Daily Papers

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Recently, evolutionary reinforcement learning has obtained much attention in various domains. Maintaining a population of actors, evolutionary reinforcement learning utilises the collected experiences to improve the behaviour policy through efficient exploration. However, the poor scalability of genetic operators limits the efficiency of optimising high-dimensional neural networks. To address this issue, this paper proposes a novel cooperative coevolutionary reinforcement learning (CoERL) algorithm. Inspired by cooperative coevolution, CoERL periodically and adaptively decomposes the policy optimisation problem into multiple subproblems and evolves a population of neural networks for each of the subproblems. Instead of using genetic operators, CoERL directly searches for partial gradients to update the policy. Updating policy with partial gradients maintains consistency between the behaviour spaces of parents and offspring across generations. The experiences collected by the population are then used to improve the entire policy, which enhances the sampling efficiency. Experiments on six benchmark locomotion tasks demonstrate that CoERL outperforms seven state-of-the-art algorithms and baselines. Ablation study verifies the unique contribution of CoERL's core ingredients.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

In recent years, instruction fine-tuning (IFT) on large language models (LLMs) has garnered considerable attention to enhance model performance on unseen tasks. Attempts have been made on automatic construction and effective selection for IFT data. However, we posit that previous methods have not fully harnessed the potential of LLMs for enhancing data quality. The responses within IFT data could be further enhanced by leveraging the capabilities of LLMs themselves. In this paper, we propose CoEvol, an LLM-based multi-agent cooperation framework for the improvement of responses to instructions. To effectively refine the responses, we develop an iterative framework following a debate-advise-edit-judge paradigm. A two-stage multi-agent debate strategy is further devised to ensure the diversity and reliability of editing suggestions within the framework. Empirically, models equipped with CoEvol outperform competitive baselines evaluated by MT-Bench and AlpacaEval, demonstrating its effectiveness in enhancing instruction-following capabilities for LLMs.

Machine learning relies heavily on data, yet the continuous growth of real-world data poses challenges for efficient dataset construction and training. A fundamental yet unsolved question is: given our current model and data, does a new data (sample/batch) need annotation/learning? Conventional approaches retain all available data, leading to non-optimal data and training efficiency. Active learning aims to reduce data redundancy by selecting a subset of samples to annotate, while it increases pipeline complexity and introduces bias. In this work, we propose Info-Coevolution, a novel framework that efficiently enables models and data to coevolve through online selective annotation with no bias. Leveraging task-specific models (and open-source models), it selectively annotates and integrates online and web data to improve datasets efficiently. For real-world datasets like ImageNet-1K, Info-Coevolution reduces annotation and training costs by 32\% without performance loss. It is able to automatically give the saving ratio without tuning the ratio. It can further reduce the annotation ratio to 50\% with semi-supervised learning. We also explore retrieval-based dataset enhancement using unlabeled open-source data. Code is available at https://github.com/NUS-HPC-AI-Lab/Info-Coevolution/.

In this position paper, we address the persistent gap between rapidly growing AI capabilities and lagging safety progress. Existing paradigms divide into ``Make AI Safe'', which applies post-hoc alignment and guardrails but remains brittle and reactive, and ``Make Safe AI'', which emphasizes intrinsic safety but struggles to address unforeseen risks in open-ended environments. We therefore propose safe-by-coevolution as a new formulation of the ``Make Safe AI'' paradigm, inspired by biological immunity, in which safety becomes a dynamic, adversarial, and ongoing learning process. To operationalize this vision, we introduce R^2AI -- Resistant and Resilient AI -- as a practical framework that unites resistance against known threats with resilience to unforeseen risks. R^2AI integrates fast and slow safe models, adversarial simulation and verification through a safety wind tunnel, and continual feedback loops that guide safety and capability to coevolve. We argue that this framework offers a scalable and proactive path to maintain continual safety in dynamic environments, addressing both near-term vulnerabilities and long-term existential risks as AI advances toward AGI and ASI.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Large Language Models (LLMs) have emerged as transformative tools in artificial intelligence, capable of processing and understanding extensive human knowledge to enhance problem-solving across various domains. This paper explores the potential of LLMs to drive the discovery of symbolic solutions within scientific and engineering disciplines, where such solutions are crucial for advancing theoretical and practical applications. We propose a novel framework that utilizes LLMs in an evolutionary search methodology, augmented by a dynamic knowledge library that integrates and refines insights in an open-ended manner. This approach aims to tackle the dual challenges of efficiently navigating complex symbolic representation spaces and leveraging both existing and newly generated knowledge to foster open-ended innovation. By enabling LLMs to interact with and expand upon a knowledge library, we facilitate the continuous generation of novel solutions in diverse forms such as language, code, and mathematical expressions. Our experimental results demonstrate that this method not only enhances the efficiency of searching for symbolic solutions but also supports the ongoing discovery process, akin to human scientific endeavors. This study represents a first effort in conceptualizing the search for symbolic solutions as a lifelong, iterative process, marking a significant step towards harnessing AI in the perpetual pursuit of scientific and engineering breakthroughs. We have open-sourced our code and data, please visit https://github.com/pgg3/CoEvo for more information.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

Zero-shot coordination in cooperative artificial intelligence (AI) remains a significant challenge, which means effectively coordinating with a wide range of unseen partners. Previous algorithms have attempted to address this challenge by optimizing fixed objectives within a population to improve strategy or behaviour diversity. However, these approaches can result in a loss of learning and an inability to cooperate with certain strategies within the population, known as cooperative incompatibility. To address this issue, we propose the Cooperative Open-ended LEarning (COLE) framework, which constructs open-ended objectives in cooperative games with two players from the perspective of graph theory to assess and identify the cooperative ability of each strategy. We further specify the framework and propose a practical algorithm that leverages knowledge from game theory and graph theory. Furthermore, an analysis of the learning process of the algorithm shows that it can efficiently overcome cooperative incompatibility. The experimental results in the Overcooked game environment demonstrate that our method outperforms current state-of-the-art methods when coordinating with different-level partners. Our demo is available at https://sites.google.com/view/cole-2023.

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

In this research, we compare four different evaluation methods in coevolution on the Majority Function problem. The size of the problem is selected such that evaluation against all possible test cases is feasible. Two measures are used for the comparisons, i.e., the objective fitness derived from evaluating solutions against all test cases, and the objective fitness correlation (OFC), which is defined as the correlation coefficient between subjective and objective fitness. The results of our experiments suggest that a combination of average score and weighted informativeness may provide a more accurate evaluation in coevolution. In order to confirm this difference, a series of t-tests on the preference between each pair of the evaluation methods is performed. The resulting significance is affirmative, and the tests for two quality measures show similar preference on four evaluation methods. %This study is the first time OFC is actually computed on a real problem. Experiments on Majority Function problems with larger sizes and Parity problems are in progress, and their results will be added in the final version.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier---AmoebaNet-A---that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-the-art 83.9% / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.

The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: https://github.com/kirjner/GGS

Developing Large Language Model (LLM) agents that exhibit human-like behavior, encompassing not only individual heterogeneity rooted in unique user profiles but also adaptive response to socially connected neighbors, is a significant research challenge. Social media platforms, with their diverse user data and explicit social structures, provide an ideal testbed for such investigations. This paper introduces EvoBot, an Evolving LLM-based social Bot that significantly enhances human-like generative capabilities through a novel adversarial learning framework. EvoBot is initialized by Supervised Fine-Tuning (SFT) on representative data from social media and then iteratively refines its generation of sophisticated, human-like content via Direct Preference Optimization (DPO). This refinement is guided by feedback from a co-adapting Detector which concurrently improves its ability to distinguish EvoBot from humans, thereby creating an increasingly challenging learning environment for EvoBot. Experiments demonstrate that EvoBot generates content aligned with diverse user profiles, increasingly bypassing the co-adapting Detector through human-like expression. Moreover, it exhibits strong social responsiveness, more accurately modeling real-world opinion dynamics and information spread in multi-agent simulations. The framework also yields a more robust Detector, underscoring its broader utility for both advanced agent development and related detection tasks. The code is available at https://github.com/kfq20/EvoBot.

In view of the problem that each subchain in the chain-of-model (CoM) relies only on the information of the previous subchain and may lose long-range dependencies due to the causal mask blocking the global context flow between multi-level subchains, this work proposes a graph of causal evolution (GoCE). Its core principle is to map the implicit token representation into a differentiable and sparse causal adjacency matrix, then permeate causal constraints through each layer of calculation using causal-masked attention and causal-MoE. By combining intervention consistency loss test and self-evolution gate, the dynamic balance between causal structure learning and adaptive updating of transformer architecture is realized. The researcher built experimental environments in sandboxes built with Claude Sonnet 4, o4-mini-high, and DeepSeek R1 respectively with the transformer variant architecture introduced in GoCE. It is evaluated on publicly available datasets including CLUTRR, CLADDER, EX-FEVER, and CausalQA and compared with the baseline LLMs. The finding proves that GoCE strengthens the transformer's ability to capture long-range causal dependencies, while the ability to self-evolve is improved. It not only surpasses the design of CoM in terms of design principles, but also provides experience for future research on causal learning and continuous adaptive improvement.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion models inherently perform evolutionary algorithms, naturally encompassing selection, mutation, and reproductive isolation. Building on this equivalence, we propose the Diffusion Evolution method: an evolutionary algorithm utilizing iterative denoising -- as originally introduced in the context of diffusion models -- to heuristically refine solutions in parameter spaces. Unlike traditional approaches, Diffusion Evolution efficiently identifies multiple optimal solutions and outperforms prominent mainstream evolutionary algorithms. Furthermore, leveraging advanced concepts from diffusion models, namely latent space diffusion and accelerated sampling, we introduce Latent Space Diffusion Evolution, which finds solutions for evolutionary tasks in high-dimensional complex parameter space while significantly reducing computational steps. This parallel between diffusion and evolution not only bridges two different fields but also opens new avenues for mutual enhancement, raising questions about open-ended evolution and potentially utilizing non-Gaussian or discrete diffusion models in the context of Diffusion Evolution.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

Scientific knowledge creation is fundamentally transforming as humans and AI systems evolve beyond tool-user relationships into co-evolutionary epistemic partnerships. When AlphaFold revolutionized protein structure prediction, researchers described engaging with an epistemic partner that reshaped how they conceptualized fundamental relationships. This article introduces Cognitio Emergens (CE), a framework addressing critical limitations in existing models that focus on static roles or narrow metrics while failing to capture how scientific understanding emerges through recursive human-AI interaction over time. CE integrates three components addressing these limitations: Agency Configurations describing how authority distributes between humans and AI (Directed, Contributory, Partnership), with partnerships dynamically oscillating between configurations rather than following linear progression; Epistemic Dimensions capturing six specific capabilities emerging through collaboration across Discovery, Integration, and Projection axes, creating distinctive "capability signatures" that guide development; and Partnership Dynamics identifying forces shaping how these relationships evolve, particularly the risk of epistemic alienation where researchers lose interpretive control over knowledge they formally endorse. Drawing from autopoiesis theory, social systems theory, and organizational modularity, CE reveals how knowledge co-creation emerges through continuous negotiation of roles, values, and organizational structures. By reconceptualizing human-AI scientific collaboration as fundamentally co-evolutionary, CE offers a balanced perspective that neither uncritically celebrates nor unnecessarily fears AI's evolving role, instead providing conceptual tools for cultivating partnerships that maintain meaningful human participation while enabling transformative scientific breakthroughs.

Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based evolution of large language models (LLMs) -- and introduces a novel framework. Starting with a population of parent LLMs, our framework enables the population to evolve through four key operations: (i) crossover, merging the weights of different parents to create offspring LLMs, (ii) mutation, introducing small, random changes to model weights to foster diversity, (iii) selection, prioritizing high-performing models, and (iv) succession, transferring the learned experience from parent to offspring LLMs. With only 200 samples per new task, the LLM population evolves rapidly to adapt to the task at hand, without any gradients. Experiments on 12 datasets show that our framework consistently outperforms existing multi-LLM merging and adaptation methods, achieving accuracy gains of up to 54.8% over the best LLM in the initial population. Moreover, our framework allows for the evolution of LLMs across multiple new tasks simultaneously, scaling effectively with populations of up to 40 LLMs, and even zero-shot generalization to unseen held-out tasks. We have open-sourced the code on GitHub and released the weights of 10 parent LLMs, fine-tuned from gemma-2-2b-it, on HuggingFace$, enabling reproduction of our proposed framework using just a single 4090 GPU with 24GB memory, without any performance degradation.

Reinforcement learning (RL) has emerged as a pivotal technique for fine-tuning large language models (LLMs) on specific tasks. However, prevailing RL fine-tuning methods predominantly rely on PPO and its variants. Though these algorithms are effective in general RL settings, they often exhibit suboptimal performance and vulnerability to distribution collapse when applied to the fine-tuning of LLMs. In this paper, we propose CORY, extending the RL fine-tuning of LLMs to a sequential cooperative multi-agent reinforcement learning framework, to leverage the inherent coevolution and emergent capabilities of multi-agent systems. In CORY, the LLM to be fine-tuned is initially duplicated into two autonomous agents: a pioneer and an observer. The pioneer generates responses based on queries, while the observer generates responses using both the queries and the pioneer's responses. The two agents are trained together. During training, the agents exchange roles periodically, fostering cooperation and coevolution between them. Experiments evaluate CORY's performance by fine-tuning GPT-2 and Llama-2 under subjective and objective reward functions on the IMDB Review and GSM8K datasets, respectively. Results show that CORY outperforms PPO in terms of policy optimality, resistance to distribution collapse, and training robustness, thereby underscoring its potential as a superior methodology for refining LLMs in real-world applications.

Model merging has become one of the key technologies for enhancing the capabilities and efficiency of Large Language Models (LLMs). However, our understanding of the expected performance gains and principles when merging any two models remains limited. In this work, we introduce model kinship, the degree of similarity or relatedness between LLMs, analogous to biological evolution. With comprehensive empirical analysis, we find that there is a certain relationship between model kinship and the performance gains after model merging, which can help guide our selection of candidate models. Inspired by this, we propose a new model merging strategy: Top-k Greedy Merging with Model Kinship, which can yield better performance on benchmark datasets. Specifically, we discover that using model kinship as a criterion can assist us in continuously performing model merging, alleviating the degradation (local optima) in model evolution, whereas model kinship can serve as a guide to escape these traps. Code is available at https://github.com/zjunlp/ModelKinship.

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large combinatorial and unstructured spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose GameOpt, a novel game-theoretical approach to combinatorial BO. GameOpt establishes a cooperative game between the different optimization variables, and selects points that are game equilibria of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate- analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making GameOpt scalable to large combinatorial spaces. We demonstrate the application of GameOpt to the challenging protein design problem and validate its performance on four real-world protein datasets. Each protein can take up to 20^{X} possible configurations, where X is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

Machine learning has achieved remarkable success in many applications. However, existing studies are largely based on the closed-world assumption, which assumes that the environment is stationary, and the model is fixed once deployed. In many real-world applications, this fundamental and rather naive assumption may not hold because an open environment is complex, dynamic, and full of unknowns. In such cases, rejecting unknowns, discovering novelties, and then incrementally learning them, could enable models to be safe and evolve continually as biological systems do. This paper provides a holistic view of open-world machine learning by investigating unknown rejection, novel class discovery, and class-incremental learning in a unified paradigm. The challenges, principles, and limitations of current methodologies are discussed in detail. Finally, we discuss several potential directions for future research. This paper aims to provide a comprehensive introduction to the emerging open-world machine learning paradigm, to help researchers build more powerful AI systems in their respective fields, and to promote the development of artificial general intelligence.

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training data that includes sequential changes and modifications, they can approximate likely changes that humans would make. To highlight the breadth of implications of such evolution through large models (ELM), in the main experiment ELM combined with MAP-Elites generates hundreds of thousands of functional examples of Python programs that output working ambulating robots in the Sodarace domain, which the original LLM had never seen in pre-training. These examples then help to bootstrap training a new conditional language model that can output the right walker for a particular terrain. The ability to bootstrap new models that can output appropriate artifacts for a given context in a domain where zero training data was previously available carries implications for open-endedness, deep learning, and reinforcement learning. These implications are explored here in depth in the hope of inspiring new directions of research now opened up by ELM.

The NeuroEvolution of Augmenting Topologies (NEAT) algorithm has received considerable recognition in the field of neuroevolution. Its effectiveness is derived from initiating with simple networks and incrementally evolving both their topologies and weights. Although its capability across various challenges is evident, the algorithm's computational efficiency remains an impediment, limiting its scalability potential. To address these limitations, this paper introduces TensorNEAT, a GPU-accelerated library that applies tensorization to the NEAT algorithm. Tensorization reformulates NEAT's diverse network topologies and operations into uniformly shaped tensors, enabling efficient parallel execution across entire populations. TensorNEAT is built upon JAX, leveraging automatic function vectorization and hardware acceleration to significantly enhance computational efficiency. In addition to NEAT, the library supports variants such as CPPN and HyperNEAT, and integrates with benchmark environments like Gym, Brax, and gymnax. Experimental evaluations across various robotic control environments in Brax demonstrate that TensorNEAT delivers up to 500x speedups compared to existing implementations, such as NEAT-Python. The source code for TensorNEAT is publicly available at: https://github.com/EMI-Group/tensorneat.

The NeuroEvolution of Augmenting Topologies (NEAT) algorithm has received considerable recognition in the field of neuroevolution. Its effectiveness is derived from initiating with simple networks and incrementally evolving both their topologies and weights. Although its capability across various challenges is evident, the algorithm's computational efficiency remains an impediment, limiting its scalability potential. In response, this paper introduces a tensorization method for the NEAT algorithm, enabling the transformation of its diverse network topologies and associated operations into uniformly shaped tensors for computation. This advancement facilitates the execution of the NEAT algorithm in a parallelized manner across the entire population. Furthermore, we develop TensorNEAT, a library that implements the tensorized NEAT algorithm and its variants, such as CPPN and HyperNEAT. Building upon JAX, TensorNEAT promotes efficient parallel computations via automated function vectorization and hardware acceleration. Moreover, the TensorNEAT library supports various benchmark environments including Gym, Brax, and gymnax. Through evaluations across a spectrum of robotics control environments in Brax, TensorNEAT achieves up to 500x speedups compared to the existing implementations such as NEAT-Python. Source codes are available at: https://github.com/EMI-Group/tensorneat.

Reinforcement learning (RL) has significantly enhanced the reasoning capabilities of large language models (LLMs), but its reliance on expensive human-labeled data or complex reward models severely limits scalability. While existing self-feedback methods aim to address this problem, they are constrained by the capabilities of a single model, which can lead to overconfidence in incorrect answers, reward hacking, and even training collapse. To this end, we propose Reinforcement Learning from Coevolutionary Collective Feedback (RLCCF), a novel RL framework that enables multi-model collaborative evolution without external supervision. Specifically, RLCCF optimizes the ability of a model collective by maximizing its Collective Consistency (CC), which jointly trains a diverse ensemble of LLMs and provides reward signals by voting on collective outputs. Moreover, each model's vote is weighted by its Self-Consistency (SC) score, ensuring that more confident models contribute more to the collective decision. Benefiting from the diverse output distributions and complementary abilities of multiple LLMs, RLCCF enables the model collective to continuously enhance its reasoning ability through coevolution. Experiments on four mainstream open-source LLMs across four mathematical reasoning benchmarks demonstrate that our framework yields significant performance gains, achieving an average relative improvement of 16.72\% in accuracy. Notably, RLCCF not only improves the performance of individual models but also enhances the group's majority-voting accuracy by 4.51\%, demonstrating its ability to extend the collective capability boundary of the model collective.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

Model merging is a powerful technique for integrating the specialized knowledge of multiple machine learning models into a single model. However, existing methods require manually partitioning model parameters into fixed groups for merging, which restricts the exploration of potential combinations and limits performance. To overcome these limitations, we propose Model Merging of Natural Niches (M2N2), an evolutionary algorithm with three key features: (1) dynamic adjustment of merging boundaries to progressively explore a broader range of parameter combinations; (2) a diversity preservation mechanism inspired by the competition for resources in nature, to maintain a population of diverse, high-performing models that are particularly well-suited for merging; and (3) a heuristicbased attraction metric to identify the most promising pairs of models for fusion. Our experimental results demonstrate, for the first time, that model merging can be used to evolve models entirely from scratch. Specifically, we apply M2N2 to evolve MNIST classifiers from scratch and achieve performance comparable to CMA-ES, while being computationally more efficient. Furthermore, M2N2 scales to merge specialized language and image generation models, achieving state-of-the-art performance. Notably, it preserves crucial model capabilities beyond those explicitly optimized by the fitness function, highlighting its robustness and versatility. Our code is available at https://github.com/SakanaAI/natural_niches

A major challenge of AI + Science lies in their inherent incompatibility: today's AI is primarily based on connectionism, while science depends on symbolism. To bridge the two worlds, we propose a framework to seamlessly synergize Kolmogorov-Arnold Networks (KANs) and science. The framework highlights KANs' usage for three aspects of scientific discovery: identifying relevant features, revealing modular structures, and discovering symbolic formulas. The synergy is bidirectional: science to KAN (incorporating scientific knowledge into KANs), and KAN to science (extracting scientific insights from KANs). We highlight major new functionalities in the pykan package: (1) MultKAN: KANs with multiplication nodes. (2) kanpiler: a KAN compiler that compiles symbolic formulas into KANs. (3) tree converter: convert KANs (or any neural networks) to tree graphs. Based on these tools, we demonstrate KANs' capability to discover various types of physical laws, including conserved quantities, Lagrangians, symmetries, and constitutive laws.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

The evolution of large language models (LLMs) toward artificial superhuman intelligence (ASI) hinges on data reproduction, a cyclical process in which models generate, curate and retrain on novel data to refine capabilities. Current methods, however, risk getting stuck in a data reproduction trap: optimizing outputs within fixed human-generated distributions in a closed loop leads to stagnation, as models merely recombine existing knowledge rather than explore new frontiers. In this paper, we propose language games as a pathway to expanded data reproduction, breaking this cycle through three mechanisms: (1) role fluidity, which enhances data diversity and coverage by enabling multi-agent systems to dynamically shift roles across tasks; (2) reward variety, embedding multiple feedback criteria that can drive complex intelligent behaviors; and (3) rule plasticity, iteratively evolving interaction constraints to foster learnability, thereby injecting continual novelty. By scaling language games into global sociotechnical ecosystems, human-AI co-evolution generates unbounded data streams that drive open-ended exploration. This framework redefines data reproduction not as a closed loop but as an engine for superhuman intelligence.

Recent advances in large language models have sparked growing interest in AI agents capable of solving complex, real-world tasks. However, most existing agent systems rely on manually crafted configurations that remain static after deployment, limiting their ability to adapt to dynamic and evolving environments. To this end, recent research has explored agent evolution techniques that aim to automatically enhance agent systems based on interaction data and environmental feedback. This emerging direction lays the foundation for self-evolving AI agents, which bridge the static capabilities of foundation models with the continuous adaptability required by lifelong agentic systems. In this survey, we provide a comprehensive review of existing techniques for self-evolving agentic systems. Specifically, we first introduce a unified conceptual framework that abstracts the feedback loop underlying the design of self-evolving agentic systems. The framework highlights four key components: System Inputs, Agent System, Environment, and Optimisers, serving as a foundation for understanding and comparing different strategies. Based on this framework, we systematically review a wide range of self-evolving techniques that target different components of the agent system. We also investigate domain-specific evolution strategies developed for specialised fields such as biomedicine, programming, and finance, where optimisation objectives are tightly coupled with domain constraints. In addition, we provide a dedicated discussion on the evaluation, safety, and ethical considerations for self-evolving agentic systems, which are critical to ensuring their effectiveness and reliability. This survey aims to provide researchers and practitioners with a systematic understanding of self-evolving AI agents, laying the foundation for the development of more adaptive, autonomous, and lifelong agentic systems.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Despite the significant advancements in text-to-image (T2I) generative models, users often face a trial-and-error challenge in practical scenarios. This challenge arises from the complexity and uncertainty of tedious steps such as crafting suitable prompts, selecting appropriate models, and configuring specific arguments, making users resort to labor-intensive attempts for desired images. This paper proposes Automatic T2I generation, which aims to automate these tedious steps, allowing users to simply describe their needs in a freestyle chatting way. To systematically study this problem, we first introduce ChatGenBench, a novel benchmark designed for Automatic T2I. It features high-quality paired data with diverse freestyle inputs, enabling comprehensive evaluation of automatic T2I models across all steps. Additionally, recognizing Automatic T2I as a complex multi-step reasoning task, we propose ChatGen-Evo, a multi-stage evolution strategy that progressively equips models with essential automation skills. Through extensive evaluation across step-wise accuracy and image quality, ChatGen-Evo significantly enhances performance over various baselines. Our evaluation also uncovers valuable insights for advancing automatic T2I. All our data, code, and models will be available in https://chengyou-jia.github.io/ChatGen-Home

In this work we introduce RITA: a suite of autoregressive generative models for protein sequences, with up to 1.2 billion parameters, trained on over 280 million protein sequences belonging to the UniRef-100 database. Such generative models hold the promise of greatly accelerating protein design. We conduct the first systematic study of how capabilities evolve with model size for autoregressive transformers in the protein domain: we evaluate RITA models in next amino acid prediction, zero-shot fitness, and enzyme function prediction, showing benefits from increased scale. We release the RITA models openly, to the benefit of the research community.

Recent advances in large multimodal models (LMMs) have enabled impressive reasoning and perception abilities, yet most existing training pipelines still depend on human-curated data or externally verified reward models, limiting their autonomy and scalability. In this work, we strive to improve LMM reasoning capabilities in a purely unsupervised fashion (without any annotated data or reward distillation). To this end, we propose a self-evolving framework, named EvoLMM, that instantiates two cooperative agents from a single backbone model: a Proposer, which generates diverse, image-grounded questions, and a Solver, which solves them through internal consistency, where learning proceeds through a continuous self-rewarding process. This dynamic feedback encourages both the generation of informative queries and the refinement of structured reasoning without relying on ground-truth or human judgments. When using the popular Qwen2.5-VL as the base model, our EvoLMM yields consistent gains upto sim3\% on multimodal math-reasoning benchmarks, including ChartQA, MathVista, and MathVision, using only raw training images. We hope our simple yet effective approach will serve as a solid baseline easing future research in self-improving LMMs in a fully-unsupervised fashion. Our code and models are available at https://github.com/mbzuai-oryx/EvoLMM.

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

Automated red teaming frameworks for Large Language Models (LLMs) have become increasingly sophisticated, yet they share a fundamental limitation: their jailbreak logic is confined to selecting, combining, or refining pre-existing attack strategies. This binds their creativity and leaves them unable to autonomously invent entirely new attack mechanisms. To overcome this gap, we introduce EvoSynth, an autonomous framework that shifts the paradigm from attack planning to the evolutionary synthesis of jailbreak methods. Instead of refining prompts, EvoSynth employs a multi-agent system to autonomously engineer, evolve, and execute novel, code-based attack algorithms. Crucially, it features a code-level self-correction loop, allowing it to iteratively rewrite its own attack logic in response to failure. Through extensive experiments, we demonstrate that EvoSynth not only establishes a new state-of-the-art by achieving an 85.5\% Attack Success Rate (ASR) against highly robust models like Claude-Sonnet-4.5, but also generates attacks that are significantly more diverse than those from existing methods. We release our framework to facilitate future research in this new direction of evolutionary synthesis of jailbreak methods. Code is available at: https://github.com/dongdongunique/EvoSynth.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

We introduce Interleaved Gibbs Diffusion (IGD), a novel generative modeling framework for mixed continuous-discrete data, focusing on constrained generation problems. Prior works on discrete and continuous-discrete diffusion models assume factorized denoising distribution for fast generation, which can hinder the modeling of strong dependencies between random variables encountered in constrained generation. IGD moves beyond this by interleaving continuous and discrete denoising algorithms via a discrete time Gibbs sampling type Markov chain. IGD provides flexibility in the choice of denoisers, allows conditional generation via state-space doubling and inference time scaling via the ReDeNoise method. Empirical evaluations on three challenging tasks-solving 3-SAT, generating molecule structures, and generating layouts-demonstrate state-of-the-art performance. Notably, IGD achieves a 7% improvement on 3-SAT out of the box and achieves state-of-the-art results in molecule generation without relying on equivariant diffusion or domain-specific architectures. We explore a wide range of modeling, and interleaving strategies along with hyperparameters in each of these problems.

In this work, we introduce CodeEvolve, an open-source evolutionary coding agent that unites Large Language Models (LLMs) with genetic algorithms to solve complex computational problems. Our framework adapts powerful evolutionary concepts to the LLM domain, building upon recent methods for generalized scientific discovery. CodeEvolve employs an island-based genetic algorithm to maintain population diversity and increase throughput, introduces a novel inspiration-based crossover mechanism that leverages the LLMs context window to combine features from successful solutions, and implements meta-prompting strategies for dynamic exploration of the solution space. We conduct a rigorous evaluation of CodeEvolve on a subset of the mathematical benchmarks used to evaluate Google DeepMind's closed-source AlphaEvolve. Our findings show that our method surpasses AlphaEvolve's performance on several challenging problems. To foster collaboration and accelerate progress, we release our complete framework as an open-source repository.

Advances in Large Language Models (LLMs) have enabled a new class of self-evolving agents that autonomously improve through interaction with the environment, demonstrating strong capabilities. However, self-evolution also introduces novel risks overlooked by current safety research. In this work, we study the case where an agent's self-evolution deviates in unintended ways, leading to undesirable or even harmful outcomes. We refer to this as Misevolution. To provide a systematic investigation, we evaluate misevolution along four key evolutionary pathways: model, memory, tool, and workflow. Our empirical findings reveal that misevolution is a widespread risk, affecting agents built even on top-tier LLMs (e.g., Gemini-2.5-Pro). Different emergent risks are observed in the self-evolutionary process, such as the degradation of safety alignment after memory accumulation, or the unintended introduction of vulnerabilities in tool creation and reuse. To our knowledge, this is the first study to systematically conceptualize misevolution and provide empirical evidence of its occurrence, highlighting an urgent need for new safety paradigms for self-evolving agents. Finally, we discuss potential mitigation strategies to inspire further research on building safer and more trustworthy self-evolving agents. Our code and data are available at https://github.com/ShaoShuai0605/Misevolution . Warning: this paper includes examples that may be offensive or harmful in nature.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Direct Preference Optimization (DPO) improves the alignment of large language models (LLMs) with human values by training directly on human preference datasets, eliminating the need for reward models. However, due to the presence of cross-domain human preferences, direct continual training can lead to catastrophic forgetting, limiting DPO's performance and efficiency. Inspired by intraspecific competition driving species evolution, we propose a Online Fast-Slow chasing DPO (OFS-DPO) for preference alignment, simulating competition through fast and slow chasing among models to facilitate rapid adaptation. Specifically, we first derive the regret upper bound for online learning, validating our motivation with a min-max optimization pattern. Based on this, we introduce two identical modules using Low-rank Adaptive (LoRA) with different optimization speeds to simulate intraspecific competition, and propose a new regularization term to guide their learning. To further mitigate catastrophic forgetting in cross-domain scenarios, we extend the OFS-DPO with LoRA modules combination strategy, resulting in the Cross domain Online Fast-Slow chasing DPO (COFS-DPO). This method leverages linear combinations of fast modules parameters from different task domains, fully utilizing historical information to achive continual value alignment. Experimental results show that OFS-DPO outperforms DPO in in-domain alignment, while COFS-DPO excels in cross-domain continual learning scenarios.

Large language models (LLMs) provide a compelling foundation for building generally-capable AI agents. These agents may soon be deployed at scale in the real world, representing the interests of individual humans (e.g., AI assistants) or groups of humans (e.g., AI-accelerated corporations). At present, relatively little is known about the dynamics of multiple LLM agents interacting over many generations of iterative deployment. In this paper, we examine whether a "society" of LLM agents can learn mutually beneficial social norms in the face of incentives to defect, a distinctive feature of human sociality that is arguably crucial to the success of civilization. In particular, we study the evolution of indirect reciprocity across generations of LLM agents playing a classic iterated Donor Game in which agents can observe the recent behavior of their peers. We find that the evolution of cooperation differs markedly across base models, with societies of Claude 3.5 Sonnet agents achieving significantly higher average scores than Gemini 1.5 Flash, which, in turn, outperforms GPT-4o. Further, Claude 3.5 Sonnet can make use of an additional mechanism for costly punishment to achieve yet higher scores, while Gemini 1.5 Flash and GPT-4o fail to do so. For each model class, we also observe variation in emergent behavior across random seeds, suggesting an understudied sensitive dependence on initial conditions. We suggest that our evaluation regime could inspire an inexpensive and informative new class of LLM benchmarks, focussed on the implications of LLM agent deployment for the cooperative infrastructure of society.

Human intelligence emerged through the process of natural selection and evolution on Earth. We investigate what it would take to re-create this process in silico. While past work has often focused on low-level processes (such as simulating physics or chemistry), we instead take a more targeted approach, aiming to evolve agents that can accumulate open-ended culture and technologies across generations. Towards this, we present JaxLife: an artificial life simulator in which embodied agents, parameterized by deep neural networks, must learn to survive in an expressive world containing programmable systems. First, we describe the environment and show that it can facilitate meaningful Turing-complete computation. We then analyze the evolved emergent agents' behavior, such as rudimentary communication protocols, agriculture, and tool use. Finally, we investigate how complexity scales with the amount of compute used. We believe JaxLife takes a step towards studying evolved behavior in more open-ended simulations. Our code is available at https://github.com/luchris429/JaxLife

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

This paper claims that machine learning (ML) largely overlooks an important facet of general intelligence: robustness to a qualitatively unknown future in an open world. Such robustness relates to Knightian uncertainty (KU) in economics, i.e. uncertainty that cannot be quantified, which is excluded from consideration in ML's key formalisms. This paper aims to identify this blind spot, argue its importance, and catalyze research into addressing it, which we believe is necessary to create truly robust open-world AI. To help illuminate the blind spot, we contrast one area of ML, reinforcement learning (RL), with the process of biological evolution. Despite staggering ongoing progress, RL still struggles in open-world situations, often failing under unforeseen situations. For example, the idea of zero-shot transferring a self-driving car policy trained only in the US to the UK currently seems exceedingly ambitious. In dramatic contrast, biological evolution routinely produces agents that thrive within an open world, sometimes even to situations that are remarkably out-of-distribution (e.g. invasive species; or humans, who do undertake such zero-shot international driving). Interestingly, evolution achieves such robustness without explicit theory, formalisms, or mathematical gradients. We explore the assumptions underlying RL's typical formalisms, showing how they limit RL's engagement with the unknown unknowns characteristic of an ever-changing complex world. Further, we identify mechanisms through which evolutionary processes foster robustness to novel and unpredictable challenges, and discuss potential pathways to algorithmically embody them. The conclusion is that the intriguing remaining fragility of ML may result from blind spots in its formalisms, and that significant gains may result from direct confrontation with the challenge of KU.

As a cornerstone in the Evolutionary Computation (EC) domain, Differential Evolution (DE) is known for its simplicity and effectiveness in handling challenging black-box optimization problems. While the advantages of DE are well-recognized, achieving peak performance heavily depends on its hyperparameters such as the mutation factor, crossover probability, and the selection of specific DE strategies. Traditional approaches to this hyperparameter dilemma have leaned towards parameter tuning or adaptive mechanisms. However, identifying the optimal settings tailored for specific problems remains a persistent challenge. In response, we introduce MetaDE, an approach that evolves DE's intrinsic hyperparameters and strategies using DE itself at a meta-level. A pivotal aspect of MetaDE is a specialized parameterization technique, which endows it with the capability to dynamically modify DE's parameters and strategies throughout the evolutionary process. To augment computational efficiency, MetaDE incorporates a design that leverages parallel processing through a GPU-accelerated computing framework. Within such a framework, DE is not just a solver but also an optimizer for its own configurations, thus streamlining the process of hyperparameter optimization and problem-solving into a cohesive and automated workflow. Extensive evaluations on the CEC2022 benchmark suite demonstrate MetaDE's promising performance. Moreover, when applied to robot control via evolutionary reinforcement learning, MetaDE also demonstrates promising performance. The source code of MetaDE is publicly accessible at: https://github.com/EMI-Group/metade.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Recent advances in large language models (LLMs) and multi-agent systems have demonstrated remarkable capabilities in complex problem-solving tasks such as deep research, vibe coding, and mathematical reasoning. However, most existing multi-agent systems are built upon manual prompt/workflow engineering with sophisticated agent frameworks, making them computationally inefficient, less capable, and can not benefit from data-centric learning. In this work, we introduce Chain-of-Agents (CoA), a novel paradigm of LLM reasoning that enables native end-to-end complex problem-solving in the same way as a multi-agent system (i.e., multi-turn problem solving with multiple tools and multiple agents) within one model. In chain-of-agents problem-solving, the model dynamically activates different tool agents and role-playing agents to simulate multi-agent collaboration in an end-to-end fashion. To elicit end-to-end chain-of-agents problem-solving abilities in LLMs, we introduce a multi-agent distillation framework to distill state-of-the-art multi-agent systems into chain-of-agents trajectories for agentic supervised fine-tuning. We then use agentic reinforcement learning on verifiable agentic tasks to further improve the models' capabilities on chain-of-agents problem solving. We call the resulting models Agent Foundation Models (AFMs). Our empirical studies demonstrate that AFM establishes new state-of-the-art performance across diverse benchmarks in both web agent and code agent settings. We make the entire research, including the model weights, code for training and evaluation, and the training data, fully open-sourced, which offers a solid starting point for future research on agent models and agentic RL.

Imitation learning (IL) has shown promise in robot locomotion but is often limited to learning a single expert policy, constraining behavior diversity and robustness in unpredictable real-world scenarios. To address this, we introduce Quality Diversity Inverse Reinforcement Learning (QD-IRL), a novel framework that integrates quality-diversity optimization with IRL methods, enabling agents to learn diverse behaviors from limited demonstrations. This work introduces Extrinsic Behavioral Curiosity (EBC), which allows agents to receive additional curiosity rewards from an external critic based on how novel the behaviors are with respect to a large behavioral archive. To validate the effectiveness of EBC in exploring diverse locomotion behaviors, we evaluate our method on multiple robot locomotion tasks. EBC improves the performance of QD-IRL instances with GAIL, VAIL, and DiffAIL across all included environments by up to 185%, 42%, and 150%, even surpassing expert performance by 20% in Humanoid. Furthermore, we demonstrate that EBC is applicable to Gradient-Arborescence-based Quality Diversity Reinforcement Learning (QD-RL) algorithms, where it substantially improves performance and provides a generic technique for diverse robot locomotion. The source code of this work is provided at https://github.com/vanzll/EBC.

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically generative modeling of protein families. ProfileBFN extends the discrete Bayesian Flow Network from an MSA profile perspective, which can be trained on single protein sequences by regarding it as a degenerate profile, thereby achieving efficient protein family design by avoiding large-scale MSA data construction and training. Empirical results show that ProfileBFN has a profound understanding of proteins. When generating diverse and novel family proteins, it can accurately capture the structural characteristics of the family. The enzyme produced by this method is more likely than the previous approach to have the corresponding function, offering better odds of generating diverse proteins with the desired functionality.

Agents based on Large Language Models (LLMs) are increasingly permeating various domains of human production and life, highlighting the importance of aligning them with human values. The current alignment of AI systems primarily focuses on passively aligning LLMs through human intervention. However, agents possess characteristics like receiving environmental feedback and self-evolution, rendering the LLM alignment methods inadequate. In response, we propose an evolutionary framework for agent evolution and alignment, named EvolutionaryAgent, which transforms agent alignment into a process of evolution and selection under the principle of survival of the fittest. In an environment where social norms continuously evolve, agents better adapted to the current social norms will have a higher probability of survival and proliferation, while those inadequately aligned dwindle over time. Experimental results assessing the agents from multiple perspectives in aligning with social norms demonstrate that EvolutionaryAgent can align progressively better with the evolving social norms while maintaining its proficiency in general tasks. Effectiveness tests conducted on various open and closed-source LLMs as the foundation for agents also prove the applicability of our approach.

Fine-tuning large pre-trained language models with Evol-Instruct has achieved encouraging results across a wide range of tasks. However, designing effective evolving methods for instruction evolution requires substantial human expertise. This paper proposes Auto Evol-Instruct, an end-to-end framework that evolves instruction datasets using large language models without any human effort. The framework automatically analyzes and summarizes suitable evolutionary strategies for the given instruction data and iteratively improves the evolving method based on issues exposed during the instruction evolution process. Our extensive experiments demonstrate that the best method optimized by Auto Evol-Instruct outperforms human-designed methods on various benchmarks, including MT-Bench, AlpacaEval, GSM8K, and HumanEval.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Self-evolution is a central research topic in enabling large language model (LLM)-based agents to continually improve their capabilities after pretraining. Recent research has witnessed a transition from reinforcement learning (RL)-free to RL-based methods. Current RL-based methods either rely on dense external reward signals or extract intrinsic reward signals from LLMs themselves. However, these approaches diverge from the self-evolution mechanisms observed in human intelligence, where individuals learn and improve through mutual discussion and collaboration. In this work, we introduce Co-Evolving Multi-Agent Systems (CoMAS), a novel framework that enables agents to improve autonomously by learning from inter-agent interactions without external supervision. CoMAS generates intrinsic rewards from rich discussion dynamics, employs an LLM-as-a-judge mechanism to formulate these rewards, and optimizes each agent's policy through RL, thereby enabling decentralized and scalable co-evolution. Experimental results demonstrate that CoMAS consistently outperforms untrained agents and achieves state-of-the-art performance across most evaluation settings. Ablation studies confirm the necessity of interaction-based reward signals and reveal promising scalability as the number and diversity of agents increase. These findings establish CoMAS as a novel and effective paradigm for self-evolution in LLM-based agents.

Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes (e.g., information diffusion, virus propagation) occurring over the unobserved network. While there have been efforts to infer networks based on such data, providing a generative probabilistic model that is able to identify the underlying time-varying network remains an open question. Here we consider the problem of inferring generative dynamic network models based on network cascade diffusion data. We propose a novel framework for providing a non-parametric dynamic network model--based on a mixture of coupled hierarchical Dirichlet processes-- based on data capturing cascade node infection times. Our approach allows us to infer the evolving community structure in networks and to obtain an explicit predictive distribution over the edges of the underlying network--including those that were not involved in transmission of any cascade, or are likely to appear in the future. We show the effectiveness of our approach using extensive experiments on synthetic as well as real-world networks.

Is the lottery ticket phenomenon an idiosyncrasy of gradient-based training or does it generalize to evolutionary optimization? In this paper we establish the existence of highly sparse trainable initializations for evolution strategies (ES) and characterize qualitative differences compared to gradient descent (GD)-based sparse training. We introduce a novel signal-to-noise iterative pruning procedure, which incorporates loss curvature information into the network pruning step. This can enable the discovery of even sparser trainable network initializations when using black-box evolution as compared to GD-based optimization. Furthermore, we find that these initializations encode an inductive bias, which transfers across different ES, related tasks and even to GD-based training. Finally, we compare the local optima resulting from the different optimization paradigms and sparsity levels. In contrast to GD, ES explore diverse and flat local optima and do not preserve linear mode connectivity across sparsity levels and independent runs. The results highlight qualitative differences between evolution and gradient-based learning dynamics, which can be uncovered by the study of iterative pruning procedures.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

We aim to understand grokking, a phenomenon where models generalize long after overfitting their training set. We present both a microscopic analysis anchored by an effective theory and a macroscopic analysis of phase diagrams describing learning performance across hyperparameters. We find that generalization originates from structured representations whose training dynamics and dependence on training set size can be predicted by our effective theory in a toy setting. We observe empirically the presence of four learning phases: comprehension, grokking, memorization, and confusion. We find representation learning to occur only in a "Goldilocks zone" (including comprehension and grokking) between memorization and confusion. We find on transformers the grokking phase stays closer to the memorization phase (compared to the comprehension phase), leading to delayed generalization. The Goldilocks phase is reminiscent of "intelligence from starvation" in Darwinian evolution, where resource limitations drive discovery of more efficient solutions. This study not only provides intuitive explanations of the origin of grokking, but also highlights the usefulness of physics-inspired tools, e.g., effective theories and phase diagrams, for understanding deep learning.

We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can traverse any series of modules in any order. DNAs are a natural generalization of the sparse methods such as Mixture-of-Experts, Mixture-of-Depths, parameter sharing, etc. Computation and communication patterns of DNA modules are learnt end-to-end during training and depend on the content and context of each token (or patch). These patterns can be shaped by further requirements added to the optimization objective such as compute/memory efficiency or load balancing. We empirically show that (i) trained DNAs are competitive with the dense baselines in both domains and (ii) compute efficiency/parameter sharing can be learnt from data. Next, we analyze the emergent connectivity and computation patterns in the trained DNAs. We find that the paths that tokens take through the models are themselves distributed according to a power-law. We show that some paths (or, equivalently, groups of modules) show emergent specialization. Finally, we demonstrate that models learn to allocate compute and active parameters in an interpretable way.

Multi-cellular robot design aims to create robots comprised of numerous cells that can be efficiently controlled to perform diverse tasks. Previous research has demonstrated the ability to generate robots for various tasks, but these approaches often optimize robots directly in the vast design space, resulting in robots with complicated morphologies that are hard to control. In response, this paper presents a novel coarse-to-fine method for designing multi-cellular robots. Initially, this strategy seeks optimal coarse-grained robots and progressively refines them. To mitigate the challenge of determining the precise refinement juncture during the coarse-to-fine transition, we introduce the Hyperbolic Embeddings for Robot Design (HERD) framework. HERD unifies robots of various granularity within a shared hyperbolic space and leverages a refined Cross-Entropy Method for optimization. This framework enables our method to autonomously identify areas of exploration in hyperbolic space and concentrate on regions demonstrating promise. Finally, the extensive empirical studies on various challenging tasks sourced from EvoGym show our approach's superior efficiency and generalization capability.

How have individuals of social animals in nature evolved to learn from each other, and what would be the optimal strategy for such learning in a specific environment? Here, we address both problems by employing a deep reinforcement learning model to optimize the social learning strategies (SLSs) of agents in a cooperative game in a multi-dimensional landscape. Throughout the training for maximizing the overall payoff, we find that the agent spontaneously learns various concepts of social learning, such as copying, focusing on frequent and well-performing neighbors, self-comparison, and the importance of balancing between individual and social learning, without any explicit guidance or prior knowledge about the system. The SLS from a fully trained agent outperforms all of the traditional, baseline SLSs in terms of mean payoff. We demonstrate the superior performance of the reinforcement learning agent in various environments, including temporally changing environments and real social networks, which also verifies the adaptability of our framework to different social settings.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.

Recent advancements in generation models have showcased remarkable capabilities in generating fantastic content. However, most of them are trained on proprietary high-quality data, and some models withhold their parameters and only provide accessible application programming interfaces (APIs), limiting their benefits for downstream tasks. To explore the feasibility of training a text-to-image generation model comparable to advanced models using publicly available resources, we introduce EvolveDirector. This framework interacts with advanced models through their public APIs to obtain text-image data pairs to train a base model. Our experiments with extensive data indicate that the model trained on generated data of the advanced model can approximate its generation capability. However, it requires large-scale samples of 10 million or more. This incurs significant expenses in time, computational resources, and especially the costs associated with calling fee-based APIs. To address this problem, we leverage pre-trained large vision-language models (VLMs) to guide the evolution of the base model. VLM continuously evaluates the base model during training and dynamically updates and refines the training dataset by the discrimination, expansion, deletion, and mutation operations. Experimental results show that this paradigm significantly reduces the required data volume. Furthermore, when approaching multiple advanced models, EvolveDirector can select the best samples generated by them to learn powerful and balanced abilities. The final trained model Edgen is demonstrated to outperform these advanced models. The code and model weights are available at https://github.com/showlab/EvolveDirector.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing and bioinformatics, and in particular, matching graphs with inherent community structure has significance related to de-anonymization of correlated social networks. Compared to the correlated Erdos-Renyi (ER) model, where various efficient algorithms have been developed, among which a few algorithms have been proven to achieve the exact matching with constant edge correlation, no low-order polynomial algorithm has been known to achieve exact matching for the correlated SBMs with constant correlation. In this work, we propose an efficient algorithm for matching graphs with community structure, based on the comparison between partition trees rooted from each vertex, by extending the idea of Mao et al. (2021) to graphs with communities. The partition tree divides the large neighborhoods of each vertex into disjoint subsets using their edge statistics to different communities. Our algorithm is the first low-order polynomial-time algorithm achieving exact matching between two correlated SBMs with high probability in dense graphs.

We propose a novel type of Artificial Immune System (AIS): Symbiotic Artificial Immune Systems (SAIS), drawing inspiration from symbiotic relationships in biology. SAIS parallels the three key stages (i.e., mutualism, commensalism and parasitism) of population updating from the Symbiotic Organisms Search (SOS) algorithm. This parallel approach effectively addresses the challenges of large population size and enhances population diversity in AIS, which traditional AIS and SOS struggle to resolve efficiently. We conducted a series of experiments, which demonstrated that our SAIS achieved comparable performance to the state-of-the-art approach SOS and outperformed other popular AIS approaches and evolutionary algorithms across 26 benchmark problems. Furthermore, we investigated the problem of parameter selection and found that SAIS performs better in handling larger population sizes while requiring fewer generations. Finally, we believe SAIS, as a novel bio-inspired and immune-inspired algorithm, paves the way for innovation in bio-inspired computing with the symbiotic paradigm.

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, and improved unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

In this paper, we propose a novel learning paradigm, termed Chain-of-Model (CoM), which incorporates the causal relationship into the hidden states of each layer as a chain style, thereby introducing great scaling efficiency in model training and inference flexibility in deployment. We introduce the concept of Chain-of-Representation (CoR), which formulates the hidden states at each layer as a combination of multiple sub-representations (i.e., chains) at the hidden dimension level. In each layer, each chain from the output representations can only view all of its preceding chains in the input representations. Consequently, the model built upon CoM framework can progressively scale up the model size by increasing the chains based on the previous models (i.e., chains), and offer multiple sub-models at varying sizes for elastic inference by using different chain numbers. Based on this principle, we devise Chain-of-Language-Model (CoLM), which incorporates the idea of CoM into each layer of Transformer architecture. Based on CoLM, we further introduce CoLM-Air by introducing a KV sharing mechanism, that computes all keys and values within the first chain and then shares across all chains. This design demonstrates additional extensibility, such as enabling seamless LM switching, prefilling acceleration and so on. Experimental results demonstrate our CoLM family can achieve comparable performance to the standard Transformer, while simultaneously enabling greater flexiblity, such as progressive scaling to improve training efficiency and offer multiple varying model sizes for elastic inference, paving a a new way toward building language models. Our code will be released in the future at: https://github.com/microsoft/CoLM.

The rapidly evolving fields of Machine Learning (ML) and Artificial Intelligence have witnessed the emergence of platforms like Hugging Face (HF) as central hubs for model development and sharing. This experience report synthesizes insights from two comprehensive studies conducted on HF, focusing on carbon emissions and the evolutionary and maintenance aspects of ML models. Our objective is to provide a practical guide for future researchers embarking on mining software repository studies within the HF ecosystem to enhance the quality of these studies. We delve into the intricacies of the replication package used in our studies, highlighting the pivotal tools and methodologies that facilitated our analysis. Furthermore, we propose a nuanced stratified sampling strategy tailored for the diverse HF Hub dataset, ensuring a representative and comprehensive analytical approach. The report also introduces preliminary guidelines, transitioning from repository mining to cohort studies, to establish causality in repository mining studies, particularly within the ML model of HF context. This transition is inspired by existing frameworks and is adapted to suit the unique characteristics of the HF model ecosystem. Our report serves as a guiding framework for researchers, contributing to the responsible and sustainable advancement of ML, and fostering a deeper understanding of the broader implications of ML models.

Model merging allows combining the capabilities of existing models into a new one - post hoc, without additional training. This has made it increasingly popular thanks to its low cost and the availability of libraries that support merging on consumer GPUs. Recent work shows that pairing merging with evolutionary algorithms can boost performance, but no framework currently supports flexible experimentation with such strategies in language models. We introduce Mergenetic, an open-source library for evolutionary model merging. Mergenetic enables easy composition of merging methods and evolutionary algorithms while incorporating lightweight fitness estimators to reduce evaluation costs. We describe its design and demonstrate that Mergenetic produces competitive results across tasks and languages using modest hardware.

We introduce **EvoGraph**, a framework that enables software systems to evolve their own source code, build pipelines, documentation, and tickets. EvoGraph represents every artefact in a typed directed graph, applies learned mutation operators driven by specialized small language models (SLMs), and selects survivors with a multi-objective fitness. On three benchmarks, EvoGraph fixes 83% of known security vulnerabilities, translates COBOL to Java with 93% functional equivalence (test verified), and maintains documentation freshness within two minutes. Experiments show a 40% latency reduction and a sevenfold drop in feature lead time compared with strong baselines. We extend our approach to **evoGraph**, leveraging language-specific SLMs for modernizing .NET, Lisp, CGI, ColdFusion, legacy Python, and C codebases, achieving 82-96% semantic equivalence across languages while reducing computational costs by 90% compared to large language models. EvoGraph's design responds to empirical failure modes in legacy modernization, such as implicit contracts, performance preservation, and integration evolution. Our results suggest a practical path toward Software 3.0, where systems adapt continuously yet remain under measurable control.

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Large Language Models (LLMs) have demonstrated strong capabilities but remain fundamentally static, unable to adapt their internal parameters to novel tasks, evolving knowledge domains, or dynamic interaction contexts. As LLMs are increasingly deployed in open-ended, interactive environments, this static nature has become a critical bottleneck, necessitating agents that can adaptively reason, act, and evolve in real time. This paradigm shift -- from scaling static models to developing self-evolving agents -- has sparked growing interest in architectures and methods enabling continual learning and adaptation from data, interactions, and experiences. This survey provides the first systematic and comprehensive review of self-evolving agents, organized around three foundational dimensions -- what to evolve, when to evolve, and how to evolve. We examine evolutionary mechanisms across agent components (e.g., models, memory, tools, architecture), categorize adaptation methods by stages (e.g., intra-test-time, inter-test-time), and analyze the algorithmic and architectural designs that guide evolutionary adaptation (e.g., scalar rewards, textual feedback, single-agent and multi-agent systems). Additionally, we analyze evaluation metrics and benchmarks tailored for self-evolving agents, highlight applications in domains such as coding, education, and healthcare, and identify critical challenges and research directions in safety, scalability, and co-evolutionary dynamics. By providing a structured framework for understanding and designing self-evolving agents, this survey establishes a roadmap for advancing adaptive agentic systems in both research and real-world deployments, ultimately shedding lights to pave the way for the realization of Artificial Super Intelligence (ASI), where agents evolve autonomously, performing at or beyond human-level intelligence across a wide array of tasks.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to 50times activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

Research in cultural evolution aims at providing causal explanations for the change of culture over time. Over the past decades, this field has generated an important body of knowledge, using experimental, historical, and computational methods. While computational models have been very successful at generating testable hypotheses about the effects of several factors, such as population structure or transmission biases, some phenomena have so far been more complex to capture using agent-based and formal models. This is in particular the case for the effect of the transformations of social information induced by evolved cognitive mechanisms. We here propose that leveraging the capacity of Large Language Models (LLMs) to mimic human behavior may be fruitful to address this gap. On top of being an useful approximation of human cultural dynamics, multi-agents models featuring generative agents are also important to study for their own sake. Indeed, as artificial agents are bound to participate more and more to the evolution of culture, it is crucial to better understand the dynamics of machine-generated cultural evolution. We here present a framework for simulating cultural evolution in populations of LLMs, allowing the manipulation of variables known to be important in cultural evolution, such as network structure, personality, and the way social information is aggregated and transformed. The software we developed for conducting these simulations is open-source and features an intuitive user-interface, which we hope will help to build bridges between the fields of cultural evolution and generative artificial intelligence.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Recent advances in multimodal large language models (MLLMs) have shown impressive reasoning capabilities. However, further enhancing existing MLLMs necessitates high-quality vision-language datasets with carefully curated task complexities, which are both costly and challenging to scale. Although recent self-improving models that iteratively refine themselves offer a feasible solution, they still suffer from two core challenges: (i) most existing methods augment visual or textual data separately, resulting in discrepancies in data complexity (e.g., over-simplified diagrams paired with redundant textual descriptions); and (ii) the evolution of data and models is also separated, leading to scenarios where models are exposed to tasks with mismatched difficulty levels. To address these issues, we propose C2-Evo, an automatic, closed-loop self-improving framework that jointly evolves both training data and model capabilities. Specifically, given a base dataset and a base model, C2-Evo enhances them by a cross-modal data evolution loop and a data-model evolution loop. The former loop expands the base dataset by generating complex multimodal problems that combine structured textual sub-problems with iteratively specified geometric diagrams, while the latter loop adaptively selects the generated problems based on the performance of the base model, to conduct supervised fine-tuning and reinforcement learning alternately. Consequently, our method continuously refines its model and training data, and consistently obtains considerable performance gains across multiple mathematical reasoning benchmarks. Our code, models, and datasets will be released.

Many proteins useful in modern medicine or bioengineering are challenging to make in the lab, fuse with other proteins in cells, or deliver to tissues in the body, because their sequences are too long. Shortening these sequences typically involves costly, time-consuming experimental campaigns. Ideally, we could instead use modern models of massive databases of sequences from nature to learn how to propose shrunken proteins that resemble sequences found in nature. Unfortunately, these models struggle to efficiently search the combinatorial space of all deletions, and are not trained with inductive biases to learn how to delete. To address this gap, we propose SCISOR, a novel discrete diffusion model that deletes letters from sequences to generate protein samples that resemble those found in nature. To do so, SCISOR trains a de-noiser to reverse a forward noising process that adds random insertions to natural sequences. As a generative model, SCISOR fits evolutionary sequence data competitively with previous large models. In evaluation, SCISOR achieves state-of-the-art predictions of the functional effects of deletions on ProteinGym. Finally, we use the SCISOR de-noiser to shrink long protein sequences, and show that its suggested deletions result in significantly more realistic proteins and more often preserve functional motifs than previous models of evolutionary sequences.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Reinforcement learning with verifiable reward (RLVR) has become a promising paradigm for post-training large language models (LLMs) to improve their reasoning capability. However, when the rollout accuracy is low on hard problems, the reward becomes sparse, limiting learning efficiency and causing exploration bottlenecks. Existing approaches either rely on teacher models for distillation or filter out difficult problems, which limits scalability or restricts reasoning improvement through exploration. We propose EvoCoT, a self-evolving curriculum learning framework based on two-stage chain-of-thought (CoT) reasoning optimization. EvoCoT constrains the exploration space by self-generating and verifying CoT trajectories, then gradually shortens CoT steps to expand the space in a controlled way. The framework enables LLMs to stably learn from initially unsolved hard problems under sparse rewards. We apply EvoCoT to multiple LLM families, including Qwen, DeepSeek, and Llama. Experiments show that EvoCoT enables LLMs to solve previously unsolved problems, improves reasoning capability without external CoT supervision, and is compatible with various RL fine-tuning methods. We release the source code to support future research.

Large deep learning models have achieved remarkable success in many scenarios. However, training large models is usually challenging, e.g., due to the high computational cost, the unstable and painfully slow optimization procedure, and the vulnerability to overfitting. To alleviate these problems, this work studies a divide-and-conquer strategy, i.e., dividing a large model into smaller modules, training them independently, and reassembling the trained modules to obtain the target model. This approach is promising since it avoids directly training large models from scratch. Nevertheless, implementing this idea is non-trivial, as it is difficult to ensure the compatibility of the independently trained modules. In this paper, we present an elegant solution to address this issue, i.e., we introduce a global, shared meta model to implicitly link all the modules together. This enables us to train highly compatible modules that collaborate effectively when they are assembled together. We further propose a module incubation mechanism that enables the meta model to be designed as an extremely shallow network. As a result, the additional overhead introduced by the meta model is minimalized. Though conceptually simple, our method significantly outperforms end-to-end (E2E) training in terms of both final accuracy and training efficiency. For example, on top of ViT-Huge, it improves the accuracy by 2.7% compared to the E2E baseline on ImageNet-1K, while saving the training cost by 43% in the meantime. Code is available at https://github.com/LeapLabTHU/Model-Assembling.

Large Language Models (LLMs) have shown remarkable performance in automated code generation. However, existing approaches often rely heavily on pre-defined test cases, which become impractical in scenarios where such cases are unavailable. While prior works explore filtering techniques between programs and test cases, they overlook the refinement of test cases. To address this limitation, we introduce CoCoEvo, a novel LLM-based co-evolution framework that simultaneously evolves programs and test cases. CoCoEvo eliminates the dependency on pre-defined test cases by generating both programs and test cases directly from natural language problem descriptions and function headers. The framework employs specialized evolutionary operators, including LLM-based crossover and mutation operators for program evolution, along with a test case generation operator for test case evolution. Additionally, we propose optimization strategies such as a crossover rate scheduler to balance exploration and convergence, and a multi-objective optimization method for test case selection. Experimental results on multiple state-of-the-art LLMs demonstrate that CoCoEvo surpasses existing methods, achieving state-of-the-art performance in automated code generation and testing. These results underscore the potential of co-evolutionary techniques in advancing the field of automated programming.

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face limitations such as suboptimal solutions from greedy methods or prohibitive computational costs and limited applicability of exact optimization approaches. To address these challenges, we propose an evolutionary optimization method for decision tree induction based on genetic programming (GP). Our key innovation is the integration of semantic priors and domain-specific knowledge about the search space into the optimization algorithm. To this end, we introduce LLEGO, a framework that incorporates semantic priors into genetic search operators through the use of Large Language Models (LLMs), thereby enhancing search efficiency and targeting regions of the search space that yield decision trees with superior generalization performance. This is operationalized through novel genetic operators that work with structured natural language prompts, effectively utilizing LLMs as conditional generative models and sources of semantic knowledge. Specifically, we introduce fitness-guided crossover to exploit high-performing regions, and diversity-guided mutation for efficient global exploration of the search space. These operators are controlled by corresponding hyperparameters that enable a more nuanced balance between exploration and exploitation across the search space. Empirically, we demonstrate across various benchmarks that LLEGO evolves superior-performing trees compared to existing tree induction methods, and exhibits significantly more efficient search performance compared to conventional GP approaches.

Coopetition refers to simultaneous cooperation and competition among actors wherein actors 'cooperate to grow the pie and compete to split it up.' Modern socio-technical systems are characterized by strategic coopetition wherein actors concomitantly cooperate to create value and compete to capture it. While conceptual modeling languages such as i* provide rich qualitative representations of strategic dependencies, they lack mechanisms for quantitative analysis of dynamic trade-offs. Conversely, classical game theory offers mathematical rigor but strips away contextual richness. This report bridges this gap by developing computational foundations that formalize two critical dimensions of coopetition: interdependence and complementarity. We ground interdependence in i* structural dependency analysis, translating depender-dependee-dependum relationships into quantitative interdependence coefficients via a structured translation framework. We formalize complementarity following Brandenburger and Nalebuff's Added Value concept, modeling synergistic value creation with validated parameterization. We integrate structural dependencies with bargaining power in value appropriation and introduce a game-theoretic formulation where Nash Equilibrium incorporates structural interdependence. Validation combines over 22,000 experimental trials across power and logarithmic specifications with the Samsung-Sony S-LCD joint venture (2004-2011). Under strict historical alignment scoring, logarithmic specifications achieve 58/60 compared to power functions (46/60), producing realistic 41% cooperation increases aligning with documented S-LCD patterns while power functions produce 166% increases exceeding realistic bounds. Statistical significance confirmed at p < 0.001, Cohen's d > 9.

Despite exceptional capabilities in knowledge-intensive tasks, Large Language Models (LLMs) face a critical gap in understanding how they internalize new knowledge, particularly how to structurally embed acquired knowledge in their neural computations. We address this issue through the lens of knowledge circuit evolution, identifying computational subgraphs that facilitate knowledge storage and processing. Our systematic analysis of circuit evolution throughout continual pre-training reveals several key findings: (1) the acquisition of new knowledge is influenced by its relevance to pre-existing knowledge; (2) the evolution of knowledge circuits exhibits a distinct phase shift from formation to optimization; (3) the evolution of knowledge circuits follows a deep-to-shallow pattern. These insights not only advance our theoretical understanding of the mechanisms of new knowledge acquisition in LLMs, but also provide potential implications for improving continual pre-training strategies to enhance model performance. Code and data will be available at https://github.com/zjunlp/DynamicKnowledgeCircuits.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

The rise of powerful large language models (LLMs) has spurred a new trend in building LLM-based autonomous agents for solving complex tasks, especially multi-agent systems. Despite the remarkable progress, we notice that existing works are heavily dependent on human-designed frameworks, which greatly limits the functional scope and scalability of agent systems. How to automatically extend the specialized agent to multi-agent systems to improve task-solving capability still remains a significant challenge. In this paper, we introduce EvoAgent, a generic method to automatically extend expert agents to multi-agent systems via the evolutionary algorithm, thereby improving the effectiveness of LLM-based agents in solving tasks. Specifically, we consider the existing agent frameworks as the initial individual and then apply a series of evolutionary operators (e.g., mutation, crossover, selection, etc.) to generate multiple agents with diverse agent settings. EvoAgent can be generalized to any LLM-based agent framework, and can automatically extend the existing agent framework to multi-agent systems without any extra human designs. Experimental results across various tasks have shown that EvoAgent can automatically generate multiple expert agents and significantly enhance the task-solving capabilities of LLM-based agents.