Lijun Wu

Yisheng Xiao, Lijun Wu, Junliang Guo et al. · microsoft-research

Non-autoregressive (NAR) generation, which is first proposed in neural machine translation (NMT) to speed up inference, has attracted much attention in both machine learning and natural language processing communities. While NAR generation can significantly accelerate inference speed for machine translation, the speedup comes at the cost of sacrificed translation accuracy compared to its counterpart, autoregressive (AR) generation. In recent years, many new models and algorithms have been designed/proposed to bridge the accuracy gap between NAR generation and AR generation. In this paper, we conduct a systematic survey with comparisons and discussions of various non-autoregressive translation (NAT) models from different aspects. Specifically, we categorize the efforts of NAT into several groups, including data manipulation, modeling methods, training criterion, decoding algorithms, and the benefit from pre-trained models. Furthermore, we briefly review other applications of NAR models beyond machine translation, such as grammatical error correction, text summarization, text style transfer, dialogue, semantic parsing, automatic speech recognition, and so on. In addition, we also discuss potential directions for future exploration, including releasing the dependency of KD, reasonable training objectives, pre-training for NAR, and wider applications, etc. We hope this survey can help researchers capture the latest progress in NAR generation, inspire the design of advanced NAR models and algorithms, and enable industry practitioners to choose appropriate solutions for their applications. The web page of this survey is at \url{https://github.com/LitterBrother-Xiao/Overview-of-Non-autoregressive-Applications}.

Qizhi Pei, Lijun Wu, Jinhua Zhu et al. · microsoft-research

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at $\href{https://github.com/QizhiPei/SSM-DTA}{Github}$.

Jinhua Zhu, Yingce Xia, Lijun Wu et al. · microsoft-research

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of all atoms. We note that most previous work handles 2D and 3D information separately, while jointly leveraging these two sources may foster a more informative representation. In this work, we explore this appealing idea and propose a new representation learning method based on a unified 2D and 3D pre-training. Atom coordinates and interatomic distances are encoded and then fused with atomic representations through graph neural networks. The model is pre-trained on three tasks: reconstruction of masked atoms and coordinates, 3D conformation generation conditioned on 2D graph, and 2D graph generation conditioned on 3D conformation. We evaluate our method on 11 downstream molecular property prediction tasks: 7 with 2D information only and 4 with both 2D and 3D information. Our method achieves state-of-the-art results on 10 tasks, and the average improvement on 2D-only tasks is 8.3%. Our method also achieves significant improvement on two 3D conformation generation tasks.

Zijie Geng, Shufang Xie, Yingce Xia et al. · microsoft-research

De novo molecular generation is an essential task for science discovery. Recently, fragment-based deep generative models have attracted much research attention due to their flexibility in generating novel molecules based on existing molecule fragments. However, the motif vocabulary, i.e., the collection of frequent fragments, is usually built upon heuristic rules, which brings difficulties to capturing common substructures from large amounts of molecules. In this work, we propose a new method, MiCaM, to generate molecules based on mined connection-aware motifs. Specifically, it leverages a data-driven algorithm to automatically discover motifs from a molecule library by iteratively merging subgraphs based on their frequency. The obtained motif vocabulary consists of not only molecular motifs (i.e., the frequent fragments), but also their connection information, indicating how the motifs are connected with each other. Based on the mined connection-aware motifs, MiCaM builds a connection-aware generator, which simultaneously picks up motifs and determines how they are connected. We test our method on distribution-learning benchmarks (i.e., generating novel molecules to resemble the distribution of a given training set) and goal-directed benchmarks (i.e., generating molecules with target properties), and achieve significant improvements over previous fragment-based baselines. Furthermore, we demonstrate that our method can effectively mine domain-specific motifs for different tasks.

Shufang Xie, Rui Yan, Peng Han et al. · microsoft-research

Retrosynthetic planning, which aims to find a reaction pathway to synthesize a target molecule, plays an important role in chemistry and drug discovery. This task is usually modeled as a search problem. Recently, data-driven methods have attracted many research interests and shown promising results for retrosynthetic planning. We observe that the same intermediate molecules are visited many times in the searching process, and they are usually independently treated in previous tree-based methods (e.g., AND-OR tree search, Monte Carlo tree search). Such redundancies make the search process inefficient. We propose a graph-based search policy that eliminates the redundant explorations of any intermediate molecules. As searching over a graph is more complicated than over a tree, we further adopt a graph neural network to guide the search over graphs. Meanwhile, our method can search a batch of targets together in the graph and remove the inter-target duplication in the tree-based search methods. Experimental results on two datasets demonstrate the effectiveness of our method. Especially on the widely used USPTO benchmark, we improve the search success rate to 99.47%, advancing previous state-of-the-art performance for 2.6 points.

Yisheng Xiao, Ruiyang Xu, Lijun Wu et al.

Transformer-based autoregressive (AR) methods have achieved appealing performance for varied sequence-to-sequence generation tasks, e.g., neural machine translation, summarization, and code generation, but suffer from low inference efficiency. To speed up the inference stage, many non-autoregressive (NAR) strategies have been proposed in the past few years. Among them, the conditional masked language model (CMLM) is one of the most versatile frameworks, as it can support many different sequence generation scenarios and achieve very competitive performance on these tasks. In this paper, we further introduce a simple yet effective adaptive masking over masking strategy to enhance the refinement capability of the decoder and make the encoder optimization easier. Experiments on \textbf{3} different tasks (neural machine translation, summarization, and code generation) with \textbf{15} datasets in total confirm that our proposed simple method achieves significant performance improvement over the strong CMLM model. Surprisingly, our proposed model yields state-of-the-art performance on neural machine translation (\textbf{34.62} BLEU on WMT16 EN$\to$RO, \textbf{34.82} BLEU on WMT16 RO$\to$EN, and \textbf{34.84} BLEU on IWSLT De$\to$En) and even better performance than the \textbf{AR} Transformer on \textbf{7} benchmark datasets with at least \textbf{2.2$\times$} speedup. Our code is available at GitHub.

Qizhi Pei, Kaiyuan Gao, Lijun Wu et al.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Kaiyuan Gao, Lijun Wu, Jinhua Zhu et al. · microsoft-research

Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the antibody patterns from data that could be complementary to human experiences. However, the computational methods heavily rely on high-quality antibody structure data, which is quite limited. Besides, the complementarity-determining region (CDR), which is the key component of an antibody that determines the specificity and binding affinity, is highly variable and hard to predict. Therefore, the data limitation issue further raises the difficulty of CDR generation for antibodies. Fortunately, there exists a large amount of sequence data of antibodies that can help model the CDR and alleviate the reliance on structure data. By witnessing the success of pre-training models for protein modeling, in this paper, we develop the antibody pre-training language model and incorporate it into the (antigen-specific) antibody design model in a systemic way. Specifically, we first pre-train an antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to avoid the heavy cost and error propagation from an autoregressive manner, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules. Through various experiments, we show that our method achieves superior performances over previous baselines on different tasks, such as sequence and structure generation and antigen-binding CDR-H3 design.

Chang Ma, Haiteng Zhao, Lin Zheng et al.

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the latest version of AlphaFold rely on Multiple Sequence Alignments (MSA) to feed in the evolutionary knowledge. Despite their success, heavy computational overheads, as well as the de novo and orphan proteins remain great challenges in protein representation learning. In this work, we show that MSAaugmented models inherently belong to retrievalaugmented methods. Motivated by this finding, we introduce Retrieved Sequence Augmentation(RSA) for protein representation learning without additional alignment or pre-processing. RSA links query protein sequences to a set of sequences with similar structures or properties in the database and combines these sequences for downstream prediction. We show that protein language models benefit from the retrieval enhancement on both structure prediction and property prediction tasks, with a 5% improvement on MSA Transformer on average while being 373 times faster. In addition, we show that our model can transfer to new protein domains better and outperforms MSA Transformer on de novo protein prediction. Our study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available on https://github.com/HKUNLP/RSA.

Keyue Qiu, Yixin Wu, Lihao Wang et al.

We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design within a single foundation model. AMix-2 is built upon two key ideas: (1) a unified protein-text formulation that embeds natural language and protein sequence in a shared token space, enabling one model to perform biological reasoning and conditional design instead of separate downstream task-specialized models; and (2) a block-wise diffusion language modeling backbone that combines causal generation across blocks with bidirectional context and iterative refinement within blocks. This scheme better matches the intrinsic nature of proteins than a strict left-to-right factorization. To evaluate protein foundation models under realistic generalization settings, we further introduce ProteinArena, a comprehensive benchmark with time-aware and homology-aware protocols across various understanding and design tasks, and with baselines covering classical bioinformatics tools, protein-specialized models and LLMs. On ProteinArena, AMix-2 outperforms frontier LLMs and demonstrates competitive performance to task-specific protein models. Controlled experiments further show that the diffusion-based paradigm generally surpasses its autoregressive counterpart, highlighting the advantage of flexible generation order for protein sequences. We release both AMix-2 and ProteinArena to facilitate open research in protein foundation models.

Zhaochen Su, Zecheng Tang, Xinyan Guan et al.

Recent research has revealed that neural language models at scale suffer from poor temporal generalization capability, i.e., the language model pre-trained on static data from past years performs worse over time on emerging data. Existing methods mainly perform continual training to mitigate such a misalignment. While effective to some extent but is far from being addressed on both the language modeling and downstream tasks. In this paper, we empirically observe that temporal generalization is closely affiliated with lexical semantic change, which is one of the essential phenomena of natural languages. Based on this observation, we propose a simple yet effective lexical-level masking strategy to post-train a converged language model. Experiments on two pre-trained language models, two different classification tasks, and four benchmark datasets demonstrate the effectiveness of our proposed method over existing temporal adaptation methods, i.e., continual training with new data. Our code is available at \url{https://github.com/zhaochen0110/LMLM}.

Qizhi Pei, Wei Zhang, Jinhua Zhu et al.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{https://github.com/QizhiPei/BioT5}{Github}$.

Kehan Wu, Yingce Xia, Yang Fan et al. · microsoft-research

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the structure of a target protein can provide novel drug candidates. In this paper, we present a generative solution named TamGent (Target-aware molecule generator with Transformer) that can directly generate candidate drugs from scratch for a given target, overcoming the limits imposed by existing compound libraries. Following the Transformer framework (a state-of-the-art framework in deep learning), we design a variant of Transformer encoder to process 3D geometric information of targets and pre-train the Transformer decoder on 10 million compounds from PubChem for candidate drug generation. Systematical evaluation on candidate compounds generated for targets from DrugBank shows that both binding affinity and drugability are largely improved. TamGent outperforms previous baselines in terms of both effectiveness and efficiency. The method is further verified by generating candidate compounds for the SARS-CoV-2 main protease and the oncogenic mutant KRAS G12C. The results show that our method not only re-discovers previously verified drug molecules , but also generates novel molecules with better docking scores, expanding the compound pool and potentially leading to the discovery of novel drugs.

Yicheng Zou, Dongsheng Zhu, Lin Zhu et al.

We introduce Intern-S1-Pro, the first one-trillion-parameter scientific multimodal foundation model. Scaling to this unprecedented size, the model delivers a comprehensive enhancement across both general and scientific domains. Beyond stronger reasoning and image-text understanding capabilities, its intelligence is augmented with advanced agent capabilities. Simultaneously, its scientific expertise has been vastly expanded to master over 100 specialized tasks across critical science fields, including chemistry, materials, life sciences, and earth sciences. Achieving this massive scale is made possible by the robust infrastructure support of XTuner and LMDeploy, which facilitates highly efficient Reinforcement Learning (RL) training at the 1-trillion parameter level while ensuring strict precision consistency between training and inference. By seamlessly integrating these advancements, Intern-S1-Pro further fortifies the fusion of general and specialized intelligence, working as a Specializable Generalist, demonstrating its position in the top tier of open-source models for general capabilities, while outperforming proprietary models in the depth of specialized scientific tasks.

Shufang Xie, Rui Yan, Junliang Guo et al.

Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. In recent years, the machine learing based retrosynthesis methods have achieved promising results. In this work, we introduce RetroKNN, a local reaction template retrieval method to further boost the performance of template-based systems with non-parametric retrieval. We first build an atom-template store and a bond-template store that contain the local templates in the training data, then retrieve from these templates with a k-nearest-neighbor (KNN) search during inference. The retrieved templates are combined with neural network predictions as the final output. Furthermore, we propose a lightweight adapter to adjust the weights when combing neural network and KNN predictions conditioned on the hidden representation and the retrieved templates. We conduct comprehensive experiments on two widely used benchmarks, the USPTO-50K and USPTO-MIT. Especially for the top-1 accuracy, we improved 7.1% on the USPTO-50K dataset and 12.0% on the USPTO-MIT dataset. These results demonstrate the effectiveness of our method.

Mengzhang Cai, Xin Gao, Yu Li et al.

The rapid evolution of Large Language Models (LLMs) is predicated on the quality and diversity of post-training datasets. However, a critical dichotomy persists: while models are rigorously benchmarked, the data fueling them remains a black box--characterized by opaque composition, uncertain provenance, and a lack of systematic evaluation. This opacity hinders reproducibility and obscures the causal link between data characteristics and model behaviors. To bridge this gap, we introduce OpenDataArena (ODA), a holistic and open platform designed to benchmark the intrinsic value of post-training data. ODA establishes a comprehensive ecosystem comprising four key pillars: (i) a unified training-evaluation pipeline that ensures fair, open comparisons across diverse models (e.g., Llama, Qwen) and domains; (ii) a multi-dimensional scoring framework that profiles data quality along tens of distinct axes; (iii) an interactive data lineage explorer to visualize dataset genealogy and dissect component sources; and (iv) a fully open-source toolkit for training, evaluation, and scoring to foster data research. Extensive experiments on ODA--covering over 120 training datasets across multiple domains on 22 benchmarks, validated by more than 600 training runs and 40 million processed data points--reveal non-trivial insights. Our analysis uncovers the inherent trade-offs between data complexity and task performance, identifies redundancy in popular benchmarks through lineage tracing, and maps the genealogical relationships across datasets. We release all results, tools, and configurations to democratize access to high-quality data evaluation. Rather than merely expanding a leaderboard, ODA envisions a shift from trial-and-error data curation to a principled science of Data-Centric AI, paving the way for rigorous studies on data mixing laws and the strategic composition of foundation models.

Zheng Liu, Honglin Lin, Chonghan Qin et al.

Chart reasoning is a critical capability for Vision Language Models (VLMs). However, the development of open-source models is severely hindered by the lack of high-quality training data. Existing datasets suffer from a dual challenge: synthetic charts are often simplistic and repetitive, while the associated QA pairs are prone to hallucinations and lack the reasoning depth required for complex tasks. To bridge this gap, we propose ChartVerse, a scalable framework designed to synthesize complex charts and reliable reasoning data from scratch. (1) To address the bottleneck of simple patterns, we first introduce Rollout Posterior Entropy (RPE), a novel metric that quantifies chart complexity. Guided by RPE, we develop complexity-aware chart coder to autonomously synthesize diverse, high-complexity charts via executable programs. (2) To guarantee reasoning rigor, we develop truth-anchored inverse QA synthesis. Diverging from standard generation, we adopt an answer-first paradigm: we extract deterministic answers directly from the source code, generate questions conditional on these anchors, and enforce strict consistency verification. To further elevate difficulty and reasoning depth, we filter samples based on model fail-rate and distill high-quality Chain-of-Thought (CoT) reasoning. We curate ChartVerse-SFT-600K and ChartVerse-RL-40K using Qwen3-VL-30B-A3B-Thinking as the teacher. Experimental results demonstrate that ChartVerse-8B achieves state-of-the-art performance, notably surpassing its teacher and rivaling the stronger Qwen3-VL-32B-Thinking.

Jinguo Zhu, Weiyun Wang, Zhe Chen et al.

We introduce InternVL3, a significant advancement in the InternVL series featuring a native multimodal pre-training paradigm. Rather than adapting a text-only large language model (LLM) into a multimodal large language model (MLLM) that supports visual inputs, InternVL3 jointly acquires multimodal and linguistic capabilities from both diverse multimodal data and pure-text corpora during a single pre-training stage. This unified training paradigm effectively addresses the complexities and alignment challenges commonly encountered in conventional post-hoc training pipelines for MLLMs. To further improve performance and scalability, InternVL3 incorporates variable visual position encoding (V2PE) to support extended multimodal contexts, employs advanced post-training techniques such as supervised fine-tuning (SFT) and mixed preference optimization (MPO), and adopts test-time scaling strategies alongside an optimized training infrastructure. Extensive empirical evaluations demonstrate that InternVL3 delivers superior performance across a wide range of multi-modal tasks. In particular, InternVL3-78B achieves a score of 72.2 on the MMMU benchmark, setting a new state-of-the-art among open-source MLLMs. Its capabilities remain highly competitive with leading proprietary models, including ChatGPT-4o, Claude 3.5 Sonnet, and Gemini 2.5 Pro, while also maintaining strong pure-language proficiency. In pursuit of open-science principles, we will publicly release both the training data and model weights to foster further research and development in next-generation MLLMs.

Honglin Lin, Zheng Liu, Yun Zhu et al.

Recent advances in Vision Language Models (VLMs) have driven significant progress in visual reasoning. However, open-source VLMs still lag behind proprietary systems, largely due to the lack of high-quality reasoning data. Existing datasets offer limited coverage of challenging domains such as STEM diagrams and visual puzzles, and lack consistent, long-form Chain-of-Thought (CoT) annotations essential for eliciting strong reasoning capabilities. To bridge this gap, we introduce MMFineReason, a large-scale multimodal reasoning dataset comprising 1.8M samples and 5.1B solution tokens, featuring high-quality reasoning annotations distilled from Qwen3-VL-235B-A22B-Thinking. The dataset is established via a systematic three-stage pipeline: (1) large-scale data collection and standardization, (2) CoT rationale generation, and (3) comprehensive selection based on reasoning quality and difficulty awareness. The resulting dataset spans STEM problems, visual puzzles, games, and complex diagrams, with each sample annotated with visually grounded reasoning traces. We fine-tune Qwen3-VL-Instruct on MMFineReason to develop MMFineReason-2B/4B/8B versions. Our models establish new state-of-the-art results for their size class. Notably, MMFineReason-4B succesfully surpasses Qwen3-VL-8B-Thinking, and MMFineReason-8B even outperforms Qwen3-VL-30B-A3B-Thinking while approaching Qwen3-VL-32B-Thinking, demonstrating remarkable parameter efficiency. Crucially, we uncover a "less is more" phenomenon via our difficulty-aware filtering strategy: a subset of just 7\% (123K samples) achieves performance comparable to the full dataset. Notably, we reveal a synergistic effect where reasoning-oriented data composition simultaneously boosts general capabilities.

Xin Gao, Xiaoyang Wang, Yun Zhu et al.

The construction of Supervised Fine-Tuning (SFT) datasets is a critical yet under-theorized stage in the post-training of Large Language Models (LLMs), as prevalent practices often rely on heuristic aggregation without a systematic understanding of how individual samples contribute to model performance. In this report, we propose a paradigm shift from ad-hoc curation to a closed-loop dataset engineering framework using OpenDataArena (ODA), which leverages value-anchored rankings and multi-dimensional analysis to transform value benchmarking into feedback signals guiding dataset construction. We instantiate this methodology through two new datasets: \textbf{ODA-Math-460k}, a specialized mathematics reasoning dataset that utilizes a novel two-stage difficulty-aware pipeline to achieve State-of-the-Art (SOTA) results on benchmarks such as AIME and HMMT, and \textbf{ODA-Mixture (100k \& 500k)}, a series of multi-domain instruction datasets built via an ``Anchor-and-Patch'' strategy that outperforms significantly larger open-source baselines. Our empirical results demonstrate that ODA-driven datasets significantly improve both domain-specific reasoning and general utility while achieving superior data efficiency, validating a transition toward data-centric AI where transparent evaluation serves as the primary engine for engineering high-quality training data.

Weiyun Wang, Zhangwei Gao, Lixin Gu et al. · cmu, pku

We introduce InternVL 3.5, a new family of open-source multimodal models that significantly advances versatility, reasoning capability, and inference efficiency along the InternVL series. A key innovation is the Cascade Reinforcement Learning (Cascade RL) framework, which enhances reasoning through a two-stage process: offline RL for stable convergence and online RL for refined alignment. This coarse-to-fine training strategy leads to substantial improvements on downstream reasoning tasks, e.g., MMMU and MathVista. To optimize efficiency, we propose a Visual Resolution Router (ViR) that dynamically adjusts the resolution of visual tokens without compromising performance. Coupled with ViR, our Decoupled Vision-Language Deployment (DvD) strategy separates the vision encoder and language model across different GPUs, effectively balancing computational load. These contributions collectively enable InternVL3.5 to achieve up to a +16.0\% gain in overall reasoning performance and a 4.05$\times$ inference speedup compared to its predecessor, i.e., InternVL3. In addition, InternVL3.5 supports novel capabilities such as GUI interaction and embodied agency. Notably, our largest model, i.e., InternVL3.5-241B-A28B, attains state-of-the-art results among open-source MLLMs across general multimodal, reasoning, text, and agentic tasks -- narrowing the performance gap with leading commercial models like GPT-5. All models and code are publicly released.

Qizhi Pei, Lijun Wu, Zhenyu He et al.

Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

Qisheng Su, Zhen Fang, Shiting Huang et al.

Recent development of agents has renewed demand for long-context reasoning capacity of LLMs. However, training LLMs for this capacity requires costly long-document curation or heuristic context synthesis. We observe that agents produce massive trajectories when solving problems, invoking tools and receiving environment observations across many turns. The evidence needed to answer the original question is thus scattered throughout these turns, requiring integration of distant context segments. Nevertheless, standard agent SFT masks tool responses and only trains turn-level tool selection, creating a supervision blind spot where these scattered signals go unused. We propose Agent Context Compilation (ACC), which converts trajectories from search, software engineering, and database querying agents into long-context QA pairs that combine the original question with tool responses and environment observations gathered across multiple turns, training the model to answer directly without tool use. This makes the dependencies between the question and the evidence explicit, enabling direct supervision of long-context reasoning over distant segments without additional annotation. ACC is a simple but effective approach that can be combined with any existing long-context extension or training method, providing scalable supervised fine-tuning data. We validate ACC on long-range dependency modeling tasks through MRCR and GraphWalks, challenging benchmarks requiring cross-turn coreference resolution and graph traversal over extended contexts. Training Qwen3-30B-A3B with ACC achieves 68.3 on MRCR (+18.1) and 77.5 on GraphWalks (+7.6), results comparable to Qwen3-235B-A22B, while preserving general capabilities on GPQA, MMLU-Pro, AIME, and IFEval. Further mechanism analysis reveals that the ACC-trained model exhibits task-adaptive attention restructuring and expert specialization.

Haote Yang, Hui Wang, Chen Zhu et al.

Optical Chemical Structure Recognition (OCSR) aims to translate molecular diagrams in scientific literature into machine-readable formats, but current systems remain unreliable on real-world images due to substantial visual and chemical complexity. We introduce MOSAIC, a dual-dimensional difficulty framework with 37 fine-grained labels that jointly characterize visual interference and chemical semantic challenges in molecular diagrams. Based on this framework, we construct MolRecBench-Wild, a benchmark of 5,029 structures from 820 recent chemistry papers, covering the full difficulty spectrum observed in real publications. To enable faithful semantic evaluation beyond SMILES and MolFile, we propose CARBON, a representation language capable of expressing valence variations, icon-based groups, and other non-standard chemical semantics. We further adopt a dual-track evaluation protocol supporting both CARBON and SMILES outputs for broad model compatibility. Comprehensive experiments over 18 OCSR-capable models reveal severe performance degradation on MolRecBench-Wild, exposing a large gap between previous patent benchmarks and real-world academic scenarios.

Qizhi Pei, Lijun Wu, Kaiyuan Gao et al.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

Qizhi Pei, Lijun Wu, Kaiyuan Gao et al.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in \url{https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling}.

Yu Li, Xiaoran Shang, Qizhi Pei et al.

Post-training data plays a pivotal role in shaping the capabilities of Large Language Models (LLMs), yet datasets are often treated as isolated artifacts, overlooking the systemic connections that underlie their evolution. To disentangle these complex relationships, we introduce the concept of \textbf{data lineage} to the LLM ecosystem and propose an automated multi-agent framework to reconstruct the evolutionary graph of dataset development. Through large-scale lineage analysis, we characterize domain-specific structural patterns, such as vertical refinement in math-oriented datasets and horizontal aggregation in general-domain corpora. Moreover, we uncover pervasive systemic issues, including \textit{structural redundancy} induced by implicit dataset intersections and the \textit{propagation of benchmark contamination} along lineage paths. To demonstrate the practical value of lineage analysis for data construction, we leverage the reconstructed lineage graph to create a \textit{lineage-aware diversity-oriented dataset}. By anchoring instruction sampling at upstream root sources, this approach mitigates downstream homogenization and hidden redundancy, yielding a more diverse post-training corpus. We further highlight lineage-centric analysis as an efficient and robust topological alternative to sample-level dataset comparison for large-scale data ecosystems. By grounding data construction in explicit lineage structures, our work advances post-training data curation toward a more systematic and controllable paradigm.

Tianyi Shang, Pengjie Xu, Zhaojun Deng et al.

Cross-modal localization using text and point clouds enables robots to localize themselves via natural language descriptions, with applications in autonomous navigation and interaction between humans and robots. In this task, objects often recur across text and point clouds, making spatial relationships the most discriminative cues for localization. Given this characteristic, we present SpatiaLoc, a framework utilizing a coarse-to-fine strategy that emphasizes spatial relationships at both the instance and global levels. In the coarse stage, we introduce a Bezier Enhanced Object Spatial Encoder (BEOSE) that models spatial relationships at the instance level using quadratic Bezier curves. Additionally, a Frequency Aware Encoder (FAE) generates spatial representations in the frequency domain at the global level. In the fine stage, an Uncertainty Aware Gaussian Fine Localizer (UGFL) regresses 2D positions by modeling predictions as Gaussian distributions with a loss function aware of uncertainty. Extensive experiments on KITTI360Pose demonstrate that SpatiaLoc significantly outperforms existing state-of-the-art (SOTA) methods.

Qizhi Pei, Lijun Wu, Zhuoshi Pan et al.

Large Language Models (LLMs) have shown impressive progress in mathematical reasoning. While data augmentation is promising to enhance mathematical problem-solving ability, current approaches are predominantly limited to instance-level modifications-such as rephrasing or generating syntactic variations-which fail to capture and leverage the intrinsic relational structures inherent in mathematical knowledge. Inspired by human learning processes, where mathematical proficiency develops through systematic exposure to interconnected concepts, we introduce MathFusion, a novel framework that enhances mathematical reasoning through cross-problem instruction synthesis. MathFusion implements this through three fusion strategies: (1) sequential fusion, which chains related problems to model solution dependencies; (2) parallel fusion, which combines analogous problems to reinforce conceptual understanding; and (3) conditional fusion, which creates context-aware selective problems to enhance reasoning flexibility. By applying these strategies, we generate a new dataset, \textbf{MathFusionQA}, followed by fine-tuning models (DeepSeekMath-7B, Mistral-7B, Llama3-8B) on it. Experimental results demonstrate that MathFusion achieves substantial improvements in mathematical reasoning while maintaining high data efficiency, boosting performance by 18.0 points in accuracy across diverse benchmarks while requiring only 45K additional synthetic instructions, representing a substantial improvement over traditional single-instruction approaches. Our datasets, models, and code are publicly available at https://github.com/QizhiPei/mathfusion.

Jikai Wang, Juntao Li, Jianye Hou et al.

Large reasoning language models such as OpenAI-o1 and Deepseek-R1 have recently attracted widespread attention due to their impressive task-solving abilities. However, the enormous model size and the generation of lengthy thought chains introduce significant reasoning costs and response latency. Existing methods for efficient reasoning mainly focus on reducing the number of model parameters or shortening the chain-of-thought length. In this paper, we introduce Speculative Chain-of-Thought (SCoT), which reduces reasoning latency from another perspective by accelerated average reasoning speed through large and small model collaboration. SCoT conducts thought-level drafting using a lightweight draft model. Then it selects the best CoT draft and corrects the error cases with the target model. The proposed thinking behavior alignment improves the efficiency of drafting and the draft selection strategy maintains the prediction accuracy of the target model for complex tasks. Experimental results on GSM8K, MATH, GaoKao, CollegeMath and Olympiad datasets show that SCoT reduces reasoning latency by 48\%$\sim$66\% and 21\%$\sim$49\% for Deepseek-R1-Distill-Qwen-32B and Deepseek-R1-Distill-Llama-70B while achieving near-target-model-level performance. Our code is available at https://github.com/Jikai0Wang/Speculative_CoT.

Kaiyuan Gao, Qizhi Pei, Gongbo Zhang et al.

Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are often slow and costly. The advent of deep learning-based approaches has shown significant promise, offering increases in both accuracy and efficiency. Building upon the foundational work of FABind, a model designed with a focus on speed and accuracy, we present FABind+, an enhanced iteration that largely boosts the performance of its predecessor. We identify pocket prediction as a critical bottleneck in molecular docking and propose a novel methodology that significantly refines pocket prediction, thereby streamlining the docking process. Furthermore, we introduce modifications to the docking module to enhance its pose generation capabilities. In an effort to bridge the gap with conventional sampling/generative methods, we incorporate a simple yet effective sampling technique coupled with a confidence model, requiring only minor adjustments to the regression framework of FABind. Experimental results and analysis reveal that FABind+ remarkably outperforms the original FABind, achieves competitive state-of-the-art performance, and delivers insightful modeling strategies. This demonstrates FABind+ represents a substantial step forward in molecular docking and drug discovery. Our code is in https://github.com/QizhiPei/FABind.

Xin Gao, Qizhi Pei, Zinan Tang et al.

While data synthesis and distillation are promising strategies to enhance small language models, current approaches heavily rely on Large Language Models (LLMs), which suffer from high computational costs, environmental inefficiency, and potential biases inherited from monolithic architectures. In contrast, smaller LLMs are more accessible and sustainable, but their individual capabilities often fall short in generating high-quality, diverse, and reliable data. Inspired by collaborative human processes (e.g., peer review), we propose a multiple small LLMs involved framework, GRA, that aggregates specialized roles across small LLMs to iterative refinement and quality control typically achieved by a single large LLM. In this collaborative framework, multiple small LLMs assume distinct roles-Generator, Reviewer, and Adjudicator-to simulate a peer-review-inspired data synthesis pipeline. The Generator proposes initial data samples, the Reviewer critiques their quality and diversity, and the Adjudicator resolves conflicts to finalize the output. By decomposing the synthesis process into specialized sub-tasks, collaborative small LLMs can achieve data-level parity with large LLM-based distillation. Through experiments across multiple benchmarks, we demonstrate that GRA-produced data matches or exceeds the quality of single large LLM outputs, e.g., Qwen-2.5-72B-Instruct. Our results challenge the necessity of monolithic large models for high-quality data synthesis, advocating instead for strategic coordination of smaller agents. Our datasets, models, and code are publicly available at https://github.com/GX-XinGao/GRA.

Runchuan Zhu, Zinco Jiang, Jiang Wu et al.

Refusal-Aware Instruction Tuning (RAIT) aims to enhance Large Language Models (LLMs) by improving their ability to refuse responses to questions beyond their knowledge, thereby reducing hallucinations and improving reliability. Effective RAIT must address two key challenges: firstly, effectively reject unknown questions to minimize hallucinations; secondly, avoid over-refusal to ensure questions that can be correctly answered are not rejected, thereby maintain the helpfulness of LLM outputs. In this paper, we address the two challenges by deriving insightful observations from the gradient-based perspective, and proposing the Gradient-driven Refusal Aware Instruction Tuning Framework GRAIT: (1) employs gradient-driven sample selection to effectively minimize hallucinations and (2) introduces an adaptive weighting mechanism during fine-tuning to reduce the risk of over-refusal, achieving the balance between accurate refusals and maintaining useful responses. Experimental evaluations on open-ended and multiple-choice question answering tasks demonstrate that GRAIT significantly outperforms existing RAIT methods in the overall performance. The source code and data will be available at https://github.com/opendatalab/GRAIT .

Yujin Zhou, Chuxue Cao, Jinluan Yang et al.

While Large Reasoning Models (LRMs) have demonstrated exceptional logical capabilities in mathematical domains, their application to the legal field remains hindered by the strict requirements for procedural rigor and adherence to legal logic. Existing legal LLMs, which rely on "closed-loop reasoning" derived solely from internal parametric knowledge, frequently suffer from lack of self-awareness regarding their knowledge boundaries, leading to confident yet incorrect conclusions. To address this challenge, we present Legal Reasoning with Agentic Search (LRAS), the first framework designed to transition legal LLMs from static and parametric "closed-loop thinking" to dynamic and interactive "Active Inquiry". By integrating Introspective Imitation Learning and Difficulty-aware Reinforcement Learning, LRAS enables LRMs to identify knowledge boundaries and handle legal reasoning complexity. Empirical results demonstrate that LRAS outperforms state-of-the-art baselines by 8.2-32\%, with the most substantial gains observed in tasks requiring deep reasoning with reliable knowledge. We will release our data and models for further exploration soon.

Honglin Lin, Zhuoshi Pan, Yu Li et al.

Large Language Models (LLMs) have demonstrated promising capabilities in solving mathematical reasoning tasks, leveraging Chain-of-Thought (CoT) data as a vital component in guiding answer generation. Current paradigms typically generate CoT and answers directly for a given problem, diverging from human problem-solving strategies to some extent. Humans often solve problems by recalling analogous cases and leveraging their solutions to reason about the current task. Inspired by this cognitive process, we propose \textbf{MetaLadder}, a novel framework that explicitly prompts LLMs to recall and reflect on meta-problems, those structurally or semantically analogous problems, alongside their CoT solutions before addressing the target problem. Additionally, we introduce a problem-restating mechanism to enhance the model's comprehension of the target problem by regenerating the original question, which further improves reasoning accuracy. Therefore, the model can achieve reasoning transfer from analogical problems, mimicking human-like "learning from examples" and generalization abilities. Extensive experiments on mathematical benchmarks demonstrate that our MetaLadder significantly boosts LLMs' problem-solving accuracy, largely outperforming standard CoT-based methods (\textbf{10.3\%} accuracy gain) and other methods. Our code and data has been released at https://github.com/LHL3341/MetaLadder.

Junyuan Gao, Jiahe Song, Jiang Wu et al.

Existing multilingual benchmarks for Large Vision Language Models (LVLMs) suffer from limitations including language-specific content biases, disjointed multimodal input formats, and a lack of safety evaluation. To address these gaps, we propose PM4Bench, the first Parallel Multilingual Multi-Modal Multi-task Benchmark for LVLMs. PM4Bench features a parallel corpus design across 10 languages, enabling fair and accurate cross-lingual comparisons. It includes the vision setting where text and queries are embedded in images, requiring LVLMs to simultaneously "see", "read", and "think", aligning with real-world applications. Additionally, PM\textsuperscript{4}Bench incorporates safety evaluations, addressing critical oversight in existing multilingual benchmarks. Using PM4Bench, we evaluate 11 mainstream LVLMs, revealing significant cross-linguistic performance disparities, particularly in vision settings, and identifying OCR capability as a key determinant of these imbalances. We will release PM4Bench at https://github.com/opendatalab/PM4Bench .

Tingyu Li, Zheng Sun, Jingxuan Wei et al.

Recent vision-language models (VLMs) achieve remarkable reasoning through reinforcement learning (RL), which provides a feasible solution for realizing continuous self-evolving large vision-language models (LVLMs) in the era of experience. However, RL for VLMs requires abundant high-quality multimodal data, especially challenging in specialized domains like chemistry, earth sciences, and multimodal mathematics. Existing strategies such as synthetic data and self-rewarding mechanisms suffer from limited distributions and alignment difficulties, ultimately causing reward hacking: models exploit high-reward patterns, collapsing policy entropy and destabilizing training. We propose DoGe (Decouple to Generalize), a dual-decoupling framework that guides models to first learn from context rather than problem solving by refocusing on the problem context scenarios overlooked by synthetic data methods. By decoupling learning process into dual components (Thinker and Solver), we reasonably quantify the reward signals of this process and propose a two-stage RL post-training approach from freely exploring context to practically solving tasks. Second, to increase the diversity of training data, DoGe constructs an evolving curriculum learning pipeline: an expanded native domain knowledge corpus and an iteratively evolving seed problems pool. Experiments show that our method consistently outperforms the baseline across various benchmarks, providing a scalable pathway for realizing self-evolving LVLMs.

Jingxuan Wei, Caijun Jia, Xi Bai et al.

The advent of Unified Multimodal Models (UMMs) signals a paradigm shift in artificial intelligence, moving from passive perception to active, cross-modal generation. Despite their unprecedented ability to synthesize information, a critical gap persists in evaluation: existing benchmarks primarily assess discriminative understanding or unconstrained image generation separately, failing to measure the integrated cognitive process of generative reasoning. To bridge this gap, we propose that geometric construction provides an ideal testbed as it inherently demands a fusion of language comprehension and precise visual generation. We introduce GGBench, a benchmark designed specifically to evaluate geometric generative reasoning. It provides a comprehensive framework for systematically diagnosing a model's ability to not only understand and reason but to actively construct a solution, thereby setting a more rigorous standard for the next generation of intelligent systems. Project website: https://opendatalab-raiser.github.io/GGBench/.

Jiahe Song, Chuang Wang, Yinfan Wang et al.

Reaction diagram parsing (RxnDP) is critical for extracting chemical synthesis information from literature. Although recent Vision-Language Models (VLMs) have emerged as a promising paradigm to automate this complex visual reasoning task, their application is fundamentally bottlenecked by the inability to align visual chemical entities with pre-trained knowledge, alongside the inherent discrepancy between token-level training and reaction-level evaluation. To address these dual challenges, this work enhances VLM-based RxnDP from two complementary perspectives: prompting representation and learning paradigms. First, we propose Identifier as Visual Prompting (IdtVP), which leverages naturally occurring molecule identifiers (e.g., bold numerals like 1a) to activate the chemical knowledge acquired during VLM pre-training. IdtVP enables powerful zero-shot and out-of-distribution capabilities, outperforming existing prompting strategies. Second, to further optimize performance within fine-tuning paradigms, we introduce Re3-DAPO, a reinforcement learning algorithm that leverages verifiable rewards to directly optimize reaction-level metrics, thereby achieving consistent gains over standard supervised fine-tuning. Additionally, we release the ScannedRxn benchmark, comprising scanned historical reaction diagrams with real-world artifacts, to rigorously assess model robustness and out-of-distribution ability. Our contributions advance the accuracy and generalization of VLM-based reaction diagram parsing. We will release data, models, and code on GitHub.

Chuxue Cao, Jinluan Yang, Haoran Li et al.

Large Language Models (LLMs) show remarkable capabilities, yet their stochastic next-token prediction creates logical inconsistencies and reward hacking that formal symbolic systems avoid. To bridge this gap, we introduce a formal logic verification-guided framework that dynamically interleaves formal symbolic verification with the natural language generation process, providing real-time feedback to detect and rectify errors as they occur. Distinguished from previous neuro-symbolic methods limited by passive post-hoc validation, our approach actively penalizes intermediate fallacies during the reasoning chain. We operationalize this framework via a novel two-stage training pipeline that synergizes formal logic verification-guided supervised fine-tuning and policy optimization. Extensive evaluation on six benchmarks spanning mathematical, logical, and general reasoning demonstrates that our 7B and 14B models outperform state-of-the-art baselines by average margins of 10.4% and 14.2%, respectively. These results validate that formal verification can serve as a scalable mechanism to significantly push the performance boundaries of advanced LLM reasoning.

Juanxi Tian, Siyuan Li, Conghui He et al.

Current multimodal models aim to transcend the limitations of single-modality representations by unifying understanding and generation, often using text-to-image (T2I) tasks to calibrate semantic consistency. However, their reliance on static, single-image generation in training and evaluation leads to overfitting to static pattern matching and semantic fusion, while fundamentally hindering their ability to model dynamic processes that unfold over time. To address these constraints, we propose Envision-a causal event progression benchmark for chained text-to-multi-image generation. Grounded in world knowledge and structured by spatiotemporal causality, it reorganizes existing evaluation dimensions and includes 1,000 four-stage prompts spanning six scientific and humanities domains. To transition evaluation from single images to sequential frames and assess whether models truly internalize world knowledge while adhering to causal-temporal constraints, we introduce Envision-Score, a holistic metric integrating multi-dimensional consistency, physicality, and aesthetics. Comprehensive evaluation of 15 models (10 specialized T2I models, 5 unified models) uncovers: specialized T2I models demonstrate proficiency in aesthetic rendering yet lack intrinsic world knowledge. Unified multimodal models bridge this gap, consistently outperforming specialized counterparts in causal narrative coherence. However, even these unified architectures remain subordinate to closed-source models and struggle to overcome the core challenge of spatiotemporal consistency. This demonstrates that a focus on causally-isolated single images impedes multi-frame reasoning and generation, promoting static pattern matching over dynamic world modeling-ultimately limiting world knowledge internalization, generation.

Chuxue Cao, Honglin Lin, Zhanping Zhong et al.

Large Language Models (LLMs) have demonstrated strong general capabilities, yet their deployment in finance remains challenging due to dense domain-specific terminology, stringent numerical reasoning requirements, and low tolerance for factual errors. We conduct a controlled empirical study showing that in specialized vertical domains, performance is largely determined by the quality and difficulty/verifiability profile of post-training data. We introduce \textbf{ODA-Fin-SFT-318k}, constructed via multi-stage distillation and verification to produce high-quality Chain-of-Thought supervision, and \textbf{ODA-Fin-RL-12k}, curated for hard-but-verifiable tasks that balance reward precision and task diversity. Using standard SFT and RL pipelines, we show that high-quality CoT distillation establishes a robust foundation during SFT, while difficulty- and verifiability-aware sampling improves RL generalization. Evaluated on nine benchmarks spanning general financial tasks, sentiment analysis, and numerical reasoning, our ODA-Fin-RL-8B consistently surpasses open-source state-of-the-art (SOTA) financial LLMs of comparable size. We release our ODA-Fin-SFT-318k and ODA-Fin-RL-12k datasets, along with trained models to advance data-centric financial AI research.

Yangzhou Liu, Yue Cao, Hao Li et al.

Diffusion language models (DLMs) have strong theoretical efficiency but are limited by fixed-length decoding and incompatibility with key-value (KV) caches. Block diffusion mitigates these issues, yet still enforces a fixed block size and requires expensive training. We introduce Next Sequence Prediction (NSP), which unifies next-token and next-block prediction, enabling the model to adaptively determine the generation length at each step. When the length is fixed to 1, NSP reduces to standard next-token prediction. Building on NSP, we propose Sequential Diffusion Language Model (SDLM), which can retrofit pre-trained autoregressive language models (ALMs) at minimal cost. Specifically, SDLM performs diffusion inference within fixed-size mask blocks, but dynamically decodes consecutive subsequences based on model confidence, thereby preserving KV-cache compatibility and improving robustness to varying uncertainty and semantics across the sequence. Experiments show that SDLM matches or surpasses strong autoregressive baselines using only 3.5M training samples, while achieving 2.1 higher throughput than Qwen-2.5. Notably, the SDLM-32B model delivers even more pronounced efficiency gains, demonstrating the strong scalability potential of our modeling paradigm. Project page and codes: https://github.com/OpenGVLab/SDLM

Jingchao Wang, Haote Yang, Jiang Wu et al.

Optical Chemical Structure Recognition (OCSR) is crucial for digitizing chemical knowledge by converting molecular images into machine-readable formats. While recent vision-language models (VLMs) have shown potential in this task, their image-captioning approach often struggles with complex molecular structures and inconsistent annotations. To overcome these challenges, we introduce GTR-Mol-VLM, a novel framework featuring two key innovations: (1) the Graph Traversal as Visual Chain of Thought mechanism that emulates human reasoning by incrementally parsing molecular graphs through sequential atom-bond predictions, and (2) the data-centric principle of Faithfully Recognize What You've Seen, which addresses the mismatch between abbreviated structures in images and their expanded annotations. To support model development, we constructed GTR-CoT-1.3M, a large-scale instruction-tuning dataset with meticulously corrected annotations, and introduced MolRec-Bench, the first benchmark designed for a fine-grained evaluation of graph-parsing accuracy in OCSR. Comprehensive experiments demonstrate that GTR-Mol-VLM achieves superior results compared to specialist models, chemistry-domain VLMs, and commercial general-purpose VLMs. Notably, in scenarios involving molecular images with functional group abbreviations, GTR-Mol-VLM outperforms the second-best baseline by approximately 14 percentage points, both in SMILES-based and graph-based metrics. We hope that this work will drive OCSR technology to more effectively meet real-world needs, thereby advancing the fields of cheminformatics and AI for Science. We will release GTR-CoT at https://github.com/opendatalab/GTR-CoT.

Bowen Jiang, Runchuan Zhu, Jiang Wu et al.

We introduce KoLasSimpleQA, the first benchmark evaluating the multilingual factual ability of Large Language Models (LLMs). Inspired by existing research, we created the question set with features such as single knowledge point coverage, absolute objectivity, unique answers, and temporal stability. These questions enable efficient evaluation using the LLM-as-judge paradigm, testing both the LLMs' factual memory and self-awareness ("know what they don't know"). KoLasSimpleQA expands existing research in two key dimensions: (1) Breadth (Multilingual Coverage): It includes 9 languages, supporting global applicability evaluation. (2) Depth (Dual Domain Design): It covers both the general domain (global facts) and the language-specific domain (such as history, culture, and regional traditions) for a comprehensive assessment of multilingual capabilities. We evaluated mainstream LLMs, including traditional LLM and emerging Large Reasoning Models. Results show significant performance differences between the two domains, particularly in performance metrics, ranking, calibration, and robustness. This highlights the need for targeted evaluation and optimization in multilingual contexts. We hope KoLasSimpleQA will help the research community better identify LLM capability boundaries in multilingual contexts and provide guidance for model optimization. We will release KoLasSimpleQA at https://github.com/opendatalab/KoLasSimpleQA .

Haote Yang, Xingjian Wei, Jiang Wu et al.

We introduce OpenHuEval, the first benchmark for LLMs focusing on the Hungarian language and specifics. OpenHuEval is constructed from a vast collection of Hungarian-specific materials sourced from multiple origins. In the construction, we incorporated the latest design principles for evaluating LLMs, such as using real user queries from the internet, emphasizing the assessment of LLMs' generative capabilities, and employing LLM-as-judge to enhance the multidimensionality and accuracy of evaluations. Ultimately, OpenHuEval encompasses eight Hungarian-specific dimensions, featuring five tasks and 3953 questions. Consequently, OpenHuEval provides the comprehensive, in-depth, and scientifically accurate assessment of LLM performance in the context of the Hungarian language and its specifics. We evaluated current mainstream LLMs, including both traditional LLMs and recently developed Large Reasoning Models. The results demonstrate the significant necessity for evaluation and model optimization tailored to the Hungarian language and specifics. We also established the framework for analyzing the thinking processes of LRMs with OpenHuEval, revealing intrinsic patterns and mechanisms of these models in non-English languages, with Hungarian serving as a representative example. We will release OpenHuEval at https://github.com/opendatalab/OpenHuEval .

Zizhuo Zhang, Lijun Wu, Kaiyuan Gao et al.

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial structural changes by assuming protein rigidity or suffer from low computational efficiency due to their reliance on generative models for structure sampling. To address these challenges, we propose FABFlex, a fast and accurate regression-based multi-task learning model designed for realistic blind flexible docking scenarios, where proteins exhibit flexibility and binding pocket sites are unknown (blind). Specifically, FABFlex's architecture comprises three specialized modules working in concert: (1) A pocket prediction module that identifies potential binding sites, addressing the challenges inherent in blind docking scenarios. (2) A ligand docking module that predicts the bound (holo) structures of ligands from their unbound (apo) states. (3) A pocket docking module that forecasts the holo structures of protein pockets from their apo conformations. Notably, FABFlex incorporates an iterative update mechanism that serves as a conduit between the ligand and pocket docking modules, enabling continuous structural refinements. This approach effectively integrates the three subtasks of blind flexible docking-pocket identification, ligand conformation prediction, and protein flexibility modeling-into a unified, coherent framework. Extensive experiments on public benchmark datasets demonstrate that FABFlex not only achieves superior effectiveness in predicting accurate binding modes but also exhibits a significant speed advantage (208 $\times$) compared to existing state-of-the-art methods. Our code is released at https://github.com/tmlr-group/FABFlex.

Jiahe Song, Chuang Wang, Bowen Jiang et al.

Large-scale chemical reaction datasets are crucial for AI research in chemistry. However, existing chemical reaction data often exist as images within papers, making them not machine-readable and unusable for training machine learning models. In response to this challenge, we propose the RxnCaption framework for the task of chemical Reaction Diagram Parsing (RxnDP). Our framework reformulates the traditional coordinate prediction driven parsing process into an image captioning problem, which Large Vision-Language Models (LVLMs) handle naturally. We introduce a strategy termed "BBox and Index as Visual Prompt" (BIVP), which uses our state-of-the-art molecular detector, MolYOLO, to pre-draw molecular bounding boxes and indices directly onto the input image. This turns the downstream parsing into a natural-language description problem. Extensive experiments show that the BIVP strategy significantly improves structural extraction quality while simplifying model design. We further construct the RxnCaption-11k dataset, an order of magnitude larger than prior real-world literature benchmarks, with a balanced test subset across four layout archetypes. Experiments demonstrate that RxnCaption-VL achieves state-of-the-art performance on multiple metrics. We believe our method, dataset, and models will advance structured information extraction from chemical literature and catalyze broader AI applications in chemistry. We will release data, models, and code on GitHub.

Dmitrii Torbunov, Yihui Ren, Lijun Wu et al.

Uncertainty quantification is critical in scientific inverse problems to distinguish identifiable parameters from those that remain ambiguous given available measurements. The Conditional Diffusion Model-based Inverse Problem Solver (CDI) has previously demonstrated effective probabilistic inference for one-dimensional temporal signals, but its applicability to higher-dimensional spatial data remains unexplored. We extend CDI to two-dimensional spatial conditioning, enabling probabilistic parameter inference directly from spatial observations. We validate this extension on convergent beam electron diffraction (CBED) parameter inference - a challenging multi-parameter inverse problem in materials characterization where sample geometry, electronic structure, and thermal properties must be extracted from 2D diffraction patterns. Using simulated CBED data with ground-truth parameters, we demonstrate that CDI produces well-calibrated posterior distributions that accurately reflect measurement constraints: tight distributions for well-determined quantities and appropriately broad distributions for ambiguous parameters. In contrast, standard regression methods - while appearing accurate on aggregate metrics - mask this underlying uncertainty by predicting training set means for poorly constrained parameters. Our results confirm that CDI successfully extends from temporal to spatial domains, providing the genuine uncertainty information required for robust scientific inference.

Kai Zhuang, Jiawei Zhang, Yumou Liu et al.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.