arXiv subjects

Nanqing Dong

Publications and source records attributed to Nanqing Dong.

At least 19 recordsLinked to original sources

arXiv2026

ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks

Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biological foundation models, specifically nucleotide foundation models (NFMs), the field lacks a unified standard for viral genomics to facilitate community development and enforce biosecurity constraints. To address this, we introduce ViroBench, the first comprehensive and large-scale benchmark specifically designed for NFMs in viral settings. ViroBench evaluates models across two critical dimensions: biological understanding and latent biosecurity risk, covering 18 diverse scenarios within 4 task types. Extensive evaluation of 66 NFMs across diverse architectures yields three critical conclusions. Firstly, NFMs exhibit a performance degradation in biological understanding under phylogenetic and temporal shifts, indicating weak extrapolation capabilities. Secondly, generation tasks reveal a decoupling between statistical likelihood and biological functional validity, posing latent biosecurity risks. Thirdly, controlled ablation studies reveal that taxonomic diversity in pretraining data outweighs parameter scale. Specifically, a lightweight baseline trained on diverse data achieves a 67.5% performance gain over its original model. Overall, ViroBench provides interpretable, diagnostic evaluations and a reproducible measurement framework for future research on viral nucleotide foundation models. The datasets and code are publicly available at https://github.com/QIANJINYDX/ViroBench.

cs.LG↗

arXiv2026

Knowledge-to-Verification: Exploring RLVR for LLMs in Knowledge-Intensive Domains

Reinforcement learning with verifiable rewards (RLVR) has demonstrated promising potential to enhance the reasoning capabilities of large language models (LLMs) in domains such as mathematics and coding. However, its applications on knowledge-intensive domains have not been effectively explored due to the scarcity of high-quality verifiable data. Furthermore, current RLVR focuses solely on the correctness of final answers, leading to the limitations of flawed reasoning and sparse reward signals. In this work, we propose Knowledge-to-Verification (K2V), a framework that extends RLVR to knowledge-intensive domains through automated verifiable data synthesis, while enabling verification of the LLM's reasoning process. Extensive experiments demonstrate that K2V enhances the reasoning of LLM in knowledge-intensive domains without significantly compromising the model's general capabilities. This study also suggests that integrating automated data synthesis with reasoning verification is a promising direction to enhance model capabilities in these broader domains. Code is available at https://github.com/SeedScientist/K2V.

cs.CL↗

arXiv2026

Project Imaging-X: A Survey of 1000+ Open-Access Medical Imaging Datasets for Foundation Model Development

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

cs.CV↗

arXiv2026

Self-evolving AI agents for protein discovery and directed evolution

Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFactory2 provides an autonomous framework that shifts from static tool usage to dynamic workflow synthesis via a self-evolving multi-agent infrastructure to address protein-related demands. It outperforms a set of well-known agents on the VenusAgentEval benchmark, and autonomously organizes the discovery and optimization of proteins from a single natural language prompt.

cs.AI↗

arXiv2026

MEMTS: Internalizing Domain Knowledge via Parameterized Memory for Retrieval-Free Domain Adaptation of Time Series Foundation Models

While Time Series Foundation Models (TSFMs) have demonstrated exceptional performance in generalized forecasting, their performance often degrades significantly when deployed in real-world vertical domains characterized by temporal distribution shifts and domain-specific periodic structures. Current solutions are primarily constrained by two paradigms: Domain-Adaptive Pretraining (DAPT), which improves short-term domain fitting but frequently disrupts previously learned global temporal patterns due to catastrophic forgetting; and Retrieval-Augmented Generation (RAG), which incorporates external knowledge but introduces substantial retrieval overhead. This creates a severe scalability bottleneck that fails to meet the high-efficiency requirements of real-time stream processing. To break this impasse, we propose Memory for Time Series (MEMTS), a lightweight and plug-and-play method for retrieval-free domain adaptation in time series forecasting. The key component of MEMTS is a Knowledge Persistence Module (KPM), which internalizes domain-specific temporal dynamics, such as recurring seasonal patterns and trends into a compact set of learnable latent prototypes. In doing so, it transforms fragmented historical observations into continuous, parameterized knowledge representations. This paradigm shift enables MEMTS to achieve accurate domain adaptation with constant-time inference and near-zero latency, while effectively mitigating catastrophic forgetting of general temporal patterns, all without requiring any architectural modifications to the frozen TSFM backbone. Extensive experiments on multiple datasets demonstrate the SOTA performance of MEMTS.

cs.LG↗

arXiv2026

SciDataCopilot: An Agentic Data Preparation Framework for AGI-driven Scientific Discovery

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30$\times$ speedup in data preparation.

cs.DB↗

arXiv2026

Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction

Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fundamental biophysical constraints. Currently, selecting candidates for wet-lab validation relies on manual expert auditing of PLM outputs, a process that is inefficient, subjective, and highly dependent on domain expertise. To address this, we propose Rank-and-Reason (VenusRAR), a two-stage agentic framework to automate this workflow and maximize expected wet-lab fitness. In the Rank-Stage, a Computational Expert and Virtual Biologist aggregate a context-aware multi-modal ensemble, establishing a new Spearman correlation record of 0.551 (vs. 0.518) on ProteinGym. In the Reason-Stage, an agentic Expert Panel employs chain-of-thought reasoning to audit candidates against geometric and structural constraints, improving the Top-5 Hit Rate by up to 367% on ProteinGym-DMS99. The wet-lab validation on Cas12i3 nuclease further confirms the framework's efficacy, achieving a 46.7% positive rate and identifying two novel mutants with 4.23-fold and 5.05-fold activity improvements. Code and datasets are released on GitHub (https://github.com/ai4protein/VenusRAR/).

q-bio.QM↗

arXiv2025

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

cs.AI↗

arXiv2025

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

cs.LG↗

arXiv2025

PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

cs.LG↗

arXiv2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

cs.LG↗

arXiv2025

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

q-bio.BM↗

arXiv2025

Intern-S1: A Scientific Multimodal Foundation Model

In recent years, a plethora of open-source foundation models have emerged, achieving remarkable progress in some widely attended fields, with performance being quite close to that of closed-source models. However, in high-value but more challenging scientific professional fields, either the fields still rely on expert models, or the progress of general foundation models lags significantly compared to those in popular areas, far from sufficient for transforming scientific research and leaving substantial gap between open-source models and closed-source models in these scientific domains. To mitigate this gap and explore a step further toward Artificial General Intelligence (AGI), we introduce Intern-S1, a specialized generalist equipped with general understanding and reasoning capabilities with expertise to analyze multiple science modal data. Intern-S1 is a multimodal Mixture-of-Experts (MoE) model with 28 billion activated parameters and 241 billion total parameters, continually pre-trained on 5T tokens, including over 2.5T tokens from scientific domains. In the post-training stage, Intern-S1 undergoes offline and then online reinforcement learning (RL) in InternBootCamp, where we propose Mixture-of-Rewards (MoR) to synergize the RL training on more than 1000 tasks simultaneously. Through integrated innovations in algorithms, data, and training systems, Intern-S1 achieved top-tier performance in online RL training. On comprehensive evaluation benchmarks, Intern-S1 demonstrates competitive performance on general reasoning tasks among open-source models and significantly outperforms open-source models in scientific domains, surpassing closed-source state-of-the-art models in professional tasks, such as molecular synthesis planning, reaction condition prediction, predicting thermodynamic stabilities for crystals. Our models are available at https://huggingface.co/internlm/Intern-S1.

cs.LG↗

arXiv2025

Dynamic Knowledge Exchange and Dual-diversity Review: Concisely Unleashing the Potential of a Multi-Agent Research Team

Scientific progress increasingly relies on effective collaboration among researchers, a dynamic that large language models (LLMs) have only begun to emulate. While recent LLM-based scientist agents show promise in autonomous scientific discovery, they often lack the interactive reasoning and evaluation mechanisms essential to real-world research. We propose IDVSCI (Internal Discussion and Vote SCIentists), a multi-agent framework built on LLMs that incorporates two key innovations: a Dynamic Knowledge Exchange mechanism enabling iterative feedback among agents, and a Dual-Diversity Review paradigm that simulates heterogeneous expert evaluation. These components jointly promote deeper reasoning and the generation of more creative and impactful scientific ideas. To evaluate the effectiveness and generalizability of our approach, we conduct experiments on two datasets: a widely used benchmark in computer science and a new dataset we introduce in the health sciences domain. Results show that IDVSCI consistently achieves the best performance across both datasets, outperforming existing systems such as AI Scientist and VIRSCI. These findings highlight the value of modeling interaction and peer review dynamics in LLM-based autonomous research.

cs.AI↗

arXiv2025

zkFL: Zero-Knowledge Proof-based Gradient Aggregation for Federated Learning

Federated learning (FL) is a machine learning paradigm, which enables multiple and decentralized clients to collaboratively train a model under the orchestration of a central aggregator. FL can be a scalable machine learning solution in big data scenarios. Traditional FL relies on the trust assumption of the central aggregator, which forms cohorts of clients honestly. However, a malicious aggregator, in reality, could abandon and replace the client's training models, or insert fake clients, to manipulate the final training results. In this work, we introduce zkFL, which leverages zero-knowledge proofs to tackle the issue of a malicious aggregator during the training model aggregation process. To guarantee the correct aggregation results, the aggregator provides a proof per round, demonstrating to the clients that the aggregator executes the intended behavior faithfully. To further reduce the verification cost of clients, we use blockchain to handle the proof in a zero-knowledge way, where miners (i.e., the participants validating and maintaining the blockchain data) can verify the proof without knowing the clients' local and aggregated models. The theoretical analysis and empirical results show that zkFL achieves better security and privacy than traditional FL, without modifying the underlying FL network structure or heavily compromising the training speed.

cs.AI↗

arXiv2025

Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing

Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model's estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species.

q-bio.BM↗

arXiv2025

ROGRAG: A Robustly Optimized GraphRAG Framework

Large language models (LLMs) commonly struggle with specialized or emerging topics which are rarely seen in the training corpus. Graph-based retrieval-augmented generation (GraphRAG) addresses this by structuring domain knowledge as a graph for dynamic retrieval. However, existing pipelines involve complex engineering workflows, making it difficult to isolate the impact of individual components. It is also challenging to evaluate the retrieval effectiveness due to the overlap between the pretraining and evaluation datasets. In this work, we introduce ROGRAG, a Robustly Optimized GraphRAG framework. Specifically, we propose a multi-stage retrieval mechanism that integrates dual-level with logic form retrieval methods to improve retrieval robustness without increasing computational cost. To further refine the system, we incorporate various result verification methods and adopt an incremental database construction approach. Through extensive ablation experiments, we rigorously assess the effectiveness of each component. Our implementation includes comparative experiments on SeedBench, where Qwen2.5-7B-Instruct initially underperformed. ROGRAG significantly improves the score from 60.0% to 75.0% and outperforms mainstream methods. Experiments on domain-specific datasets reveal that dual-level retrieval enhances fuzzy matching, while logic form retrieval improves structured reasoning, highlighting the importance of multi-stage retrieval.ROGRAG is released as an open-source resource and supports installation with pip.

cs.IR↗

arXiv2025

Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

cs.LG↗