Attention with bias, which extends standard attention by introducing prior knowledge as an additive bias matrix to the query-key scores, has been widely deployed in vision, language, protein-folding and other advanced scientific models, underscoring its status as a key evolution of this foundational module. However, introducing bias terms creates a severe efficiency bottleneck in attention computation. It disrupts the tightly fused memory-compute pipeline that underlies the speed of accelerators like FlashAttention, thereby stripping away most of their performance gains and leaving biased attention computationally expensive. Surprisingly, despite its common usage, targeted efficiency optimization for attention with bias remains absent, which seriously hinders its application in complex tasks. Diving into the computation of FlashAttention, we prove that its optimal efficiency is determined by the rank of the attention weight matrix. Inspired by this theoretical result, this paper presents FlashBias based on the low-rank compressed sensing theory, which can provide fast-exact computation for many widely used attention biases and a fast-accurate approximation for biases in general formalizations. FlashBias can fully take advantage of the extremely optimized matrix multiplication operation in modern GPUs, achieving 1.5 speedup for Pairformer in AlphaFold 3, and over 2 speedup for attention with bias in vision and language models without loss of accuracy. Code is available at this repository: https://github.com/thuml/FlashBias.

The rapid advancement of generative AI enables highly realistic synthetic videos, posing significant challenges for content authentication and raising urgent concerns about misuse.

Previous research has investigated the application of Multimodal Large Language Models (MLLMs) in understanding 3D scenes by interpreting them as videos. These approaches generally depend on comprehensive 3D data inputs, such as point clouds or reconstructed Bird's-Eye View (BEV) maps. In our research, we advance this field by enhancing the capability of MLLMs to understand and reason in 3D spaces directly from video data, without the need for additional 3D input. We propose a novel and efficient method called the Video-3D Geometry Large Language Model (VG LLM). Our approach utilizes a 3D visual geometry encoder to extract 3D prior information from video sequences. This information is then integrated with visual tokens and input into the MLLM. Extensive experiments have shown that our method has achieved substantial improvements in various tasks related to 3D scene understanding and spatial reasoning, all directly learned from video sources. Impressively, our 4B model, which does not rely on explicit 3D data inputs, achieves competitive results compared to existing state-of-the-art methods, and even surpasses the Gemini-1.5-Pro in the VSI-Bench evaluations.

Recent reasoning adv through ances in the lar ef ge fecti language ve use of models Chain-of-Thought have significantly (CoT) and impro reinforcement ved textual learning.

Rotary Positional Encodings (RoPE) have emerged as a highly effective technique for one-dimensional sequences in Natural Language Processing spurring recent progress towards generalizing RoPE to higher-dimensional data such as images and videos. The success of RoPE has been thought to be due to its positional equivariance, i.e. its status as a relative positional encoding. In this paper, we mathematically show RoPE to be one of the most general solutions for equivariant positional embedding in one-dimensional data. Moreover, we show Mixed RoPE to be the analogously general solution for M-dimensional data, if we require commutative generators - a property necessary for RoPE's equivariance. However, we question whether strict equivariance plays a large role in RoPE's performance. We propose Spherical RoPE, a method analogous to Mixed RoPE, but assumes non-commutative generators. Empirically, we find Spherical RoPE to have the equivalent or better learning behavior compared to its equivariant analogues. This suggests that relative positional embeddings are not as important as is commonly believed, at least within computer vision. We expect this discovery to facilitate future work in positional encodings for vision that can be faster and generalize better by removing the preconception that they must be relative.

The rapid advancement of reasoning capabilities in large language models (LLMs) has led to notable improvements on mathematical benchmarks. However, many of the most commonly used evaluation datasets (e.g., AIME 2024) are widely available online, making it difficult to disentangle genuine reasoning from potential memorization. Furthermore, these benchmarks do not evaluate proof-writing capabilities, which are crucial for many mathematical tasks. To address this, we introduce MATHARENA, a new benchmark based on the following key insight: recurring math competitions provide a stream of high-quality, challenging problems that can be used for real-time evaluation of LLMs. By evaluating models as soon as new problems are released, we effectively eliminate the risk of contamination.

We introduce BikeBench, an engineering design benchmark for evaluating generative models on problems with multiple real-world objectives and constraints. As generative AI's reach continues to grow, evaluating its capability to understand physical laws, human guidelines, and hard constraints grows increasingly important. Engineering product design lies at the intersection of these difficult tasks, providing new challenges for AI capabilities. BikeBench evaluates AI models' capabilities to generate bicycle designs that not only resemble the dataset, but meet specific performance objectives and constraints. To do so, BikeBench quantifies a variety of human-centered and multiphysics performance characteristics, such as aerodynamics, ergonomics, structural mechanics, human-rated usability, and similarity to subjective text or image prompts. Supporting the benchmark are several datasets of simulation results, a dataset of 10,000 human-rated bicycle assessments, and a synthetically generated dataset of 1.6M designs, each with a parametric, CAD/XML, SVG, and PNG representation. BikeBench is uniquely configured to evaluate tabular generative models, large language models (LLMs), design optimization, and hybrid algorithms side-by-side. Our experiments indicate that LLMs and tabular generative models fall short of hybrid GenAI+optimization algorithms in design quality, constraint satisfaction, and similarity scores, suggesting significant room for improvement. We hope that BikeBench, a first-of-its-kind benchmark, will help catalyze progress in generative AI for constrained multi-objective engineering design problems.

The quality of foundation models depends heavily on their training data. Consequently, great efforts have been put into dataset curation. Yet most approaches rely on manual tuning of coarse-grained mixtures of large buckets of data, or filtering by hand-crafted heuristics. An approach that is ultimately more scalable (let alone more satisfying) is to learn which data is actually valuable for training. This type of meta-learning could allow more sophisticated, fine-grained, and effective curation. Our proposed DataRater is an instance of this idea. It estimates the value of training on any particular data point. This is done by meta-learning using'meta-gradients', with the objective of improving training efficiency on held out data. In extensive experiments across a range of model scales and datasets, we find that using our DataRater to filter data is highly effective, resulting in significantly improved compute efficiency.

Paucity of medical data severely limits the generalizability of diagnostic ML models, as the full spectrum of disease variability can not be represented by a small clinical dataset. To address this, diffusion models (DMs) have been considered as a promising avenue for synthetic image generation and augmentation. However, they frequently produce medically inaccurate images, deteriorating the model performance. Expert domain knowledge is critical for synthesizing images that correctly encode clinical information, especially when data is scarce and quality outweighs quantity. Existing approaches for incorporating human feedback, such as reinforcement learning (RL) and Direct Preference Optimization (DPO), rely on robust reward functions or demand labor-intensive expert evaluations. Recent progress in Multimodal Large Language Models (MLLMs) reveals their strong visual reasoning capabilities, making them adept candidates as evaluators. In this work, we propose a novel framework, coined MAGIC (Medically Accurate Generation of Images through AI-Expert Collaboration), that synthesizes clinically accurate skin disease images for data augmentation.

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce PRODVA, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, PRODVA achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.62%. 1