Daily Papers

We introduce Skywork UniPic, a 1.5 billion-parameter autoregressive model that unifies image understanding, text-to-image generation, and image editing within a single architecture-eliminating the need for task-specific adapters or inter-module connectors-and demonstrate that compact multimodal systems can achieve state-of-the-art performance on commodity hardware. Skywork UniPic achieves a GenEval score of 0.86, surpassing most existing unified models; sets a new DPG-Bench complex-generation record of 85.5; attains 5.83 on GEditBench-EN and 3.49 on ImgEdit-Bench for image editing; and generates 1024 x 1024 images with under 15 GB of GPU memory (e.g., RTX 4090). (1) a decoupled encoding strategy that leverages a masked autoregressive encoder for synthesis and a SigLIP2 encoder for understanding, all feeding a shared autoregressive decoder; (2) a progressive, resolution-aware training schedule scaling from 256 x 256 to 1024 x 1024 while dynamically unfreezing parameters to balance capacity and stability; and (3) meticulously curated, 100 million-scale datasets augmented with task-specific reward models to refine generation and editing objectives. By demonstrating that high-fidelity multimodal integration need not incur prohibitive resource demands, Skywork UniPic establishes a practical paradigm for deployable, high-fidelity multimodal AI. Code and weights are publicly available at https://huggingface.co/Skywork/Skywork-UniPic-1.5B.

We present Jina-VLM, a 2.4B parameter vision-language model that achieves state-of-the-art multilingual visual question answering among open 2B-scale VLMs. The model couples a SigLIP2 vision encoder with a Qwen3 language backbone through an attention-pooling connector that enables token-efficient processing of arbitrary-resolution images. Across standard VQA benchmarks and multilingual evaluations, Jina-VLM outperforms comparable models while preserving competitive text-only performance.

We introduce SigLIP 2, a family of new multilingual vision-language encoders that build on the success of the original SigLIP. In this second iteration, we extend the original image-text training objective with several prior, independently developed techniques into a unified recipe -- this includes captioning-based pretraining, self-supervised losses (self-distillation, masked prediction) and online data curation. With these changes, SigLIP 2 models outperform their SigLIP counterparts at all model scales in core capabilities, including zero-shot classification, image-text retrieval, and transfer performance when extracting visual representations for Vision-Language Models (VLMs). Furthermore, the new training recipe leads to significant improvements on localization and dense prediction tasks. We also train variants which support multiple resolutions and preserve the input's native aspect ratio. Finally, we train on a more diverse data-mixture that includes de-biasing techniques, leading to much better multilingual understanding and improved fairness. To allow users to trade off inference cost with performance, we release model checkpoints at four sizes: ViT-B (86M), L (303M), So400m (400M), and g (1B).

Vision encoders are increasingly used in modern applications, from vision-only models to multimodal systems such as vision-language models. Despite their remarkable success, it remains unclear how these architectures represent features internally. Here, we propose a novel approach for interpreting vision features via image reconstruction. We compare two related model families, SigLIP and SigLIP2, which differ only in their training objective, and show that encoders pre-trained on image-based tasks retain significantly more image information than those trained on non-image tasks such as contrastive learning. We further apply our method to a range of vision encoders, ranking them by the informativeness of their feature representations. Finally, we demonstrate that manipulating the feature space yields predictable changes in reconstructed images, revealing that orthogonal rotations (rather than spatial transformations) control color encoding. Our approach can be applied to any vision encoder, shedding light on the inner structure of its feature space. The code and model weights to reproduce the experiments are available in GitHub.

We introduce a novel method for pre-training of large-scale vision encoders. Building on recent advancements in autoregressive pre-training of vision models, we extend this framework to a multimodal setting, i.e., images and text. In this paper, we present AIMV2, a family of generalist vision encoders characterized by a straightforward pre-training process, scalability, and remarkable performance across a range of downstream tasks. This is achieved by pairing the vision encoder with a multimodal decoder that autoregressively generates raw image patches and text tokens. Our encoders excel not only in multimodal evaluations but also in vision benchmarks such as localization, grounding, and classification. Notably, our AIMV2-3B encoder achieves 89.5% accuracy on ImageNet-1k with a frozen trunk. Furthermore, AIMV2 consistently outperforms state-of-the-art contrastive models (e.g., CLIP, SigLIP) in multimodal image understanding across diverse settings.

Artificial intelligence (AI) has significant potential in healthcare applications, but its training and deployment faces challenges due to healthcare's diverse data, complex tasks, and the need to preserve privacy. Foundation models that perform well on medical tasks and require less task-specific tuning data are critical to accelerate the development of healthcare AI applications. We introduce MedGemma, a collection of medical vision-language foundation models based on Gemma 3 4B and 27B. MedGemma demonstrates advanced medical understanding and reasoning on images and text, significantly exceeding the performance of similar-sized generative models and approaching the performance of task-specific models, while maintaining the general capabilities of the Gemma 3 base models. For out-of-distribution tasks, MedGemma achieves 2.6-10% improvement on medical multimodal question answering, 15.5-18.1% improvement on chest X-ray finding classification, and 10.8% improvement on agentic evaluations compared to the base models. Fine-tuning MedGemma further improves performance in subdomains, reducing errors in electronic health record information retrieval by 50% and reaching comparable performance to existing specialized state-of-the-art methods for pneumothorax classification and histopathology patch classification. We additionally introduce MedSigLIP, a medically-tuned vision encoder derived from SigLIP. MedSigLIP powers the visual understanding capabilities of MedGemma and as an encoder achieves comparable or better performance than specialized medical image encoders. Taken together, the MedGemma collection provides a strong foundation of medical image and text capabilities, with potential to significantly accelerate medical research and development of downstream applications. The MedGemma collection, including tutorials and model weights, can be found at https://goo.gle/medgemma.

PaliGemma 2 is an upgrade of the PaliGemma open Vision-Language Model (VLM) based on the Gemma 2 family of language models. We combine the SigLIP-So400m vision encoder that was also used by PaliGemma with the whole range of Gemma 2 models, from the 2B one all the way up to the 27B model. We train these models at three resolutions (224px, 448px, and 896px) in multiple stages to equip them with broad knowledge for transfer via fine-tuning. The resulting family of base models covering different model sizes and resolutions allows us to investigate factors impacting transfer performance (such as learning rate) and to analyze the interplay between the type of task, model size, and resolution. We further increase the number and breadth of transfer tasks beyond the scope of PaliGemma including different OCR-related tasks such as table structure recognition, molecular structure recognition, music score recognition, as well as long fine-grained captioning and radiography report generation, on which PaliGemma 2 obtains state-of-the-art results.

We introduce VL-JEPA, a vision-language model built on a Joint Embedding Predictive Architecture (JEPA). Instead of autoregressively generating tokens as in classical VLMs, VL-JEPA predicts continuous embeddings of the target texts. By learning in an abstract representation space, the model focuses on task-relevant semantics while abstracting away surface-level linguistic variability. In a strictly controlled comparison against standard token-space VLM training with the same vision encoder and training data, VL-JEPA achieves stronger performance while having 50% fewer trainable parameters. At inference time, a lightweight text decoder is invoked only when needed to translate VL-JEPA predicted embeddings into text. We show that VL-JEPA natively supports selective decoding that reduces the number of decoding operations by 2.85x while maintaining similar performance compared to non-adaptive uniform decoding. Beyond generation, the VL-JEPA's embedding space naturally supports open-vocabulary classification, text-to-video retrieval, and discriminative VQA without any architecture modification. On eight video classification and eight video retrieval datasets, the average performance VL-JEPA surpasses that of CLIP, SigLIP2, and Perception Encoder. At the same time, the model achieves comparable performance as classical VLMs (InstructBLIP, QwenVL) on four VQA datasets: GQA, TallyQA, POPE and POPEv2, despite only having 1.6B parameters.

The objective in this paper is to improve the performance of text-to-image retrieval. To this end, we introduce a new framework that can boost the performance of large-scale pre-trained vision-language models, so that they can be used for text-to-image re-ranking. The approach, Enhanced Language-Image Pre-training (ELIP), uses the text query, via a simple MLP mapping network, to predict a set of visual prompts to condition the ViT image encoding. ELIP can easily be applied to the commonly used CLIP, SigLIP and BLIP-2 networks. To train the architecture with limited computing resources, we develop a 'student friendly' best practice, involving global hard sample mining, and curation of a large-scale dataset. On the evaluation side, we set up two new out-of-distribution (OOD) benchmarks, Occluded COCO and ImageNet-R, to assess the zero-shot generalisation of the models to different domains. The results demonstrate that ELIP significantly boosts CLIP/SigLIP/SigLIP-2 text-to-image retrieval performance and outperforms BLIP-2 on several benchmarks, as well as providing an easy means to adapt to OOD datasets.

Large-scale and high-quality image-text pair datasets play an important role in developing high-performing Vision-Language Models (VLMs). In this work, we introduce WAON, a large-scale and high-quality Japanese image-text pair dataset containing approximately 155 million examples, collected from Common Crawl. Our dataset construction pipeline employs various techniques, including filtering and deduplication, which have been shown to be effective in previous studies. To evaluate its effectiveness, we also construct WAON-Bench, a manually curated benchmark for Japanese cultural image classification, consisting of 374 classes. To assess the effectiveness of our dataset, we conduct experiments using both WAON and the Japanese subset of ReLAION, one of the most widely used vision-language datasets. We fine-tune SigLIP2, a strong multilingual model, on both datasets. The results demonstrate that WAON enhances model performance on WAON-Bench more efficiently than ReLAION and achieves higher accuracy across all evaluated benchmarks. Furthermore, the model fine-tuned on WAON achieves state-of-the-art performance on several Japanese cultural benchmarks. We release our dataset, model, and code at https://speed1313.github.io/WAON.

This paper presents PaLI-3, a smaller, faster, and stronger vision language model (VLM) that compares favorably to similar models that are 10x larger. As part of arriving at this strong performance, we compare Vision Transformer (ViT) models pretrained using classification objectives to contrastively (SigLIP) pretrained ones. We find that, while slightly underperforming on standard image classification benchmarks, SigLIP-based PaLI shows superior performance across various multimodal benchmarks, especially on localization and visually-situated text understanding. We scale the SigLIP image encoder up to 2 billion parameters, and achieves a new state-of-the-art on multilingual cross-modal retrieval. We hope that PaLI-3, at only 5B parameters, rekindles research on fundamental pieces of complex VLMs, and could fuel a new generation of scaled-up models.

Unified multimodal large language models (MLLMs) have shown promise in jointly advancing multimodal understanding and generation, with visual codebooks discretizing images into tokens for autoregressive modeling. Existing codebook-based methods either rely on small vocabularies (~16K entries) that lack fine-grained semantics or naively scale up, resulting in low token utilization and unstable training. We propose UniCode^2, a cascaded codebook framework enabling large-scale, semantically aligned, and stable visual tokenization. By clustering millions of SigLIP sequence embeddings, we build a 500K-entry codebook that preserves vision-language alignment while expanding capacity. Stability is ensured via a cascaded design: a frozen codebook anchors the embedding space, and a trainable codebook refines task-specific semantics. This decoupling promotes high utilization and robust learning. Moreover, the alignment of our visual tokens with textual semantics enables seamless integration with pretrained diffusion decoders, supporting high-quality visual synthesis with minimal adaptation. UniCode^2 delivers strong performance across diverse benchmarks, demonstrating the viability of scaling visual token spaces without sacrificing stability, semantics, or modularity.

Self-supervised vision-language models trained with contrastive objectives form the basis of current state-of-the-art methods in AI vision tasks. The success of these models is a direct consequence of the huge web-scale datasets used to train them, but they require correspondingly large vision components to properly learn powerful and general representations from such a broad data domain. This poses a challenge for deploying large vision-language models, especially in resource-constrained environments. To address this, we propose an alternate vision-language architecture, called HyperCLIP, that uses a small image encoder along with a hypernetwork that dynamically adapts image encoder weights to each new set of text inputs. All three components of the model (hypernetwork, image encoder, and text encoder) are pre-trained jointly end-to-end, and with a trained HyperCLIP model, we can generate new zero-shot deployment-friendly image classifiers for any task with a single forward pass through the text encoder and hypernetwork. HyperCLIP increases the zero-shot accuracy of SigLIP trained models with small image encoders by up to 3% on ImageNet and 5% on CIFAR-100 with minimal training throughput overhead.

OpenAI's CLIP, released in early 2021, have long been the go-to choice of vision encoder for building multimodal foundation models. Although recent alternatives such as SigLIP have begun to challenge this status quo, to our knowledge none are fully open: their training data remains proprietary and/or their training recipes are not released. This paper fills this gap with OpenVision, a fully-open, cost-effective family of vision encoders that match or surpass the performance of OpenAI's CLIP when integrated into multimodal frameworks like LLaVA. OpenVision builds on existing works -- e.g., CLIPS for training framework and Recap-DataComp-1B for training data -- while revealing multiple key insights in enhancing encoder quality and showcasing practical benefits in advancing multimodal models. By releasing vision encoders spanning from 5.9M to 632.1M parameters, OpenVision offers practitioners a flexible trade-off between capacity and efficiency in building multimodal models: larger models deliver enhanced multimodal performance, while smaller versions enable lightweight, edge-ready multimodal deployments.

Storing open-source fine-tuned models separately introduces redundancy and increases response times in applications utilizing multiple models. Delta-parameter pruning (DPP), particularly the random drop and rescale (DARE) method proposed by Yu et al., addresses this by pruning the majority of delta parameters--the differences between fine-tuned and pre-trained model weights--while typically maintaining minimal performance loss. However, DARE fails when either the pruning rate or the magnitude of the delta parameters is large. We highlight two key reasons for this failure: (1) an excessively large rescaling factor as pruning rates increase, and (2) high mean and variance in the delta parameters. To push DARE's limits, we introduce DAREx (DARE the eXtreme), which features two algorithmic improvements: (1) DAREx-q, a rescaling factor modification that significantly boosts performance at high pruning rates (e.g., >30 % on COLA and SST2 for encoder models, with even greater gains in decoder models), and (2) DAREx-L2, which combines DARE with AdamR, an in-training method that applies appropriate delta regularization before DPP. We also demonstrate that DAREx-q can be seamlessly combined with vanilla parameter-efficient fine-tuning techniques like LoRA and can facilitate structural DPP. Additionally, we revisit the application of importance-based pruning techniques within DPP, demonstrating that they outperform random-based methods when delta parameters are large. Through this comprehensive study, we develop a pipeline for selecting the most appropriate DPP method under various practical scenarios.

Zero-shot medical detection can further improve detection performance without relying on annotated medical images even upon the fine-tuned model, showing great clinical value. Recent studies leverage grounded vision-language models (GLIP) to achieve this by using detailed disease descriptions as prompts for the target disease name during the inference phase. However, these methods typically treat prompts as equivalent context to the target name, making it difficult to assign specific disease knowledge based on visual information, leading to a coarse alignment between images and target descriptions. In this paper, we propose StructuralGLIP, which introduces an auxiliary branch to encode prompts into a latent knowledge bank layer-by-layer, enabling more context-aware and fine-grained alignment. Specifically, in each layer, we select highly similar features from both the image representation and the knowledge bank, forming structural representations that capture nuanced relationships between image patches and target descriptions. These features are then fused across modalities to further enhance detection performance. Extensive experiments demonstrate that StructuralGLIP achieves a +4.1\% AP improvement over prior state-of-the-art methods across seven zero-shot medical detection benchmarks, and consistently improves fine-tuned models by +3.2\% AP on endoscopy image datasets.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

DINO and DINOv2 are two model families being widely used to learn representations from unlabeled imagery data at large scales. Their learned representations often enable state-of-the-art performance for downstream tasks, such as image classification and segmentation. However, they employ many empirically motivated design choices and their training pipelines are highly complex and unstable -- many hyperparameters need to be carefully tuned to ensure that the representations do not collapse -- which poses considerable difficulty to improving them or adapting them to new domains. In this work, we posit that we can remove most such-motivated idiosyncrasies in the pre-training pipelines, and only need to add an explicit coding rate term in the loss function to avoid collapse of the representations. As a result, we obtain highly simplified variants of the DINO and DINOv2 which we call SimDINO and SimDINOv2, respectively. Remarkably, these simplified models are more robust to different design choices, such as network architecture and hyperparameters, and they learn even higher-quality representations, measured by performance on downstream tasks, offering a Pareto improvement over the corresponding DINO and DINOv2 models. This work highlights the potential of using simplifying design principles to improve the empirical practice of deep learning.

Pre-trained Vision Foundation Models (VFMs) provide strong visual representations for a wide range of applications. In this paper, we continually pre-train prevailing VFMs in a multimodal manner such that they can effortlessly process visual inputs of varying sizes and produce visual representations that are more aligned with language representations, regardless of their original pre-training process. To this end, we introduce CoMP, a carefully designed multimodal pre-training pipeline. CoMP uses a Continual Rotary Position Embedding to support native resolution continual pre-training, and an Alignment Loss between visual and textual features through language prototypes to align multimodal representations. By three-stage training, our VFMs achieve remarkable improvements not only in multimodal understanding but also in other downstream tasks such as classification and segmentation. Remarkably, CoMP-SigLIP achieves scores of 66.7 on ChartQA and 75.9 on DocVQA with a 0.5B LLM, while maintaining an 87.4% accuracy on ImageNet-1K and a 49.5 mIoU on ADE20K under frozen chunk evaluation.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

Frontier AI models have achieved remarkable progress, yet recent studies suggest they struggle with compositional reasoning, often performing at or below random chance on established benchmarks. We revisit this problem and show that widely used evaluation metrics systematically underestimate model capability. To address this, we introduce a group matching score that better exploits group structure and reveals substantial hidden capability in both contrastive vision-language models (VLMs) and multimodal large language models (MLLMs). Moreover, simply overfitting to the induced group matchings at test time transfers this hidden capability into higher scores under standard evaluation metrics, closing much of the reported gap. This adjustment enables SigLIP-B16 to surpass all previous results and GPT-4.1 to yield the first result surpassing estimated human performance on Winoground. Building on this insight, we propose Test-Time Matching (TTM), an iterative, self-improving algorithm that further bootstraps model performance without any external supervision. TTM delivers additional, non-trivial improvements: for example, TTM enables SigLIP-B16 to surpass GPT-4.1 on MMVP-VLM, establishing a new state of the art. Importantly, TTM remains broadly effective even on benchmarks without metric-induced effects or group structures, achieving relative gains up to 85.7% on challenging datasets such as WhatsUp. Across 16 dataset variants spanning diverse setups, our experiments demonstrate that TTM consistently improves model performance and advances the frontier of compositional reasoning.

In the realm of Virtual Reality (VR) and Human-Computer Interaction (HCI), real-time emotion recognition shows promise for supporting individuals with Autism Spectrum Disorder (ASD) in improving social skills. This task requires a strict latency-accuracy trade-off, with motion-to-photon (MTP) latency kept below 140 ms to maintain contingency. However, most off-the-shelf Deep Learning models prioritize accuracy over the strict timing constraints of commodity hardware. As a first step toward accessible VR therapy, we benchmark State-of-the-Art (SOTA) models for Zero-Shot Facial Expression Recognition (FER) on virtual characters using the UIBVFED dataset. We evaluate Medium and Nano variants of YOLO (v8, v11, and v12) for face detection, alongside general-purpose Vision Transformers including CLIP, SigLIP, and ViT-FER.Our results on CPU-only inference demonstrate that while face detection on stylized avatars is robust (100% accuracy), a "Latency Wall" exists in the classification stage. The YOLOv11n architecture offers the optimal balance for detection (~54 ms). However, general-purpose Transformers like CLIP and SigLIP fail to achieve viable accuracy (<23%) or speed (>150 ms) for real-time loops. This study highlights the necessity for lightweight, domain-specific architectures to enable accessible, real-time AI in therapeutic settings.

Discrete diffusion models enable parallel token sampling for faster inference than autoregressive approaches. However, prior diffusion models use a decoder-only architecture, which requires sampling algorithms that invoke the full network at every denoising step and incur high computational cost. Our key insight is that discrete diffusion models perform two types of computation: 1) representing clean tokens and 2) denoising corrupted tokens, which enables us to use separate modules for each task. We propose an encoder-decoder architecture to accelerate discrete diffusion inference, which relies on an encoder to represent clean tokens and a lightweight decoder to iteratively refine a noised sequence. We also show that this architecture enables faster training of block diffusion models, which partition sequences into blocks for better quality and are commonly used in diffusion language model inference. We introduce a framework for Efficient Encoder-Decoder Diffusion (E2D2), consisting of an architecture with specialized training and sampling algorithms, and we show that E2D2 achieves superior trade-offs between generation quality and inference throughput on summarization, translation, and mathematical reasoning tasks. We provide the code, model weights, and blog post on the project page: https://m-arriola.com/e2d2

Benefiting from the simplicity and effectiveness of Dense O2O and MAL, DEIM has become the mainstream training framework for real-time DETRs, significantly outperforming the YOLO series. In this work, we extend it with DINOv3 features, resulting in DEIMv2. DEIMv2 spans eight model sizes from X to Atto, covering GPU, edge, and mobile deployment. For the X, L, M, and S variants, we adopt DINOv3-pretrained or distilled backbones and introduce a Spatial Tuning Adapter (STA), which efficiently converts DINOv3's single-scale output into multi-scale features and complements strong semantics with fine-grained details to enhance detection. For ultra-lightweight models (Nano, Pico, Femto, and Atto), we employ HGNetv2 with depth and width pruning to meet strict resource budgets. Together with a simplified decoder and an upgraded Dense O2O, this unified design enables DEIMv2 to achieve a superior performance-cost trade-off across diverse scenarios, establishing new state-of-the-art results. Notably, our largest model, DEIMv2-X, achieves 57.8 AP with only 50.3 million parameters, surpassing prior X-scale models that require over 60 million parameters for just 56.5 AP. On the compact side, DEIMv2-S is the first sub-10 million model (9.71 million) to exceed the 50 AP milestone on COCO, reaching 50.9 AP. Even the ultra-lightweight DEIMv2-Pico, with just 1.5 million parameters, delivers 38.5 AP, matching YOLOv10-Nano (2.3 million) with around 50 percent fewer parameters. Our code and pre-trained models are available at https://github.com/Intellindust-AI-Lab/DEIMv2

We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity (ΔG) and mutation-induced affinity changes (ΔΔG) using only protein sequence information. Our approach offers a significant advancement over existing methods by employing specialized prediction heads that operate on a shared representation network, allowing direct and optimized prediction of both values. To ensure robust generalization, we integrated complementary datasets from SKEMPI v2 and PDBbind with a rigorous protein domain-based splitting strategy that prevents information leakage between training and validation sets. Our architecture combines transformer-based encoders with a novel cross-attention mechanism that processes paired protein sequences directly, without requiring any structural information. The network embeds input sequences using ESM3 representations, then employs a learnable sliced window embedding layer to manage variable-length sequences efficiently. A multi-layer transformer encoder with bidirectional self-attention captures intra-protein patterns, while cross-attention layers enable explicit modeling of interactions between protein pairs. This shared representation network feeds into separate ΔG and ΔΔG prediction heads, allowing task-specific optimization while leveraging common features. The model achieves ΔΔG validation of Pearson correlation at 0.485, while maintaining strong ΔG predictions (Pearson: 0.638). While existing approaches require protein structure data and binding interface information, our model eliminates these constraints. This provides a critical advantage for the numerous proteins with unknown structures or those challenging to crystallize, such as viral and intrinsically disordered proteins.

Recent progress in Multimodal Large Language Models (MLLMs) has highlighted the critical roles of both the visual backbone and the underlying language model. While prior work has primarily focused on scaling these components to billions of parameters, the trade-offs between model size, architecture, and performance remain underexplored. Additionally, inconsistencies in training data and evaluation protocols have hindered direct comparisons, making it difficult to derive optimal design choices. In this paper, we introduce LLaVA-MORE, a new family of MLLMs that integrates recent language models with diverse visual backbones. To ensure fair comparisons, we employ a unified training protocol applied consistently across all architectures. Our analysis systematically explores both small- and medium-scale LLMs -- including Phi-4, LLaMA-3.1, and Gemma-2 -- to evaluate multimodal reasoning, generation, and instruction following, while examining the relationship between model size and performance. Beyond evaluating the LLM impact on final results, we conduct a comprehensive study of various visual encoders, ranging from CLIP-based architectures to alternatives such as DINOv2, SigLIP, and SigLIP2. Additional experiments investigate the effects of increased image resolution and variations in pre-training datasets. Overall, our results provide insights into the design of more effective MLLMs, offering a reproducible evaluation framework that facilitates direct comparisons and can guide future model development. Our source code and trained models are publicly available at: https://github.com/aimagelab/LLaVA-MORE.

We study the effectiveness of data-balancing for mitigating biases in contrastive language-image pretraining (CLIP), identifying areas of strength and limitation. First, we reaffirm prior conclusions that CLIP models can inadvertently absorb societal stereotypes. To counter this, we present a novel algorithm, called Multi-Modal Moment Matching (M4), designed to reduce both representation and association biases (i.e. in first- and second-order statistics) in multimodal data. We use M4 to conduct an in-depth analysis taking into account various factors, such as the model, representation, and data size. Our study also explores the dynamic nature of how CLIP learns and unlearns biases. In particular, we find that fine-tuning is effective in countering representation biases, though its impact diminishes for association biases. Also, data balancing has a mixed impact on quality: it tends to improve classification but can hurt retrieval. Interestingly, data and architectural improvements seem to mitigate the negative impact of data balancing on performance; e.g. applying M4 to SigLIP-B/16 with data quality filters improves COCO image-to-text retrieval @5 from 86% (without data balancing) to 87% and ImageNet 0-shot classification from 77% to 77.5%! Finally, we conclude with recommendations for improving the efficacy of data balancing in multimodal systems.

Determining the necessity of resecting malignant polyps during colonoscopy screen is crucial for patient outcomes, yet challenging due to the time-consuming and costly nature of histopathology examination. While deep learning-based classification models have shown promise in achieving optical biopsy with endoscopic images, they often suffer from a lack of explainability. To overcome this limitation, we introduce EndoFinder, a content-based image retrieval framework to find the 'digital twin' polyp in the reference database given a newly detected polyp. The clinical semantics of the new polyp can be inferred referring to the matched ones. EndoFinder pioneers a polyp-aware image encoder that is pre-trained on a large polyp dataset in a self-supervised way, merging masked image modeling with contrastive learning. This results in a generic embedding space ready for different downstream clinical tasks based on image retrieval. We validate the framework on polyp re-identification and optical biopsy tasks, with extensive experiments demonstrating that EndoFinder not only achieves explainable diagnostics but also matches the performance of supervised classification models. EndoFinder's reliance on image retrieval has the potential to support diverse downstream decision-making tasks during real-time colonoscopy procedures.

Recent advances in Neural Fields have enabled powerful, discretization-invariant methods for learning neural operators that approximate solutions of Partial Differential Equations (PDEs) on general geometries. Building on these developments, we introduce enf2enf, an encoder--decoder methodology for predicting steady-state Partial Differential Equations with non-parameterized geometric variability, based on recently proposed Equivariant Neural Field architectures. In enf2enf, input geometries are encoded into latent point cloud embeddings that inherently preserve geometric grounding and capture local phenomena. The resulting representations are then combined with global parameters and directly decoded into continuous output fields, thus efficiently modeling the coupling between geometry and physics. By leveraging the inductive biases of locality and translation invariance, our approach is able to capture fine-scale physical features as well as complex shape variations, thereby enhancing generalization and physical compliance. Extensive experiments on a high-fidelity aerodynamic dataset, a hyper-elastic material benchmark, and multi-element airfoil geometries, demonstrate that the proposed model achieves superior or competitive performance compared to state-of-the-art graph based, operator learning, and neural field methods. Notably, our method supports real time inference and zero-shot super-resolution, enabling efficient training on low-resolution meshes while maintaining high accuracy on full-scale discretizations.

While decoder-only large language models (LLMs) have shown impressive results, encoder-decoder models are still widely adopted in real-world applications for their inference efficiency and richer encoder representation. In this paper, we study a novel problem: adapting pretrained decoder-only LLMs to encoder-decoder, with the goal of leveraging the strengths of both approaches to achieve a more favorable quality-efficiency trade-off. We argue that adaptation not only enables inheriting the capability of decoder-only LLMs but also reduces the demand for computation compared to pretraining from scratch. We rigorously explore different pretraining objectives and parameter initialization/optimization techniques. Through extensive experiments based on Gemma 2 (2B and 9B) and a suite of newly pretrained mT5-sized models (up to 1.6B), we demonstrate the effectiveness of adaptation and the advantage of encoder-decoder LLMs. Under similar inference budget, encoder-decoder LLMs achieve comparable (often better) pretraining performance but substantially better finetuning performance than their decoder-only counterpart. For example, Gemma 2B-2B outperforms Gemma 2B by sim7\% after instruction tuning. Encoder-decoder adaptation also allows for flexible combination of different-sized models, where Gemma 9B-2B significantly surpasses Gemma 2B-2B by >3\%. The adapted encoder representation also yields better results on SuperGLUE. We will release our checkpoints to facilitate future research.

Neural Implicit Representation (NIR) has recently gained significant attention due to its remarkable ability to encode complex and high-dimensional data into representation space and easily reconstruct it through a trainable mapping function. However, NIR methods assume a one-to-one mapping between the target data and representation models regardless of data relevancy or similarity. This results in poor generalization over multiple complex data and limits their efficiency and scalability. Motivated by continual learning, this work investigates how to accumulate and transfer neural implicit representations for multiple complex video data over sequential encoding sessions. To overcome the limitation of NIR, we propose a novel method, Progressive Fourier Neural Representation (PFNR), that aims to find an adaptive and compact sub-module in Fourier space to encode videos in each training session. This sparsified neural encoding allows the neural network to hold free weights, enabling an improved adaptation for future videos. In addition, when learning a representation for a new video, PFNR transfers the representation of previous videos with frozen weights. This design allows the model to continuously accumulate high-quality neural representations for multiple videos while ensuring lossless decoding that perfectly preserves the learned representations for previous videos. We validate our PFNR method on the UVG8/17 and DAVIS50 video sequence benchmarks and achieve impressive performance gains over strong continual learning baselines. The PFNR code is available at https://github.com/ihaeyong/PFNR.git.

We study speech intent classification and slot filling (SICSF) by proposing to use an encoder pretrained on speech recognition (ASR) to initialize an end-to-end (E2E) Conformer-Transformer model, which achieves the new state-of-the-art results on the SLURP dataset, with 90.14% intent accuracy and 82.27% SLURP-F1. We compare our model with encoders pretrained on self-supervised learning (SSL), and show that ASR pretraining is much more effective than SSL for SICSF. To explore parameter efficiency, we freeze the encoder and add Adapter modules, and show that parameter efficiency is only achievable with an ASR-pretrained encoder, while the SSL encoder needs full finetuning to achieve comparable results. In addition, we provide an in-depth comparison on end-to-end models versus cascading models (ASR+NLU), and show that E2E models are better than cascaded models unless an oracle ASR model is provided. Last but not least, our model is the first E2E model that achieves the same performance as cascading models with oracle ASR. Code, checkpoints and configs are available.

We present Waver, a high-performance foundation model for unified image and video generation. Waver can directly generate videos with durations ranging from 5 to 10 seconds at a native resolution of 720p, which are subsequently upscaled to 1080p. The model simultaneously supports text-to-video (T2V), image-to-video (I2V), and text-to-image (T2I) generation within a single, integrated framework. We introduce a Hybrid Stream DiT architecture to enhance modality alignment and accelerate training convergence. To ensure training data quality, we establish a comprehensive data curation pipeline and manually annotate and train an MLLM-based video quality model to filter for the highest-quality samples. Furthermore, we provide detailed training and inference recipes to facilitate the generation of high-quality videos. Building on these contributions, Waver excels at capturing complex motion, achieving superior motion amplitude and temporal consistency in video synthesis. Notably, it ranks among the Top 3 on both the T2V and I2V leaderboards at Artificial Analysis (data as of 2025-07-30 10:00 GMT+8), consistently outperforming existing open-source models and matching or surpassing state-of-the-art commercial solutions. We hope this technical report will help the community more efficiently train high-quality video generation models and accelerate progress in video generation technologies. Official page: https://github.com/FoundationVision/Waver.

The BigCode project, an open-scientific collaboration focused on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder2. In partnership with Software Heritage (SWH), we build The Stack v2 on top of the digital commons of their source code archive. Alongside the SWH repositories spanning 619 programming languages, we carefully select other high-quality data sources, such as GitHub pull requests, Kaggle notebooks, and code documentation. This results in a training set that is 4x larger than the first StarCoder dataset. We train StarCoder2 models with 3B, 7B, and 15B parameters on 3.3 to 4.3 trillion tokens and thoroughly evaluate them on a comprehensive set of Code LLM benchmarks. We find that our small model, StarCoder2-3B, outperforms other Code LLMs of similar size on most benchmarks, and also outperforms StarCoderBase-15B. Our large model, StarCoder2- 15B, significantly outperforms other models of comparable size. In addition, it matches or outperforms CodeLlama-34B, a model more than twice its size. Although DeepSeekCoder- 33B is the best-performing model at code completion for high-resource languages, we find that StarCoder2-15B outperforms it on math and code reasoning benchmarks, as well as several low-resource languages. We make the model weights available under an OpenRAIL license and ensure full transparency regarding the training data by releasing the SoftWare Heritage persistent IDentifiers (SWHIDs) of the source code data.

Code generation using large language models (LLMs) is highly sensitive to the choice of tokens during decoding, especially at points of uncertainty that critically affect the generated program's logic. Conventional decoding methods such as greedy search and beam search apply uniform treatment to all tokens, neglecting the unique uncertainty characteristics inherent in code generation, which can result in suboptimal outputs. In this work, we conduct an empirical analysis demonstrating that a significant portion of generation errors arises from incorrect token ranking at high-uncertainty steps, where the ground truth token exists in the candidate set but fails to be ranked first. Inspired by this insight, we introduce AdaDec, an adaptive decoding framework guided by token-level uncertainty quantified via Shannon entropy. AdaDec dynamically learns uncertainty thresholds tailored to each model and employs a pause-then-rerank mechanism with lookahead when the uncertainty surpasses these thresholds. Evaluation on the HumanEval and MBPP benchmarks reveals that AdaDec achieves up to a 15.5% improvement in Pass@1 accuracy compared to greedy decoding, matches or outperforms traditional beam search, and reduces both computational overhead and latency through targeted, selective pausing. Our findings suggest that uncertainty-aware adaptive decoding holds considerable potential for enhancing both the reliability and efficiency of code generation with LLMs.

Foundation image-text models such as CLIP with zero-shot capabilities enable a wide array of applications. MobileCLIP is a recent family of image-text models at 3-15ms latency and 50-150M parameters with state-of-the-art zero-shot accuracy. The main ingredients in MobileCLIP were its low-latency and light architectures and a novel multi-modal reinforced training that made knowledge distillation from multiple caption-generators and CLIP teachers efficient, scalable, and reproducible. In this paper, we improve the multi-modal reinforced training of MobileCLIP through: 1) better CLIP teacher ensembles trained on the DFN dataset, 2) improved captioner teachers trained on the DFN dataset and fine-tuned on a diverse selection of high-quality image-caption datasets. We discover new insights through ablations such as the importance of temperature tuning in contrastive knowledge distillation, the effectiveness of caption-generator fine-tuning for caption diversity, and the additive improvement from combining synthetic captions generated by multiple models. We train a new family of models called MobileCLIP2 and achieve state-of-the-art ImageNet-1k zero-shot accuracies at low latencies. In particular, we observe 2.2% improvement in ImageNet-1k accuracy for MobileCLIP2-B compared with MobileCLIP-B architecture. Notably, MobileCLIP2-S4 matches the zero-shot accuracy of SigLIP-SO400M/14 on ImageNet-1k while being 2times smaller and improves on DFN ViT-L/14 at 2.5times lower latency. We release our pretrained models (https://github.com/apple/ml-mobileclip) and the data generation code (https://github.com/apple/ml-mobileclip-dr). The data generation code makes it easy to create new reinforced datasets with arbitrary teachers using distributed scalable processing.

Recent studies have highlighted the potential of adapting the Segment Anything Model (SAM) for various downstream tasks. However, constructing a more powerful and generalizable encoder to further enhance performance remains an open challenge. In this work, we propose SAM2-UNeXT, an advanced framework that builds upon the core principles of SAM2-UNet while extending the representational capacity of SAM2 through the integration of an auxiliary DINOv2 encoder. By incorporating a dual-resolution strategy and a dense glue layer, our approach enables more accurate segmentation with a simple architecture, relaxing the need for complex decoder designs. Extensive experiments conducted on four benchmarks, including dichotomous image segmentation, camouflaged object detection, marine animal segmentation, and remote sensing saliency detection, demonstrate the superior performance of our proposed method. The code is available at https://github.com/WZH0120/SAM2-UNeXT.

Large Language Models (LLMs) have demonstrated exceptional performance across diverse natural language processing tasks. However, these models exhibit a critical limitation in output diversity, often generating highly similar content across multiple attempts. This limitation significantly affects tasks requiring diverse outputs, from creative writing to reasoning. Existing solutions, like temperature scaling, enhance diversity by modifying probability distributions but compromise output quality. We propose Guide-to-Generation (G2), a training-free plug-and-play method that enhances output diversity while preserving generation quality. G2 employs a base generator alongside dual Guides, which guide the generation process through decoding-based interventions to encourage more diverse outputs conditioned on the original query. Comprehensive experiments demonstrate that G2 effectively improves output diversity while maintaining an optimal balance between diversity and quality.

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time.

The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce Prot2Token, a unified framework that overcomes these challenges by converting a wide spectrum of protein-related predictions, from sequence-level properties and residue-specific attributes to complex inter-protein interactions, into a standardized next-token prediction format. At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens, to perform diverse predictions. This architecture uniquely facilitates multi-task learning, enabling a single model to master numerous tasks with improved efficiency. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks. Key results include significant speedups (e.g., near 1000x over AlphaFold2 with MSA) and performance often matching or exceeding specialized approaches. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a significant step towards a versatile, high-throughput paradigm for protein modeling, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .

Vision-Language Pre-training (VLP) models demonstrate strong performance across various downstream tasks by learning from large-scale image-text pairs through contrastive pretraining. The release of extensive English image-text datasets (e.g., COYO-700M and LAION-400M) has enabled widespread adoption of models such as CLIP and SigLIP in tasks including cross-modal retrieval and image captioning. However, the advancement of Chinese vision-language pretraining has substantially lagged behind, due to the scarcity of high-quality Chinese image-text data. To address this gap, we develop a comprehensive pipeline for constructing a high-quality Chinese cross-modal dataset. As a result, we propose DanQing, which contains 100 million image-text pairs collected from Common Crawl. Different from existing datasets, DanQing is curated through a more rigorous selection process, yielding superior data quality. Moreover, DanQing is primarily built from 2024-2025 web data, enabling models to better capture evolving semantic trends and thus offering greater practical utility. We compare DanQing with existing datasets by continual pre-training of the SigLIP2 model. Experimental results show that DanQing consistently achieves superior performance across a range of Chinese downstream tasks, including zero-shot classification, cross-modal retrieval, and LMM-based evaluations. To facilitate further research in Chinese vision-language pre-training, we will open-source the DanQing dataset under the Creative Common CC-BY 4.0 license.

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.

Protein inverse folding, the design of an amino acid sequence based on a target 3D structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models (PLMs). The former omits the evolutionary information stored in protein databases, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called retrieval-augmented denoising diffusion (RadDiff), for protein inverse folding. Given the target protein backbone, RadDiff uses a hierarchical search strategy to efficiently retrieve structurally similar proteins from large protein databases. The retrieved structures are then aligned residue-by-residue to the target to construct a position-specific amino acid profile, which serves as an evolutionary-informed prior that conditions the denoising process. A lightweight integration module is further designed to incorporate this prior effectively. Experimental results on the CATH, PDB, and TS50 datasets show that RadDiff consistently outperforms existing methods, improving sequence recovery rate by up to 19%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

Sequence-to-sequence (seq2seq) learning is a popular fashion for large-scale pretraining language models. However, the prior seq2seq pretraining models generally focus on reconstructive objectives on the decoder side and neglect the effect of encoder-side supervision, which we argue may lead to sub-optimal performance. To verify our hypothesis, we first empirically study the functionalities of the encoder and decoder in seq2seq pretrained language models, and find that the encoder takes an important but under-exploitation role than the decoder regarding the downstream performance and neuron activation. Therefore, we propose an encoding-enhanced seq2seq pretraining strategy, namely E2S2, which improves the seq2seq models via integrating more efficient self-supervised information into the encoders. Specifically, E2S2 adopts two self-supervised objectives on the encoder side from two aspects: 1) locally denoising the corrupted sentence (denoising objective); and 2) globally learning better sentence representations (contrastive objective). With the help of both objectives, the encoder can effectively distinguish the noise tokens and capture high-level (i.e. syntactic and semantic) knowledge, thus strengthening the ability of seq2seq model to accurately achieve the conditional generation. On a large diversity of downstream natural language understanding and generation tasks, E2S2 dominantly improves the performance of its powerful backbone models, e.g. BART and T5. For example, upon BART backbone, we achieve +1.1% averaged gain on the general language understanding evaluation (GLUE) benchmark and +1.75% F_0.5 score improvement on CoNLL2014 dataset. We also provide in-depth analyses to show the improvement stems from better linguistic representation. We hope that our work will foster future self-supervision research on seq2seq language model pretraining.

Implicit Neural Representations (INRs) have become an essential tool for modeling continuous 2D images, enabling high-fidelity reconstruction, super-resolution, and compression. Popular architectures such as SIREN, WIRE, and FINER demonstrate the potential of INR for capturing fine-grained image details. However, traditional INRs often lack explicit geometric structure and have limited capabilities for local editing or integration with physical simulation, restricting their applicability in dynamic or interactive settings. To address these limitations, we propose GaINeR: Geometry-Aware Implicit Network Representation, a novel framework for 2D images that combines trainable Gaussian distributions with a neural network-based INR. For a given image coordinate, the model retrieves the K nearest Gaussians, aggregates distance-weighted embeddings, and predicts the RGB value via a neural network. This design enables continuous image representation, interpretable geometric structure, and flexible local editing, providing a foundation for physically aware and interactive image manipulation. The official implementation of our method is publicly available at https://github.com/WJakubowska/GaINeR.

A naive application of state-of-the-art bidirectional encoders for streaming sequence tagging would require encoding each token from scratch for each new token in an incremental streaming input (like transcribed speech). The lack of re-usability of previous computation leads to a higher number of Floating Point Operations (or FLOPs) and higher number of unnecessary label flips. Increased FLOPs consequently lead to higher wall-clock time and increased label flipping leads to poorer streaming performance. In this work, we present a Hybrid Encoder with Adaptive Restart (HEAR) that addresses these issues while maintaining the performance of bidirectional encoders over the offline (or complete) inputs while improving performance on streaming (or incomplete) inputs. HEAR has a Hybrid unidirectional-bidirectional encoder architecture to perform sequence tagging, along with an Adaptive Restart Module (ARM) to selectively guide the restart of bidirectional portion of the encoder. Across four sequence tagging tasks, HEAR offers FLOP savings in streaming settings upto 71.1% and also outperforms bidirectional encoders for streaming predictions by upto +10% streaming exact match.

We present DeepSeek-Coder-V2, an open-source Mixture-of-Experts (MoE) code language model that achieves performance comparable to GPT4-Turbo in code-specific tasks. Specifically, DeepSeek-Coder-V2 is further pre-trained from an intermediate checkpoint of DeepSeek-V2 with additional 6 trillion tokens. Through this continued pre-training, DeepSeek-Coder-V2 substantially enhances the coding and mathematical reasoning capabilities of DeepSeek-V2, while maintaining comparable performance in general language tasks. Compared to DeepSeek-Coder-33B, DeepSeek-Coder-V2 demonstrates significant advancements in various aspects of code-related tasks, as well as reasoning and general capabilities. Additionally, DeepSeek-Coder-V2 expands its support for programming languages from 86 to 338, while extending the context length from 16K to 128K. In standard benchmark evaluations, DeepSeek-Coder-V2 achieves superior performance compared to closed-source models such as GPT4-Turbo, Claude 3 Opus, and Gemini 1.5 Pro in coding and math benchmarks.

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: https://github.com/kaist-silab/bootgen{https://github.com/kaist-silab/bootgen}.

Text-to-Image (T2I) diffusion models have made remarkable advancements in generative modeling; however, they face a trade-off between inference speed and image quality, posing challenges for efficient deployment. Existing distilled T2I models can generate high-fidelity images with fewer sampling steps, but often struggle with diversity and quality, especially in one-step models. From our analysis, we observe redundant computations in the UNet encoders. Our findings suggest that, for T2I diffusion models, decoders are more adept at capturing richer and more explicit semantic information, while encoders can be effectively shared across decoders from diverse time steps. Based on these observations, we introduce the first Time-independent Unified Encoder TiUE for the student model UNet architecture, which is a loop-free image generation approach for distilling T2I diffusion models. Using a one-pass scheme, TiUE shares encoder features across multiple decoder time steps, enabling parallel sampling and significantly reducing inference time complexity. In addition, we incorporate a KL divergence term to regularize noise prediction, which enhances the perceptual realism and diversity of the generated images. Experimental results demonstrate that TiUE outperforms state-of-the-art methods, including LCM, SD-Turbo, and SwiftBrushv2, producing more diverse and realistic results while maintaining the computational efficiency.

Recent advances in dense 3D reconstruction have led to significant progress, yet achieving accurate unified geometric prediction remains a major challenge. Most existing methods are limited to predicting a single geometry quantity from input images. However, geometric quantities such as depth, surface normals, and point maps are inherently correlated, and estimating them in isolation often fails to ensure consistency, thereby limiting both accuracy and practical applicability. This motivates us to explore a unified framework that explicitly models the structural coupling among different geometric properties to enable joint regression. In this paper, we present Dens3R, a 3D foundation model designed for joint geometric dense prediction and adaptable to a wide range of downstream tasks. Dens3R adopts a two-stage training framework to progressively build a pointmap representation that is both generalizable and intrinsically invariant. Specifically, we design a lightweight shared encoder-decoder backbone and introduce position-interpolated rotary positional encoding to maintain expressive power while enhancing robustness to high-resolution inputs. By integrating image-pair matching features with intrinsic invariance modeling, Dens3R accurately regresses multiple geometric quantities such as surface normals and depth, achieving consistent geometry perception from single-view to multi-view inputs. Additionally, we propose a post-processing pipeline that supports geometrically consistent multi-view inference. Extensive experiments demonstrate the superior performance of Dens3R across various dense 3D prediction tasks and highlight its potential for broader applications.

Recent advancements in subject-driven image generation have led to zero-shot generation, yet precise selection and focus on crucial subject representations remain challenging. Addressing this, we introduce the SSR-Encoder, a novel architecture designed for selectively capturing any subject from single or multiple reference images. It responds to various query modalities including text and masks, without necessitating test-time fine-tuning. The SSR-Encoder combines a Token-to-Patch Aligner that aligns query inputs with image patches and a Detail-Preserving Subject Encoder for extracting and preserving fine features of the subjects, thereby generating subject embeddings. These embeddings, used in conjunction with original text embeddings, condition the generation process. Characterized by its model generalizability and efficiency, the SSR-Encoder adapts to a range of custom models and control modules. Enhanced by the Embedding Consistency Regularization Loss for improved training, our extensive experiments demonstrate its effectiveness in versatile and high-quality image generation, indicating its broad applicability. Project page: https://ssr-encoder.github.io

Methods for image-to-video generation have achieved impressive, photo-realistic quality. However, adjusting specific elements in generated videos, such as object motion or camera movement, is often a tedious process of trial and error, e.g., involving re-generating videos with different random seeds. Recent techniques address this issue by fine-tuning a pre-trained model to follow conditioning signals, such as bounding boxes or point trajectories. Yet, this fine-tuning procedure can be computationally expensive, and it requires datasets with annotated object motion, which can be difficult to procure. In this work, we introduce SG-I2V, a framework for controllable image-to-video generation that is self-guidedx2013offering zero-shot control by relying solely on the knowledge present in a pre-trained image-to-video diffusion model without the need for fine-tuning or external knowledge. Our zero-shot method outperforms unsupervised baselines while being competitive with supervised models in terms of visual quality and motion fidelity.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

By leveraging multi-teacher distillation, agglomerative vision backbones provide a unified student model that retains and improves the distinct capabilities of multiple teachers. In this tech report, we describe the most recent release of the C-RADIO family of models, C-RADIOv4, which builds upon AM-RADIO/RADIOv2.5 in design, offering strong improvements on key downstream tasks at the same computational complexity. We release -SO400M (412M params), and -H (631M) model variants, both trained with an updated set of teachers: SigLIP2, DINOv3, and SAM3. In addition to improvements on core metrics and new capabilities from imitating SAM3, the C-RADIOv4 model family further improves any-resolution support, brings back the ViTDet option for drastically enhanced efficiency at high-resolution, and comes with a permissive license.

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

General-purpose multilingual vector representations, used in retrieval, regression and classification, are traditionally obtained from bidirectional encoder models. Despite their wide applicability, encoders have been recently overshadowed by advances in generative decoder-only models. However, many innovations driving this progress are not inherently tied to decoders. In this paper, we revisit the development of multilingual encoders through the lens of these advances, and introduce EuroBERT, a family of multilingual encoders covering European and widely spoken global languages. Our models outperform existing alternatives across a diverse range of tasks, spanning multilingual capabilities, mathematics, and coding, and natively supporting sequences of up to 8,192 tokens. We also examine the design decisions behind EuroBERT, offering insights into our dataset composition and training pipeline. We publicly release the EuroBERT models, including intermediate training checkpoints, together with our training framework.

Perspective projection has been extensively utilized in monocular 3D object detection methods. It introduces geometric priors from 2D bounding boxes and 3D object dimensions to reduce the uncertainty of depth estimation. However, due to depth errors originating from the object's visual surface, the height of the bounding box often fails to represent the actual projected central height, which undermines the effectiveness of geometric depth. Direct prediction for the projected height unavoidably results in a loss of 2D priors, while multi-depth prediction with complex branches does not fully leverage geometric depth. This paper presents a Transformer-based monocular 3D object detection method called MonoDGP, which adopts perspective-invariant geometry errors to modify the projection formula. We also try to systematically discuss and explain the mechanisms and efficacy behind geometry errors, which serve as a simple but effective alternative to multi-depth prediction. Additionally, MonoDGP decouples the depth-guided decoder and constructs a 2D decoder only dependent on visual features, providing 2D priors and initializing object queries without the disturbance of 3D detection. To further optimize and fine-tune input tokens of the transformer decoder, we also introduce a Region Segment Head (RSH) that generates enhanced features and segment embeddings. Our monocular method demonstrates state-of-the-art performance on the KITTI benchmark without extra data. Code is available at https://github.com/PuFanqi23/MonoDGP.

Recently diffusion models have shown improvement in synthetic image quality as well as better control in generation. We motivate and present Gen2Det, a simple modular pipeline to create synthetic training data for object detection for free by leveraging state-of-the-art grounded image generation methods. Unlike existing works which generate individual object instances, require identifying foreground followed by pasting on other images, we simplify to directly generating scene-centric images. In addition to the synthetic data, Gen2Det also proposes a suite of techniques to best utilize the generated data, including image-level filtering, instance-level filtering, and better training recipe to account for imperfections in the generation. Using Gen2Det, we show healthy improvements on object detection and segmentation tasks under various settings and agnostic to detection methods. In the long-tailed detection setting on LVIS, Gen2Det improves the performance on rare categories by a large margin while also significantly improving the performance on other categories, e.g. we see an improvement of 2.13 Box AP and 1.84 Mask AP over just training on real data on LVIS with Mask R-CNN. In the low-data regime setting on COCO, Gen2Det consistently improves both Box and Mask AP by 2.27 and 1.85 points. In the most general detection setting, Gen2Det still demonstrates robust performance gains, e.g. it improves the Box and Mask AP on COCO by 0.45 and 0.32 points.

Video synthesis has recently made remarkable strides benefiting from the rapid development of diffusion models. However, it still encounters challenges in terms of semantic accuracy, clarity and spatio-temporal continuity. They primarily arise from the scarcity of well-aligned text-video data and the complex inherent structure of videos, making it difficult for the model to simultaneously ensure semantic and qualitative excellence. In this report, we propose a cascaded I2VGen-XL approach that enhances model performance by decoupling these two factors and ensures the alignment of the input data by utilizing static images as a form of crucial guidance. I2VGen-XL consists of two stages: i) the base stage guarantees coherent semantics and preserves content from input images by using two hierarchical encoders, and ii) the refinement stage enhances the video's details by incorporating an additional brief text and improves the resolution to 1280times720. To improve the diversity, we collect around 35 million single-shot text-video pairs and 6 billion text-image pairs to optimize the model. By this means, I2VGen-XL can simultaneously enhance the semantic accuracy, continuity of details and clarity of generated videos. Through extensive experiments, we have investigated the underlying principles of I2VGen-XL and compared it with current top methods, which can demonstrate its effectiveness on diverse data. The source code and models will be publicly available at https://i2vgen-xl.github.io.

With the recent focus on Large Language Models (LLMs), both StarCoder (Li et al., 2023) and Code Llama (Rozi\`ere et al., 2023) have demonstrated remarkable performance in code generation. However, there is still a need for improvement in code translation functionality with efficient training techniques. In response to this, we introduce SteloCoder, a decoder-only StarCoder-based LLM designed specifically for multi-programming language-to-Python code translation. In particular, SteloCoder achieves C++, C#, JavaScript, Java, or PHP-to-Python code translation without specifying the input programming language. We modified StarCoder model architecture by incorporating a Mixture-of-Experts (MoE) technique featuring five experts and a gating network for multi-task handling. Experts are obtained by StarCoder fine-tuning. Specifically, we use a Low-Rank Adaptive Method (LoRA) technique, limiting each expert size as only 0.06% of number of StarCoder's parameters. At the same time, to enhance training efficiency in terms of time, we adopt curriculum learning strategy and use self-instruct data for efficient fine-tuning. As a result, each expert takes only 6 hours to train on one single 80Gb A100 HBM. With experiments on XLCoST datasets, SteloCoder achieves an average of 73.76 CodeBLEU score in multi-programming language-to-Python translation, surpassing the top performance from the leaderboard by at least 3.5. This accomplishment is attributed to only 45M extra parameters with StarCoder as the backbone and 32 hours of valid training on one 80GB A100 HBM. The source code is release here: https://github.com/sade-adrien/SteloCoder.

Despite the recent success of image-text contrastive models like CLIP and SigLIP, these models often struggle with vision-centric tasks that demand high-fidelity image understanding, such as counting, depth estimation, and fine-grained object recognition. These models, by performing language alignment, tend to prioritize high-level semantics over visual understanding, weakening their image understanding. On the other hand, vision-focused models are great at processing visual information but struggle to understand language, limiting their flexibility for language-driven tasks. In this work, we introduce TULIP, an open-source, drop-in replacement for existing CLIP-like models. Our method leverages generative data augmentation, enhanced image-image and text-text contrastive learning, and image/text reconstruction regularization to learn fine-grained visual features while preserving global semantic alignment. Our approach, scaling to over 1B parameters, outperforms existing state-of-the-art (SOTA) models across multiple benchmarks, establishing a new SOTA zero-shot performance on ImageNet-1K, delivering up to a 2times enhancement over SigLIP on RxRx1 in linear probing for few-shot classification, and improving vision-language models, achieving over 3times higher scores than SigLIP on MMVP. Our code/checkpoints are available at https://tulip-berkeley.github.io

Text-to-image (T2I) generative models have attracted significant attention and found extensive applications within and beyond academic research. For example, the Civitai community, a platform for T2I innovation, currently hosts an impressive array of 74,492 distinct models. However, this diversity presents a formidable challenge in selecting the most appropriate model and parameters, a process that typically requires numerous trials. Drawing inspiration from the tool usage research of large language models (LLMs), we introduce DiffAgent, an LLM agent designed to screen the accurate selection in seconds via API calls. DiffAgent leverages a novel two-stage training framework, SFTA, enabling it to accurately align T2I API responses with user input in accordance with human preferences. To train and evaluate DiffAgent's capabilities, we present DABench, a comprehensive dataset encompassing an extensive range of T2I APIs from the community. Our evaluations reveal that DiffAgent not only excels in identifying the appropriate T2I API but also underscores the effectiveness of the SFTA training framework. Codes are available at https://github.com/OpenGVLab/DiffAgent.

This paper introduces VALL-E 2, the latest advancement in neural codec language models that marks a milestone in zero-shot text-to-speech synthesis (TTS), achieving human parity for the first time. Based on its predecessor, VALL-E, the new iteration introduces two significant enhancements: Repetition Aware Sampling refines the original nucleus sampling process by accounting for token repetition in the decoding history. It not only stabilizes the decoding but also circumvents the infinite loop issue. Grouped Code Modeling organizes codec codes into groups to effectively shorten the sequence length, which not only boosts inference speed but also addresses the challenges of long sequence modeling. Our experiments on the LibriSpeech and VCTK datasets show that VALL-E 2 surpasses previous systems in speech robustness, naturalness, and speaker similarity. It is the first of its kind to reach human parity on these benchmarks. Moreover, VALL-E 2 consistently synthesizes high-quality speech, even for sentences that are traditionally challenging due to their complexity or repetitive phrases. The advantages of this work could contribute to valuable endeavors, such as generating speech for individuals with aphasia or people with amyotrophic lateral sclerosis. Demos of VALL-E 2 will be posted to https://aka.ms/valle2.

Ultra-fine-grained image recognition (UFGIR) categorizes objects with extremely small differences between classes, such as distinguishing between cultivars within the same species, as opposed to species-level classification in fine-grained image recognition (FGIR). The difficulty of this task is exacerbated due to the scarcity of samples per category. To tackle these challenges we introduce a novel approach employing down-sampling inter-layer adapters in a parameter-efficient setting, where the backbone parameters are frozen and we only fine-tune a small set of additional modules. By integrating dual-branch down-sampling, we significantly reduce the number of parameters and floating-point operations (FLOPs) required, making our method highly efficient. Comprehensive experiments on ten datasets demonstrate that our approach obtains outstanding accuracy-cost performance, highlighting its potential for practical applications in resource-constrained environments. In particular, our method increases the average accuracy by at least 6.8\% compared to other methods in the parameter-efficient setting while requiring at least 123x less trainable parameters compared to current state-of-the-art UFGIR methods and reducing the FLOPs by 30\% in average compared to other methods.

In this work, we question the necessity of adaptive gradient methods for training deep neural networks. SGD-SaI is a simple yet effective enhancement to stochastic gradient descent with momentum (SGDM). SGD-SaI performs learning rate Scaling at Initialization (SaI) to distinct parameter groups, guided by their respective gradient signal-to-noise ratios (g-SNR). By adjusting learning rates without relying on adaptive second-order momentum, SGD-SaI helps prevent training imbalances from the very first iteration and cuts the optimizer's memory usage by half compared to AdamW. Despite its simplicity and efficiency, SGD-SaI consistently matches or outperforms AdamW in training a variety of Transformer-based tasks, effectively overcoming a long-standing challenge of using SGD for training Transformers. SGD-SaI excels in ImageNet-1K classification with Vision Transformers(ViT) and GPT-2 pretraining for large language models (LLMs, transformer decoder-only), demonstrating robustness to hyperparameter variations and practicality for diverse applications. We further tested its robustness on tasks like LoRA fine-tuning for LLMs and diffusion models, where it consistently outperforms state-of-the-art optimizers. From a memory efficiency perspective, SGD-SaI achieves substantial memory savings for optimizer states, reducing memory usage by 5.93 GB for GPT-2 (1.5B parameters) and 25.15 GB for Llama2-7B compared to AdamW in full-precision training settings.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Object detection in point clouds is an important aspect of many robotics applications such as autonomous driving. In this paper we consider the problem of encoding a point cloud into a format appropriate for a downstream detection pipeline. Recent literature suggests two types of encoders; fixed encoders tend to be fast but sacrifice accuracy, while encoders that are learned from data are more accurate, but slower. In this work we propose PointPillars, a novel encoder which utilizes PointNets to learn a representation of point clouds organized in vertical columns (pillars). While the encoded features can be used with any standard 2D convolutional detection architecture, we further propose a lean downstream network. Extensive experimentation shows that PointPillars outperforms previous encoders with respect to both speed and accuracy by a large margin. Despite only using lidar, our full detection pipeline significantly outperforms the state of the art, even among fusion methods, with respect to both the 3D and bird's eye view KITTI benchmarks. This detection performance is achieved while running at 62 Hz: a 2 - 4 fold runtime improvement. A faster version of our method matches the state of the art at 105 Hz. These benchmarks suggest that PointPillars is an appropriate encoding for object detection in point clouds.

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

We propose SegGen, a highly-effective training data generation method for image segmentation, which pushes the performance limits of state-of-the-art segmentation models to a significant extent. SegGen designs and integrates two data generation strategies: MaskSyn and ImgSyn. (i) MaskSyn synthesizes new mask-image pairs via our proposed text-to-mask generation model and mask-to-image generation model, greatly improving the diversity in segmentation masks for model supervision; (ii) ImgSyn synthesizes new images based on existing masks using the mask-to-image generation model, strongly improving image diversity for model inputs. On the highly competitive ADE20K and COCO benchmarks, our data generation method markedly improves the performance of state-of-the-art segmentation models in semantic segmentation, panoptic segmentation, and instance segmentation. Notably, in terms of the ADE20K mIoU, Mask2Former R50 is largely boosted from 47.2 to 49.9 (+2.7); Mask2Former Swin-L is also significantly increased from 56.1 to 57.4 (+1.3). These promising results strongly suggest the effectiveness of our SegGen even when abundant human-annotated training data is utilized. Moreover, training with our synthetic data makes the segmentation models more robust towards unseen domains. Project website: https://seggenerator.github.io

Deep learning model inference on embedded devices is challenging due to the limited availability of computation resources. A popular alternative is to perform model inference on the cloud, which requires transmitting images from the embedded device to the cloud. Image compression techniques are commonly employed in such cloud-based architectures to reduce transmission latency over low bandwidth networks. This work proposes an end-to-end image compression framework that learns domain-specific features to achieve higher compression ratios than standard HEVC/JPEG compression techniques while maintaining accuracy on downstream tasks (e.g., recognition). Our framework does not require fine-tuning of the downstream task, which allows us to drop-in any off-the-shelf downstream task model without retraining. We choose faces as an application domain due to the ready availability of datasets and off-the-shelf recognition models as representative downstream tasks. We present a novel Identity Preserving Reconstruction (IPR) loss function which achieves Bits-Per-Pixel (BPP) values that are ~38% and ~42% of CRF-23 HEVC compression for LFW (low-resolution) and CelebA-HQ (high-resolution) datasets, respectively, while maintaining parity in recognition accuracy. The superior compression ratio is achieved as the model learns to retain the domain-specific features (e.g., facial features) while sacrificing details in the background. Furthermore, images reconstructed by our proposed compression model are robust to changes in downstream model architectures. We show at-par recognition performance on the LFW dataset with an unseen recognition model while retaining a lower BPP value of ~38% of CRF-23 HEVC compression.

Lossy image compression aims to represent images in as few bits as possible while maintaining fidelity to the original. Theoretical results indicate that optimizing distortion metrics such as PSNR or MS-SSIM necessarily leads to a discrepancy in the statistics of original images from those of reconstructions, in particular at low bitrates, often manifested by the blurring of the compressed images. Previous work has leveraged adversarial discriminators to improve statistical fidelity. Yet these binary discriminators adopted from generative modeling tasks may not be ideal for image compression. In this paper, we introduce a non-binary discriminator that is conditioned on quantized local image representations obtained via VQ-VAE autoencoders. Our evaluations on the CLIC2020, DIV2K and Kodak datasets show that our discriminator is more effective for jointly optimizing distortion (e.g., PSNR) and statistical fidelity (e.g., FID) than the state-of-the-art HiFiC model. On the CLIC2020 test set, we obtain the same FID as HiFiC with 30-40% fewer bits.

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

Background: We evaluate SAM 2 for surgical scene understanding by examining its semantic segmentation capabilities for organs/tissues both in zero-shot scenarios and after fine-tuning. Methods: We utilized five public datasets to evaluate and fine-tune SAM 2 for segmenting anatomical tissues in surgical videos/images. Fine-tuning was applied to the image encoder and mask decoder. We limited training subsets from 50 to 400 samples per class to better model real-world constraints with data acquisition. The impact of dataset size on fine-tuning performance was evaluated with weighted mean Dice coefficient (WMDC), and the results were also compared against previously reported state-of-the-art (SOTA) results. Results: SurgiSAM 2, a fine-tuned SAM 2 model, demonstrated significant improvements in segmentation performance, achieving a 17.9% relative WMDC gain compared to the baseline SAM 2. Increasing prompt points from 1 to 10 and training data scale from 50/class to 400/class enhanced performance; the best WMDC of 0.92 on the validation subset was achieved with 10 prompt points and 400 samples per class. On the test subset, this model outperformed prior SOTA methods in 24/30 (80%) of the classes with a WMDC of 0.91 using 10-point prompts. Notably, SurgiSAM 2 generalized effectively to unseen organ classes, achieving SOTA on 7/9 (77.8%) of them. Conclusion: SAM 2 achieves remarkable zero-shot and fine-tuned performance for surgical scene segmentation, surpassing prior SOTA models across several organ classes of diverse datasets. This suggests immense potential for enabling automated/semi-automated annotation pipelines, thereby decreasing the burden of annotations facilitating several surgical applications.

Large language models (LLMs) have shown remarkable progress in code generation, but their generated code often suffers from inefficiency, resulting in longer execution times and higher memory consumption. To address this issue, we propose EffiLearner, a self-optimization framework that utilizes execution overhead profiles to improve the efficiency of LLM-generated code. EffiLearner first generates code using an LLM, then executes it locally to capture execution time and memory usage profiles. These profiles are fed back to the LLM, which then revises the code to reduce overhead. To evaluate the effectiveness of EffiLearner, we conduct extensive experiments on the EffiBench, HumanEval, and MBPP with 16 open-source and 6 closed-source models. Our evaluation results demonstrate that through iterative self-optimization, EffiLearner significantly enhances the efficiency of LLM-generated code. For example, the execution time (ET) of StarCoder2-15B for the EffiBench decreases from 0.93 (s) to 0.12 (s) which reduces 87.1% the execution time requirement compared with the initial code. The total memory usage (TMU) of StarCoder2-15B also decreases from 22.02 (Mb*s) to 2.03 (Mb*s), which decreases 90.8% of total memory consumption during the execution process. The source code of EffiLearner was released in https://github.com/huangd1999/EffiLearner

In this paper, we present an encoder-decoder model leveraging Flan-T5 for post-Automatic Speech Recognition (ASR) Generative Speech Error Correction (GenSEC), and we refer to it as FlanEC. We explore its application within the GenSEC framework to enhance ASR outputs by mapping n-best hypotheses into a single output sentence. By utilizing n-best lists from ASR models, we aim to improve the linguistic correctness, accuracy, and grammaticality of final ASR transcriptions. Specifically, we investigate whether scaling the training data and incorporating diverse datasets can lead to significant improvements in post-ASR error correction. We evaluate FlanEC using the HyPoradise dataset, providing a comprehensive analysis of the model's effectiveness in this domain. Furthermore, we assess the proposed approach under different settings to evaluate model scalability and efficiency, offering valuable insights into the potential of instruction-tuned encoder-decoder models for this task.

We present SegFormer, a simple, efficient yet powerful semantic segmentation framework which unifies Transformers with lightweight multilayer perception (MLP) decoders. SegFormer has two appealing features: 1) SegFormer comprises a novel hierarchically structured Transformer encoder which outputs multiscale features. It does not need positional encoding, thereby avoiding the interpolation of positional codes which leads to decreased performance when the testing resolution differs from training. 2) SegFormer avoids complex decoders. The proposed MLP decoder aggregates information from different layers, and thus combining both local attention and global attention to render powerful representations. We show that this simple and lightweight design is the key to efficient segmentation on Transformers. We scale our approach up to obtain a series of models from SegFormer-B0 to SegFormer-B5, reaching significantly better performance and efficiency than previous counterparts. For example, SegFormer-B4 achieves 50.3% mIoU on ADE20K with 64M parameters, being 5x smaller and 2.2% better than the previous best method. Our best model, SegFormer-B5, achieves 84.0% mIoU on Cityscapes validation set and shows excellent zero-shot robustness on Cityscapes-C. Code will be released at: github.com/NVlabs/SegFormer.

We propose GE2E-KWS -- a generalized end-to-end training and evaluation framework for customized keyword spotting. Specifically, enrollment utterances are separated and grouped by keywords from the training batch and their embedding centroids are compared to all other test utterance embeddings to compute the loss. This simulates runtime enrollment and verification stages, and improves convergence stability and training speed by optimizing matrix operations compared to SOTA triplet loss approaches. To benchmark different models reliably, we propose an evaluation process that mimics the production environment and compute metrics that directly measure keyword matching accuracy. Trained with GE2E loss, our 419KB quantized conformer model beats a 7.5GB ASR encoder by 23.6% relative AUC, and beats a same size triplet loss model by 60.7% AUC. Our KWS models are natively streamable with low memory footprints, and designed to continuously run on-device with no retraining needed for new keywords (zero-shot).

Pre-training by numerous image data has become de-facto for robust 2D representations. In contrast, due to the expensive data acquisition and annotation, a paucity of large-scale 3D datasets severely hinders the learning for high-quality 3D features. In this paper, we propose an alternative to obtain superior 3D representations from 2D pre-trained models via Image-to-Point Masked Autoencoders, named as I2P-MAE. By self-supervised pre-training, we leverage the well learned 2D knowledge to guide 3D masked autoencoding, which reconstructs the masked point tokens with an encoder-decoder architecture. Specifically, we first utilize off-the-shelf 2D models to extract the multi-view visual features of the input point cloud, and then conduct two types of image-to-point learning schemes on top. For one, we introduce a 2D-guided masking strategy that maintains semantically important point tokens to be visible for the encoder. Compared to random masking, the network can better concentrate on significant 3D structures and recover the masked tokens from key spatial cues. For another, we enforce these visible tokens to reconstruct the corresponding multi-view 2D features after the decoder. This enables the network to effectively inherit high-level 2D semantics learned from rich image data for discriminative 3D modeling. Aided by our image-to-point pre-training, the frozen I2P-MAE, without any fine-tuning, achieves 93.4% accuracy for linear SVM on ModelNet40, competitive to the fully trained results of existing methods. By further fine-tuning on on ScanObjectNN's hardest split, I2P-MAE attains the state-of-the-art 90.11% accuracy, +3.68% to the second-best, demonstrating superior transferable capacity. Code will be available at https://github.com/ZrrSkywalker/I2P-MAE.

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: [email protected] or [email protected] Key words: Protein Q&A, Early-Fusion, LLM

One of the key components within diffusion models is the UNet for noise prediction. While several works have explored basic properties of the UNet decoder, its encoder largely remains unexplored. In this work, we conduct the first comprehensive study of the UNet encoder. We empirically analyze the encoder features and provide insights to important questions regarding their changes at the inference process. In particular, we find that encoder features change gently, whereas the decoder features exhibit substantial variations across different time-steps. This finding inspired us to omit the encoder at certain adjacent time-steps and reuse cyclically the encoder features in the previous time-steps for the decoder. Further based on this observation, we introduce a simple yet effective encoder propagation scheme to accelerate the diffusion sampling for a diverse set of tasks. By benefiting from our propagation scheme, we are able to perform in parallel the decoder at certain adjacent time-steps. Additionally, we introduce a prior noise injection method to improve the texture details in the generated image. Besides the standard text-to-image task, we also validate our approach on other tasks: text-to-video, personalized generation and reference-guided generation. Without utilizing any knowledge distillation technique, our approach accelerates both the Stable Diffusion (SD) and the DeepFloyd-IF models sampling by 41% and 24% respectively, while maintaining high-quality generation performance. Our code is available in https://github.com/hutaiHang/Faster-Diffusion{FasterDiffusion}.

Current dense text retrieval models face two typical challenges. First, they adopt a siamese dual-encoder architecture to encode queries and documents independently for fast indexing and searching, while neglecting the finer-grained term-wise interactions. This results in a sub-optimal recall performance. Second, their model training highly relies on a negative sampling technique to build up the negative documents in their contrastive losses. To address these challenges, we present Adversarial Retriever-Ranker (AR2), which consists of a dual-encoder retriever plus a cross-encoder ranker. The two models are jointly optimized according to a minimax adversarial objective: the retriever learns to retrieve negative documents to cheat the ranker, while the ranker learns to rank a collection of candidates including both the ground-truth and the retrieved ones, as well as providing progressive direct feedback to the dual-encoder retriever. Through this adversarial game, the retriever gradually produces harder negative documents to train a better ranker, whereas the cross-encoder ranker provides progressive feedback to improve retriever. We evaluate AR2 on three benchmarks. Experimental results show that AR2 consistently and significantly outperforms existing dense retriever methods and achieves new state-of-the-art results on all of them. This includes the improvements on Natural Questions R@5 to 77.9%(+2.1%), TriviaQA R@5 to 78.2%(+1.4), and MS-MARCO MRR@10 to 39.5%(+1.3%). Code and models are available at https://github.com/microsoft/AR2.

Implicit neural representations store videos as neural networks and have performed well for various vision tasks such as video compression and denoising. With frame index or positional index as input, implicit representations (NeRV, E-NeRV, \etc) reconstruct video from fixed and content-agnostic embeddings. Such embedding largely limits the regression capacity and internal generalization for video interpolation. In this paper, we propose a Hybrid Neural Representation for Videos (HNeRV), where a learnable encoder generates content-adaptive embeddings, which act as the decoder input. Besides the input embedding, we introduce HNeRV blocks, which ensure model parameters are evenly distributed across the entire network, such that higher layers (layers near the output) can have more capacity to store high-resolution content and video details. With content-adaptive embeddings and re-designed architecture, HNeRV outperforms implicit methods in video regression tasks for both reconstruction quality (+4.7 PSNR) and convergence speed (16times faster), and shows better internal generalization. As a simple and efficient video representation, HNeRV also shows decoding advantages for speed, flexibility, and deployment, compared to traditional codecs~(H.264, H.265) and learning-based compression methods. Finally, we explore the effectiveness of HNeRV on downstream tasks such as video compression and video inpainting. We provide project page at https://haochen-rye.github.io/HNeRV, and Code at https://github.com/haochen-rye/HNeRV

Classifier-free guidance (CFG) has become an essential component of modern diffusion models to enhance both generation quality and alignment with input conditions. However, CFG requires specific training procedures and is limited to conditional generation. To address these limitations, we propose Token Perturbation Guidance (TPG), a novel method that applies perturbation matrices directly to intermediate token representations within the diffusion network. TPG employs a norm-preserving shuffling operation to provide effective and stable guidance signals that improve generation quality without architectural changes. As a result, TPG is training-free and agnostic to input conditions, making it readily applicable to both conditional and unconditional generation. We further analyze the guidance term provided by TPG and show that its effect on sampling more closely resembles CFG compared to existing training-free guidance techniques. Extensive experiments on SDXL and Stable Diffusion 2.1 show that TPG achieves nearly a 2times improvement in FID for unconditional generation over the SDXL baseline, while closely matching CFG in prompt alignment. These results establish TPG as a general, condition-agnostic guidance method that brings CFG-like benefits to a broader class of diffusion models. The code is available at https://github.com/TaatiTeam/Token-Perturbation-Guidance

This paper studies a novel pre-training technique with unpaired speech data, Speech2C, for encoder-decoder based automatic speech recognition (ASR). Within a multi-task learning framework, we introduce two pre-training tasks for the encoder-decoder network using acoustic units, i.e., pseudo codes, derived from an offline clustering model. One is to predict the pseudo codes via masked language modeling in encoder output, like HuBERT model, while the other lets the decoder learn to reconstruct pseudo codes autoregressively instead of generating textual scripts. In this way, the decoder learns to reconstruct original speech information with codes before learning to generate correct text. Comprehensive experiments on the LibriSpeech corpus show that the proposed Speech2C can relatively reduce the word error rate (WER) by 19.2% over the method without decoder pre-training, and also outperforms significantly the state-of-the-art wav2vec 2.0 and HuBERT on fine-tuning subsets of 10h and 100h. We release our code and model at https://github.com/microsoft/SpeechT5/tree/main/Speech2C.

Large-scale text encoders in text-to-image (T2I) diffusion models have demonstrated exceptional performance in generating high-quality images from textual prompts. Unlike denoising modules that rely on multiple iterative steps, text encoders require only a single forward pass to produce text embeddings. However, despite their minimal contribution to total inference time and floating-point operations (FLOPs), text encoders demand significantly higher memory usage, up to eight times more than denoising modules. To address this inefficiency, we propose Skip and Re-use layers (Skrr), a simple yet effective pruning strategy specifically designed for text encoders in T2I diffusion models. Skrr exploits the inherent redundancy in transformer blocks by selectively skipping or reusing certain layers in a manner tailored for T2I tasks, thereby reducing memory consumption without compromising performance. Extensive experiments demonstrate that Skrr maintains image quality comparable to the original model even under high sparsity levels, outperforming existing blockwise pruning methods. Furthermore, Skrr achieves state-of-the-art memory efficiency while preserving performance across multiple evaluation metrics, including the FID, CLIP, DreamSim, and GenEval scores.

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance performance in specialized tasks. In this work, we introduce Protap, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Specifically, Protap covers five applications: three general tasks and two novel specialized tasks, i.e., enzyme-catalyzed protein cleavage site prediction and targeted protein degradation, which are industrially relevant yet missing from existing benchmarks. For each application, Protap compares various domain-specific models and general architectures under multiple pretraining settings. Our empirical studies imply that: (i) Though large-scale pretraining encoders achieve great results, they often underperform supervised encoders trained on small downstream training sets. (ii) Incorporating structural information during downstream fine-tuning can match or even outperform protein language models pretrained on large-scale sequence corpora. (iii) Domain-specific biological priors can enhance performance on specialized downstream tasks. Code and datasets are publicly available at https://github.com/Trust-App-AI-Lab/protap.

This technical report describes the MERaLiON Speech Encoder, a foundation model designed to support a wide range of downstream speech applications. Developed as part of Singapore's National Multimodal Large Language Model Programme, the MERaLiON Speech Encoder is tailored to address the speech processing needs in Singapore and the surrounding Southeast Asian region. The model currently supports mainly English, including the variety spoken in Singapore. We are actively expanding our datasets to gradually cover other languages in subsequent releases. The MERaLiON Speech Encoder was pre-trained from scratch on 200K hours of unlabelled speech data using a self-supervised learning approach based on masked language modelling. We describe our training procedure and hyperparameter tuning experiments in detail below. Our evaluation demonstrates improvements to spontaneous and Singapore speech benchmarks for speech recognition, while remaining competitive to other state-of-the-art speech encoders across ten other speech tasks. We commit to releasing our model, supporting broader research endeavours, both in Singapore and beyond.

Categorical variables often appear in datasets for classification and regression tasks, and they need to be encoded into numerical values before training. Since many encoders have been developed and can significantly impact performance, choosing the appropriate encoder for a task becomes a time-consuming yet important practical issue. This study broadly classifies machine learning models into three categories: 1) ATI models that implicitly perform affine transformations on inputs, such as multi-layer perceptron neural network; 2) Tree-based models that are based on decision trees, such as random forest; and 3) the rest, such as kNN. Theoretically, we prove that the one-hot encoder is the best choice for ATI models in the sense that it can mimic any other encoders by learning suitable weights from the data. We also explain why the target encoder and its variants are the most suitable encoders for tree-based models. This study conducted comprehensive computational experiments to evaluate 14 encoders, including one-hot and target encoders, along with eight common machine-learning models on 28 datasets. The computational results agree with our theoretical analysis. The findings in this study shed light on how to select the suitable encoder for data scientists in fields such as fraud detection, disease diagnosis, etc.

Despite the prominence of decoder-only language models, encoders remain crucial for resource-constrained applications. We introduce ModernGBERT (134M, 1B), a fully transparent family of German encoder models trained from scratch, incorporating architectural innovations from ModernBERT. To evaluate the practical trade-offs of training encoders from scratch, we also present LL\"aMmlein2Vec (120M, 1B, 7B), a family of encoders derived from German decoder-only models via LLM2Vec. We benchmark all models on natural language understanding, text embedding, and long-context reasoning tasks, enabling a controlled comparison between dedicated encoders and converted decoders. Our results show that ModernGBERT 1B outperforms prior state-of-the-art German encoders as well as encoders adapted via LLM2Vec, with regard to performance and parameter-efficiency. All models, training data, checkpoints and code are publicly available, advancing the German NLP ecosystem with transparent, high-performance encoder models.

We present Marian, an efficient and self-contained Neural Machine Translation framework with an integrated automatic differentiation engine based on dynamic computation graphs. Marian is written entirely in C++. We describe the design of the encoder-decoder framework and demonstrate that a research-friendly toolkit can achieve high training and translation speed.

Plane geometry problem solving (PGPS) has recently gained significant attention as a benchmark to assess the multi-modal reasoning capabilities of large vision-language models. Despite the growing interest in PGPS, the research community still lacks a comprehensive overview that systematically synthesizes recent work in PGPS. To fill this gap, we present a survey of existing PGPS studies. We first categorize PGPS methods into an encoder-decoder framework and summarize the corresponding output formats used by their encoders and decoders. Subsequently, we classify and analyze these encoders and decoders according to their architectural designs. Finally, we outline major challenges and promising directions for future research. In particular, we discuss the hallucination issues arising during the encoding phase within encoder-decoder architectures, as well as the problem of data leakage in current PGPS benchmarks.

The existing model compression methods via structured pruning typically require complicated multi-stage procedures. Each individual stage necessitates numerous engineering efforts and domain-knowledge from the end-users which prevent their wider applications onto broader scenarios. We propose the second generation of Only-Train-Once (OTOv2), which first automatically trains and compresses a general DNN only once from scratch to produce a more compact model with competitive performance without fine-tuning. OTOv2 is automatic and pluggable into various deep learning applications, and requires almost minimal engineering efforts from the users. Methodologically, OTOv2 proposes two major improvements: (i) Autonomy: automatically exploits the dependency of general DNNs, partitions the trainable variables into Zero-Invariant Groups (ZIGs), and constructs the compressed model; and (ii) Dual Half-Space Projected Gradient (DHSPG): a novel optimizer to more reliably solve structured-sparsity problems. Numerically, we demonstrate the generality and autonomy of OTOv2 on a variety of model architectures such as VGG, ResNet, CARN, ConvNeXt, DenseNet and StackedUnets, the majority of which cannot be handled by other methods without extensive handcrafting efforts. Together with benchmark datasets including CIFAR10/100, DIV2K, Fashion-MNIST, SVNH and ImageNet, its effectiveness is validated by performing competitively or even better than the state-of-the-arts. The source code is available at https://github.com/tianyic/only_train_once.

Speculative Decoding (SD) enforces strict distributional equivalence to the target model when accepting candidate tokens. While it maintains the target model's generation quality, this strict equivalence limits the speedup achievable by SD and prevents users from trading deviations from the target distribution in exchange for further inference speed gains. To address these limitations, we introduce Fuzzy Speculative Decoding (FSD) - a decoding algorithm that generalizes SD by accepting candidate tokens based on the divergences between the target and draft model distributions. By allowing for controlled divergence from the target model, FSD enables users to flexibly trade generation quality for inference speed. Across several benchmarks, our method is able to achieve significant runtime improvements of over 5 tokens per second faster than SD at only an approximate 2% absolute reduction in benchmark accuracy. In many cases, FSD is even able to match SD benchmark accuracy at over 2 tokens per second faster, demonstrating that distributional equivalence is not necessary to maintain target model performance. Furthermore, FSD can be seamlessly integrated into existing SD extensions; we demonstrate this by applying FSD to EAGLE-2, greatly enhancing this existing extension's efficiency while allowing it to leverage FSD's tunable quality-speed trade-off.

Recent advances in scene understanding benefit a lot from depth maps because of the 3D geometry information, especially in complex conditions (e.g., low light and overexposed). Existing approaches encode depth maps along with RGB images and perform feature fusion between them to enable more robust predictions. Taking into account that depth can be regarded as a geometry supplement for RGB images, a straightforward question arises: Do we really need to explicitly encode depth information with neural networks as done for RGB images? Based on this insight, in this paper, we investigate a new way to learn RGBD feature representations and present DFormerv2, a strong RGBD encoder that explicitly uses depth maps as geometry priors rather than encoding depth information with neural networks. Our goal is to extract the geometry clues from the depth and spatial distances among all the image patch tokens, which will then be used as geometry priors to allocate attention weights in self-attention. Extensive experiments demonstrate that DFormerv2 exhibits exceptional performance in various RGBD semantic segmentation benchmarks. Code is available at: https://github.com/VCIP-RGBD/DFormer.

The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alignment (MSA), which requires extensive exploration of a large protein database for similar sequences. However, not all protein sequences possess abundant homologous families, and consequently, AF2's performance can degrade on such queries, at times failing to produce meaningful results. To address this, we introduce a novel generative language model, MSA-Augmenter, which leverages protein-specific attention mechanisms and large-scale MSAs to generate useful, novel protein sequences not currently found in databases. These sequences supplement shallow MSAs, enhancing the accuracy of structural property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter can generate de novo sequences that retain co-evolutionary information from inferior MSAs, thereby improving protein structure prediction quality on top of strong AF2.

Existing codecs are designed to eliminate intrinsic redundancies to create a compact representation for compression. However, strong external priors from Multimodal Large Language Models (MLLMs) have not been explicitly explored in video compression. Herein, we introduce a unified paradigm for Cross-Modality Video Coding (CMVC), which is a pioneering approach to explore multimodality representation and video generative models in video coding. Specifically, on the encoder side, we disentangle a video into spatial content and motion components, which are subsequently transformed into distinct modalities to achieve very compact representation by leveraging MLLMs. During decoding, previously encoded components and video generation models are leveraged to create multiple encoding-decoding modes that optimize video reconstruction quality for specific decoding requirements, including Text-Text-to-Video (TT2V) mode to ensure high-quality semantic information and Image-Text-to-Video (IT2V) mode to achieve superb perceptual consistency. In addition, we propose an efficient frame interpolation model for IT2V mode via Low-Rank Adaption (LoRA) tuning to guarantee perceptual quality, which allows the generated motion cues to behave smoothly. Experiments on benchmarks indicate that TT2V achieves effective semantic reconstruction, while IT2V exhibits competitive perceptual consistency. These results highlight potential directions for future research in video coding.

Modern transformer architectures achieve remarkable performance across tasks and domains but remain rigid in how they allocate computation at inference time. Real-world deployment often requires models to adapt to diverse hardware and latency constraints, yet most approaches to dynamic computation focus on a single axis -- such as reducing the number of tokens. We present a novel capability: AdaPerceiver, the first transformer architecture with unified adaptivity across depth, width, and tokens within a single model. We propose an architecture that supports adaptivity along these axes. We couple this with an efficient joint training regime that ensures the model maintains performance across its various configurations. We evaluate AdaPerceiver on image classification, semantic segmentation, and depth estimation tasks. On image classification, AdaPerceiver expands the accuracy-throughput Pareto front. It achieves 85.4% accuracy while yielding 36% higher throughput than FlexiViT-L. On dense prediction, AdaPerceiver matches ViT-H/14 while having sim26x fewer encoder FLOPs (floating-point operations) on semantic segmentation and depth estimation. Finally, we show how AdaPerceiver equipped with a policy can maintain ImageNet1K accuracy (pm0.1 percentage points) while reducing FLOPs by 24-33%.

Automated diagnostic systems (ADS) have shown significant potential in the early detection of polyps during endoscopic examinations, thereby reducing the incidence of colorectal cancer. However, due to high annotation costs and strict privacy concerns, acquiring high-quality endoscopic images poses a considerable challenge in the development of ADS. Despite recent advancements in generating synthetic images for dataset expansion, existing endoscopic image generation algorithms failed to accurately generate the details of polyp boundary regions and typically required medical priors to specify plausible locations and shapes of polyps, which limited the realism and diversity of the generated images. To address these limitations, we present Polyp-Gen, the first full-automatic diffusion-based endoscopic image generation framework. Specifically, we devise a spatial-aware diffusion training scheme with a lesion-guided loss to enhance the structural context of polyp boundary regions. Moreover, to capture medical priors for the localization of potential polyp areas, we introduce a hierarchical retrieval-based sampling strategy to match similar fine-grained spatial features. In this way, our Polyp-Gen can generate realistic and diverse endoscopic images for building reliable ADS. Extensive experiments demonstrate the state-of-the-art generation quality, and the synthetic images can improve the downstream polyp detection task. Additionally, our Polyp-Gen has shown remarkable zero-shot generalizability on other datasets. The source code is available at https://github.com/CUHK-AIM-Group/Polyp-Gen.

Neural audio codecs form the foundational building blocks for language model (LM)-based speech generation. Typically, there is a trade-off between frame rate and audio quality. This study introduces a low-frame-rate, semantically enhanced codec model. Existing approaches distill semantically rich self-supervised (SSL) representations into the first-layer codec tokens. This work proposes DualCodec, a dual-stream encoding approach that integrates SSL and waveform representations within an end-to-end codec framework. In this setting, DualCodec enhances the semantic information in the first-layer codec and enables the codec system to maintain high audio quality while operating at a low frame rate. Note that a low-frame-rate codec improves the efficiency of speech generation. Experimental results on audio codec and speech generation tasks confirm the effectiveness of the proposed DualCodec compared to state-of-the-art codec systems, such as Mimi Codec, SpeechTokenizer, DAC, and Encodec. Demos and codes are available at: https://dualcodec.github.io

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

There are a thousand ways to caption an image. Contrastive Language Pretraining (CLIP) on the other hand, works by mapping an image and its caption to a single vector -- limiting how well CLIP-like models can represent the diverse ways to describe an image. In this work, we introduce Llip, Latent Language Image Pretraining, which models the diversity of captions that could match an image. Llip's vision encoder outputs a set of visual features that are mixed into a final representation by conditioning on information derived from the text. We show that Llip outperforms non-contextualized baselines like CLIP and SigLIP on a variety of tasks even with large-scale encoders. Llip improves zero-shot classification by an average of 2.9% zero-shot classification benchmarks with a ViT-G/14 encoder. Specifically, Llip attains a zero-shot top-1 accuracy of 83.5% on ImageNet outperforming a similarly sized CLIP by 1.4%. We also demonstrate improvement on zero-shot retrieval on MS-COCO by 6.0%. We provide a comprehensive analysis of the components introduced by the method and demonstrate that Llip leads to richer visual representations.

Recent studies have identified Direct Preference Optimization (DPO) as an efficient and reward-free approach to improving video generation quality. However, existing methods largely follow image-domain paradigms and are mainly developed on small-scale models (approximately 2B parameters), limiting their ability to address the unique challenges of video tasks, such as costly data construction, unstable training, and heavy memory consumption. To overcome these limitations, we introduce a GT-Pair that automatically builds high-quality preference pairs by using real videos as positives and model-generated videos as negatives, eliminating the need for any external annotation. We further present Reg-DPO, which incorporates the SFT loss as a regularization term into the DPO objective to enhance training stability and generation fidelity. Additionally, by combining the FSDP framework with multiple memory optimization techniques, our approach achieves nearly three times higher training capacity than using FSDP alone. Extensive experiments on both I2V and T2V tasks across multiple datasets demonstrate that our method consistently outperforms existing approaches, delivering superior video generation quality.

We introduce CADE 2.5 (Comfy Adaptive Detail Enhancer), a sampler-level guidance stack for SD/SDXL latent diffusion models. The central module, ZeResFDG, unifies (i) frequency-decoupled guidance that reweights low- and high-frequency components of the guidance signal, (ii) energy rescaling that matches the per-sample magnitude of the guided prediction to the positive branch, and (iii) zero-projection that removes the component parallel to the unconditional direction. A lightweight spectral EMA with hysteresis switches between a conservative and a detail-seeking mode as structure crystallizes during sampling. Across SD/SDXL samplers, ZeResFDG improves sharpness, prompt adherence, and artifact control at moderate guidance scales without any retraining. In addition, we employ a training-free inference-time stabilizer, QSilk Micrograin Stabilizer (quantile clamp + depth/edge-gated micro-detail injection), which improves robustness and yields natural high-frequency micro-texture at high resolutions with negligible overhead. For completeness we note that the same rule is compatible with alternative parameterizations (e.g., velocity), which we briefly discuss in the Appendix; however, this paper focuses on SD/SDXL latent diffusion models.

Zero-shot quantization is a promising approach for developing lightweight deep neural networks when data is inaccessible owing to various reasons, including cost and issues related to privacy. By exploiting the learned parameters (mu and sigma) of batch normalization layers in an FP32-pre-trained model, zero-shot quantization schemes focus on generating synthetic data. Subsequently, they distill knowledge from the pre-trained model (teacher) to the quantized model (student) such that the quantized model can be optimized with the synthetic dataset. However, thus far, zero-shot quantization has primarily been discussed in the context of quantization-aware training methods, which require task-specific losses and long-term optimization as much as retraining. We thus introduce a post-training quantization scheme for zero-shot quantization that produces high-quality quantized networks within a few hours. Furthermore, we propose a framework called Genie~that generates data suited for quantization. With the data synthesized by Genie, we can produce robust quantized models without real datasets, which is comparable to few-shot quantization. We also propose a post-training quantization algorithm to enhance the performance of quantized models. By combining them, we can bridge the gap between zero-shot and few-shot quantization while significantly improving the quantization performance compared to that of existing approaches. In other words, we can obtain a unique state-of-the-art zero-shot quantization approach. The code is available at https://github.com/SamsungLabs/Genie.

We present Kaleido, a subject-to-video~(S2V) generation framework, which aims to synthesize subject-consistent videos conditioned on multiple reference images of target subjects. Despite recent progress in S2V generation models, existing approaches remain inadequate at maintaining multi-subject consistency and at handling background disentanglement, often resulting in lower reference fidelity and semantic drift under multi-image conditioning. These shortcomings can be attributed to several factors. Primarily, the training dataset suffers from a lack of diversity and high-quality samples, as well as cross-paired data, i.e., paired samples whose components originate from different instances. In addition, the current mechanism for integrating multiple reference images is suboptimal, potentially resulting in the confusion of multiple subjects. To overcome these limitations, we propose a dedicated data construction pipeline, incorporating low-quality sample filtering and diverse data synthesis, to produce consistency-preserving training data. Moreover, we introduce Reference Rotary Positional Encoding (R-RoPE) to process reference images, enabling stable and precise multi-image integration. Extensive experiments across numerous benchmarks demonstrate that Kaleido significantly outperforms previous methods in consistency, fidelity, and generalization, marking an advance in S2V generation.

We present MIPS, a novel method for program synthesis based on automated mechanistic interpretability of neural networks trained to perform the desired task, auto-distilling the learned algorithm into Python code. We test MIPS on a benchmark of 62 algorithmic tasks that can be learned by an RNN and find it highly complementary to GPT-4: MIPS solves 32 of them, including 13 that are not solved by GPT-4 (which also solves 30). MIPS uses an integer autoencoder to convert the RNN into a finite state machine, then applies Boolean or integer symbolic regression to capture the learned algorithm. As opposed to large language models, this program synthesis technique makes no use of (and is therefore not limited by) human training data such as algorithms and code from GitHub. We discuss opportunities and challenges for scaling up this approach to make machine-learned models more interpretable and trustworthy.

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

Encoder-free architectures have been preliminarily explored in the 2D visual domain, yet it remains an open question whether they can be effectively applied to 3D understanding scenarios. In this paper, we present the first comprehensive investigation into the potential of encoder-free architectures to overcome the challenges of encoder-based 3D Large Multimodal Models (LMMs). These challenges include the failure to adapt to varying point cloud resolutions and the point features from the encoder not meeting the semantic needs of Large Language Models (LLMs). We identify key aspects for 3D LMMs to remove the encoder and enable the LLM to assume the role of the 3D encoder: 1) We propose the LLM-embedded Semantic Encoding strategy in the pre-training stage, exploring the effects of various point cloud self-supervised losses. And we present the Hybrid Semantic Loss to extract high-level semantics. 2) We introduce the Hierarchical Geometry Aggregation strategy in the instruction tuning stage. This incorporates inductive bias into the LLM early layers to focus on the local details of the point clouds. To the end, we present the first Encoder-free 3D LMM, ENEL. Our 7B model rivals the current state-of-the-art model, ShapeLLM-13B, achieving 55.0%, 50.92%, and 42.7% on the classification, captioning, and VQA tasks, respectively. Our results demonstrate that the encoder-free architecture is highly promising for replacing encoder-based architectures in the field of 3D understanding. The code is released at https://github.com/Ivan-Tang-3D/ENEL

Pre-trained encoders for offline feature extraction followed by multiple instance learning (MIL) aggregators have become the dominant paradigm in computational pathology (CPath), benefiting cancer diagnosis and prognosis. However, performance limitations arise from the absence of encoder fine-tuning for downstream tasks and disjoint optimization with MIL. While slide-level supervised end-to-end (E2E) learning is an intuitive solution to this issue, it faces challenges such as high computational demands and suboptimal results. These limitations motivate us to revisit E2E learning. We argue that prior work neglects inherent E2E optimization challenges, leading to performance disparities compared to traditional two-stage methods. In this paper, we pioneer the elucidation of optimization challenge caused by sparse-attention MIL and propose a novel MIL called ABMILX. It mitigates this problem through global correlation-based attention refinement and multi-head mechanisms. With the efficient multi-scale random patch sampling strategy, an E2E trained ResNet with ABMILX surpasses SOTA foundation models under the two-stage paradigm across multiple challenging benchmarks, while remaining computationally efficient (<10 RTX3090 hours). We show the potential of E2E learning in CPath and calls for greater research focus in this area. The code is https://github.com/DearCaat/E2E-WSI-ABMILX.

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

The conversion from 2D X-ray to 3D shape holds significant potential for improving diagnostic efficiency and safety. However, existing reconstruction methods often rely on hand-crafted features, manual intervention, and prior knowledge, resulting in unstable shape errors and additional processing costs. In this paper, we introduce Swin-X2S, an end-to-end deep learning method for directly reconstructing 3D segmentation and labeling from 2D biplanar orthogonal X-ray images. Swin-X2S employs an encoder-decoder architecture: the encoder leverages 2D Swin Transformer for X-ray information extraction, while the decoder employs 3D convolution with cross-attention to integrate structural features from orthogonal views. A dimension-expanding module is introduced to bridge the encoder and decoder, ensuring a smooth conversion from 2D pixels to 3D voxels. We evaluate proposed method through extensive qualitative and quantitative experiments across nine publicly available datasets covering four anatomies (femur, hip, spine, and rib), with a total of 54 categories. Significant improvements over previous methods have been observed not only in the segmentation and labeling metrics but also in the clinically relevant parameters that are of primary concern in practical applications, which demonstrates the promise of Swin-X2S to provide an effective option for anatomical shape reconstruction in clinical scenarios. Code implementation is available at: https://github.com/liukuan5625/Swin-X2S.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Multilingual understanding models (or encoder-based), pre-trained via masked language modeling, have achieved promising results on many language understanding tasks (e.g., mBERT). However, these non-autoregressive (NAR) models still struggle to generate high-quality texts compared with autoregressive (AR) models. Considering that encoder-based models have the advantage of efficient generation and self-correction abilities, this paper explores methods to empower multilingual understanding models the generation abilities to get a unified model. Specifically, we start from a multilingual encoder (XLM-R) and propose a Semantic-Guided Alignment-then-Denoising (SGA) approach to adapt an encoder to a multilingual generator with a small number of new parameters. Experiments show that the proposed approach is an effective adaption method, outperforming widely-used initialization-based methods with gains of 9.4 BLEU on machine translation, 8.1 Rouge-L on question generation, and 5.5 METEOR on story generation on XLM-R_{large}. On the other hand, we observe that XLM-R is still inferior to mBART in supervised settings despite better results on zero-shot settings, indicating that more exploration is required to make understanding models strong generators.

Error correcting codes play a central role in digital communication, ensuring that transmitted information can be accurately reconstructed despite channel impairments. Recently, autoencoder (AE) based approaches have gained attention for the end-to-end design of communication systems, offering a data driven alternative to conventional coding schemes. However, enforcing binary codewords within differentiable AE architectures remains difficult, as discretization breaks gradient flow and often leads to unstable convergence. To overcome this limitation, a simplified two stage training procedure is proposed, consisting of a continuous pretraining phase followed by direct binarization and fine tuning without gradient approximation techniques. For the (7,4) block configuration over a binary symmetric channel (BSC), the learned encoder-decoder pair learns a rotated version (coset code) of the optimal Hamming code, naturally recovering its linear and distance properties and thereby achieving the same block error rate (BLER) with maximum likelihood (ML) decoding. These results indicate that compact AE architectures can effectively learn structured, algebraically optimal binary codes through stable and straightforward training.

In this paper, we provide the observation that too few queries assigned as positive samples in DETR with one-to-one set matching leads to sparse supervision on the encoder's output which considerably hurt the discriminative feature learning of the encoder and vice visa for attention learning in the decoder. To alleviate this, we present a novel collaborative hybrid assignments training scheme, namely Co-DETR, to learn more efficient and effective DETR-based detectors from versatile label assignment manners. This new training scheme can easily enhance the encoder's learning ability in end-to-end detectors by training the multiple parallel auxiliary heads supervised by one-to-many label assignments such as ATSS and Faster RCNN. In addition, we conduct extra customized positive queries by extracting the positive coordinates from these auxiliary heads to improve the training efficiency of positive samples in the decoder. In inference, these auxiliary heads are discarded and thus our method introduces no additional parameters and computational cost to the original detector while requiring no hand-crafted non-maximum suppression (NMS). We conduct extensive experiments to evaluate the effectiveness of the proposed approach on DETR variants, including DAB-DETR, Deformable-DETR, and DINO-Deformable-DETR. The state-of-the-art DINO-Deformable-DETR with Swin-L can be improved from 58.5% to 59.5% AP on COCO val. Surprisingly, incorporated with ViT-L backbone, we achieve 66.0% AP on COCO test-dev and 67.9% AP on LVIS val, outperforming previous methods by clear margins with much fewer model sizes. Codes are available at https://github.com/Sense-X/Co-DETR.

Text-to-video (T2V) generation has gained significant attention due to its wide applications to video generation, editing, enhancement and translation, \etc. However, high-quality (HQ) video synthesis is extremely challenging because of the diverse and complex motions existed in real world. Most existing works struggle to address this problem by collecting large-scale HQ videos, which are inaccessible to the community. In this work, we show that publicly available limited and low-quality (LQ) data are sufficient to train a HQ video generator without recaptioning or finetuning. We factorize the whole T2V generation process into two steps: generating an image conditioned on a highly descriptive caption, and synthesizing the video conditioned on the generated image and a concise caption of motion details. Specifically, we present Factorized-Dreamer, a factorized spatiotemporal framework with several critical designs for T2V generation, including an adapter to combine text and image embeddings, a pixel-aware cross attention module to capture pixel-level image information, a T5 text encoder to better understand motion description, and a PredictNet to supervise optical flows. We further present a noise schedule, which plays a key role in ensuring the quality and stability of video generation. Our model lowers the requirements in detailed captions and HQ videos, and can be directly trained on limited LQ datasets with noisy and brief captions such as WebVid-10M, largely alleviating the cost to collect large-scale HQ video-text pairs. Extensive experiments in a variety of T2V and image-to-video generation tasks demonstrate the effectiveness of our proposed Factorized-Dreamer. Our source codes are available at https://github.com/yangxy/Factorized-Dreamer/.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.