arXiv subjects

Xuezhi Wang

Publications and source records attributed to Xuezhi Wang.

At least 19 recordsLinked to original sources

arXiv2026

Scientific Data Skills: Enabling Agent-Ready Scientific Data Services at Scale

Scientific data are increasingly used by AI agents, yet existing dataset representations provide limited support for reliable dataset discovery and interpretation, constraining their effective use in scientific workflows. This limitation arises because agents must search across heterogeneous repositories and reconstruct dataset-specific semantics and operating procedures from documentation designed primarily for human use. To address this limitation, we introduce the Scientific Data Skill (SciDSK), an agent-ready representation that packages dataset-specific knowledge and operational guidance as a reusable agent skill. A SciDSK integrates dataset descriptions, scientific context, file organization, task-specific usage procedures, quality checks, and provenance information while retaining the underlying data in its original repository. We define a structured SciDSK specification and develop a systematic construction pipeline that grounds each SciDSK in authoritative dataset records and associated supporting materials. We further establish the Scientific Data Skill Bank, a unified platform that publishes SciDSK resources across six scientific disciplines and supports package access, persistent identification, and traceability to source datasets. We evaluate SciDSK through a retrieval benchmark for dataset discovery and controlled cases for dataset interpretation. On the query retrieval benchmark, Agent-SciDSK achieves 80.77% Hit@1, exceeding Agent-Raw by 9.62 percentage points. Across controlled interpretation cases, the SciDSK condition satisfies 23 of 24 assessment criteria, compared with 22 under the web-page condition. These results indicate that SciDSK improves how agents locate and understand scientific datasets, providing a stronger foundation for actionable scientific data use.

cs.AI↗

arXiv2026

From Snapshots to Trajectories: Learning Single-Cell Gene Expression Dynamics via Conditional Flow Matching

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points as unpaired snapshot populations, leaving substantial temporal gaps. This motivates trajectory inference at unmeasured time points. Existing methods mainly follow two directions, optimal-transport (OT) alignment provides distribution-level matching between observed snapshots, while continuous-time generative models support forecasting via learned dynamics. However, two challenges remain: (i) unpaired snapshots render local transitions between adjacent time points ambiguous, leading to unstable supervision; and (ii) long-horizon prediction relies on repeated integration, where small modeling errors compound and cause distribution drift. To address these challenges, we propose single-cell Flow Matching (scFM), a latent generative framework based on coupling-conditioned flow matching. First, we compute entropically regularized OT couplings between adjacent snapshots and use them to construct soft, weighted flow-matching targets for learning time-dependent velocity fields. Second, we learn bidirectional velocity fields and leverage their consistency to refine couplings and improve temporal coherence under sparse supervision. Third, we introduce distribution-level alignment and latent dynamic regularization to anchor long rollouts and mitigate drift. Experiments on real-world time-series scRNA-seq datasets show that scFM consistently improves distributional prediction performance for both temporal interpolation and extrapolation. Moreover, scFM yields more accurate trajectory reconstruction and temporally coherent visualizations where intermediate time points are absent, indicating a more faithful recovery of underlying temporal gene expression dynamics.

cs.LG↗

arXiv2026

DeepEra: A Deep Evidence Reranking Agent for Scientific Retrieval-Augmented Generated Question Answering

With the rapid growth of scientific literature, scientific question answering (SciQA) has become increasingly critical for exploring and utilizing scientific knowledge. Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating knowledge from external sources, thereby providing credible evidence for scientific question answering. But existing retrieval and reranking methods remain vulnerable to passages that are semantically similar but logically irrelevant, often reducing factual reliability and amplifying hallucinations.To address this challenge, we propose a Deep Evidence Reranking Agent (DeepEra) that integrates step-by-step reasoning, enabling more precise evaluation of candidate passages beyond surface-level semantics. To support systematic evaluation, we construct SciRAG-SSLI (Scientific RAG - Semantically Similar but Logically Irrelevant), a large-scale dataset comprising about 300K SciQA instances across 10 subjects, constructed from 10M scientific corpus. The dataset combines naturally retrieved contexts with systematically generated distractors to test logical robustness and factual grounding. Comprehensive evaluations confirm that our approach achieves superior retrieval performance compared to leading rerankers. To our knowledge, this work is the first to comprehensively study and empirically validate innegligible SSLI issues in two-stage RAG frameworks.

cs.CL↗

arXiv2026

ScienceDB AI: An LLM-Driven Agentic Recommender System for Large-Scale Scientific Data Sharing Services

The rapid growth of AI for Science (AI4S) has underscored the significance of scientific datasets, leading to the establishment of numerous national scientific data centers and sharing platforms. Despite this progress, efficiently promoting dataset sharing and utilization for scientific research remains challenging. Scientific datasets contain intricate domain-specific knowledge and contexts, rendering traditional collaborative filtering-based recommenders inadequate. Recent advances in Large Language Models (LLMs) offer unprecedented opportunities to build conversational agents capable of deep semantic understanding and personalized recommendations. In response, we present ScienceDB AI, a novel LLM-driven agentic recommender system developed on Science Data Bank (ScienceDB), one of the largest global scientific data-sharing platforms. ScienceDB AI leverages natural language conversations and deep reasoning to accurately recommend datasets aligned with researchers' scientific intents and evolving requirements. The system introduces several innovations: a Scientific Intention Perceptor to extract structured experimental elements from complicated queries, a Structured Memory Compressor to manage multi-turn dialogues effectively, and a Trustworthy Retrieval-Augmented Generation (Trustworthy RAG) framework. The Trustworthy RAG employs a two-stage retrieval mechanism and provides citable dataset references via Citable Scientific Task Record (CSTR) identifiers, enhancing recommendation trustworthiness and reproducibility. Through extensive offline and online experiments using over 10 million real-world datasets, ScienceDB AI has demonstrated significant effectiveness. To our knowledge, ScienceDB AI is the first LLM-driven conversational recommender tailored explicitly for large-scale scientific dataset sharing services. The platform is publicly accessible at: https://ai.scidb.cn/en.

cs.IR↗

arXiv2025

Quantifying the advantage of vector over scalar magnetic sensor networks for undersea surveillance

Magnetic monitoring of maritime environments is an important problem for monitoring and optimising shipping, as well as national security. New developments in compact, fibre-coupled quantum magnetometers have led to the opportunity to critically evaluate how best to create such a sensor network. Here we explore various magnetic sensor network architectures for target identification. Our modelling compares networks of scalar vs vector magnetometers. We implement an unscented Kalman filter approach to perform target tracking, and we find that vector networks provide a significant improvement in target tracking, specifically tracking accuracy and resilience compared with scalar networks.

eess.SP↗

arXiv2025

Ming-Flash-Omni: A Sparse, Unified Architecture for Multimodal Perception and Generation

We propose Ming-Flash-Omni, an upgraded version of Ming-Omni, built upon a sparser Mixture-of-Experts (MoE) variant of Ling-Flash-2.0 with 100 billion total parameters, of which only 6.1 billion are active per token. This architecture enables highly efficient scaling (dramatically improving computational efficiency while significantly expanding model capacity) and empowers stronger unified multimodal intelligence across vision, speech, and language, representing a key step toward Artificial General Intelligence (AGI). Compared to its predecessor, the upgraded version exhibits substantial improvements across multimodal understanding and generation. Notably, it achieves strong performance on vision-language understanding benchmarks, with overall scores on par with Gemini 2.5 Pro, and enables seamless switching among multimodal tasks in multi-turn interactions. In speech, it achieves strong performance in contextual and dialect-aware ASR while enabling joint, continuous-generation of speech, sound, and music. In vision, it introduces generative semantic segmentation that achieves competitive standalone performance and enhances spatial control and editing consistency, alongside marked improvements in identity preservation, and high-fidelity in-image text rendering. Together, these capabilities demonstrate that a single unified model can serve as a practical foundation for general-purpose multimodal intelligence.

cs.CV↗

arXiv2025

Ming-UniAudio: Speech LLM for Joint Understanding, Generation and Editing with Unified Representation

Existing speech models suffer from competing requirements on token representations by understanding and generation tasks. This discrepancy in representation prevents speech language models from performing instruction-based free-form editing. To solve this challenge, we introduce a novel framework that unifies speech understanding, generation, and editing. The core of our unified model is a unified continuous speech tokenizer MingTok-Audio, the first continuous tokenizer to effectively integrate semantic and acoustic features, which makes it suitable for both understanding and generation tasks. Based on this unified continuous audio tokenizer, we developed the speech language model Ming-UniAudio, which achieved a balance between generation and understanding capabilities. Ming-UniAudio sets new state-of-the-art (SOTA) records on 8 out of 12 metrics on the ContextASR benchmark. Notably, for Chinese voice cloning, it achieves a highly competitive Seed-TTS-WER of 0.95. Leveraging this foundational model, we further trained a dedicated speech editing model Ming-UniAudio-Edit, the first speech language model that enables universal, free-form speech editing guided solely by natural language instructions, handling both semantic and acoustic modifications without timestamp condition. To rigorously assess the editing capability and establish a foundation for future research, we introduce Ming-Freeform-Audio-Edit, the first comprehensive benchmark tailored for instruction-based free-form speech editing, featuring diverse scenarios and evaluation dimensions spanning semantic correctness, acoustic quality, and instruction alignment. We open-sourced the continuous audio tokenizer, the unified foundational model, and the free-form instruction-based editing model to facilitate the development of unified audio understanding, generation, and manipulation.

cs.CL↗

arXiv2025

Nontrivial topology in one- and two-dimensional asymmetric systems with chiral boundary states

Symmetry plays an important role in the topological band theory. In contrary, study on the topological properties of the asymmetric systems is rather limited, especially in higher-dimensional systems. In this work, we explore a new theory to study the topology in various one-dimensional (1D) and two-dimensional (2D) asymmetric systems with chiral boundary states. Starting from the simple SSHm model, we show the chiral topology of its edge states by redefining sublattices. Meanwhile, based on its Rice-Mele-like effective Hamiltonian, a new topological invariant $\bar{Z}$ can be defined and the bulk-edge correspondence is established. With this clear physical picture, our theory can be extended to the more complex asymmetric ladder models, or even the 2D asymmetric systems. In the 2D BBH3 model, new chiral corner states with redefined lattices are found based on our method. These corner states are independent of any spatial symmetry and exhibit the characteristics of topological bound states in the continuum (TBICs). Moreover, the topological invariant can be calculated by introducing $\bar{Z}$ into 2D. At last, we propose an acoustic experiment of the BBH3 model where chiral corner states are numerically observed. Our work exhibits a new approach to study the topological properties of asymmetric systems. By redefining sublattices, we find that the models with entirely different structures might share the same topological origins.

cond-mat.mes-hall↗

arXiv2025

SciRerankBench: Benchmarking Rerankers Towards Scientific Retrieval-Augmented Generated LLMs

Scientific literature question answering is a pivotal step towards new scientific discoveries. Recently, \textit{two-stage} retrieval-augmented generated large language models (RAG-LLMs) have shown impressive advancements in this domain. Such a two-stage framework, especially the second stage (reranker), is particularly essential in the scientific domain, where subtle differences in terminology may have a greatly negative impact on the final factual-oriented or knowledge-intensive answers. Despite this significant progress, the potential and limitations of these works remain unexplored. In this work, we present a Scientific Rerank-oriented RAG Benchmark (SciRerankBench), for evaluating rerankers within RAG-LLMs systems, spanning five scientific subjects. To rigorously assess the reranker performance in terms of noise resilience, relevance disambiguation, and factual consistency, we develop three types of question-context-answer (Q-C-A) pairs, i.e., Noisy Contexts (NC), Semantically Similar but Logically Irrelevant Contexts (SSLI), and Counterfactual Contexts (CC). Through systematic evaluation of 13 widely used rerankers on five families of LLMs, we provide detailed insights into their relative strengths and limitations. To the best of our knowledge, SciRerankBench is the first benchmark specifically developed to evaluate rerankers within RAG-LLMs, which provides valuable observations and guidance for their future development.

cs.CL↗

arXiv2025

Comprehensive Metapath-based Heterogeneous Graph Transformer for Gene-Disease Association Prediction

Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital for efficient and scalable gene-disease association prediction. Graph-based learning models, which leverage node features and network relationships, are commonly employed for biomolecular predictions. However, existing methods often struggle to effectively integrate node features, heterogeneous structures, and semantic information. To address these challenges, we propose COmprehensive MEtapath-based heterogeneous graph Transformer(COMET) for predicting gene-disease associations. COMET integrates diverse datasets to construct comprehensive heterogeneous networks, initializing node features with BioGPT. We define seven Metapaths and utilize a transformer framework to aggregate Metapath instances, capturing global contexts and long-distance dependencies. Through intra- and inter-metapath aggregation using attention mechanisms, COMET fuses latent vectors from multiple Metapaths to enhance GDA prediction accuracy. Our method demonstrates superior robustness compared to state-of-the-art approaches. Ablation studies and visualizations validate COMET's effectiveness, providing valuable insights for advancing human health research.

cs.AI↗

arXiv2024

GeneSUM: Large Language Model-based Gene Summary Extraction

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and formidable challenges for researchers striving to keep abreast of the latest advancements. One significant challenge is navigating the vast corpus of literature to extract vital gene-related information, a time-consuming and cumbersome task. To enhance the efficiency of this process, it is crucial to address several key challenges: (1) the overwhelming volume of literature, (2) the complexity of gene functions, and (3) the automated integration and generation. In response, we propose GeneSUM, a two-stage automated gene summary extractor utilizing a large language model (LLM). Our approach retrieves and eliminates redundancy of target gene literature and then fine-tunes the LLM to refine and streamline the summarization process. We conducted extensive experiments to validate the efficacy of our proposed framework. The results demonstrate that LLM significantly enhances the integration of gene-specific information, allowing more efficient decision-making in ongoing research.

q-bio.GN↗

arXiv2024

BioRAG: A RAG-LLM Framework for Biological Question Reasoning

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

cs.CL↗

arXiv2024

MSR-86K: An Evolving, Multilingual Corpus with 86,300 Hours of Transcribed Audio for Speech Recognition Research

Recently, multilingual artificial intelligence assistants, exemplified by ChatGPT, have gained immense popularity. As a crucial gateway to human-computer interaction, multilingual automatic speech recognition (ASR) has also garnered significant attention, as evidenced by systems like Whisper. However, the proprietary nature of the training data has impeded researchers' efforts to study multilingual ASR. This paper introduces MSR-86K, an evolving, large-scale multilingual corpus for speech recognition research. The corpus is derived from publicly accessible videos on YouTube, comprising 15 languages and a total of 86,300 hours of transcribed ASR data. We also introduce how to use the MSR-86K corpus and other open-source corpora to train a robust multilingual ASR model that is competitive with Whisper. MSR-86K will be publicly released on HuggingFace, and we believe that such a large corpus will pave new avenues for research in multilingual ASR.

eess.AS↗

arXiv2024

A Minimalist Prompt for Zero-Shot Policy Learning

Transformer-based methods have exhibited significant generalization ability when prompted with target-domain demonstrations or example solutions during inference. Although demonstrations, as a way of task specification, can capture rich information that may be hard to specify by language, it remains unclear what information is extracted from the demonstrations to help generalization. Moreover, assuming access to demonstrations of an unseen task is impractical or unreasonable in many real-world scenarios, especially in robotics applications. These questions motivate us to explore what the minimally sufficient prompt could be to elicit the same level of generalization ability as the demonstrations. We study this problem in the contextural RL setting which allows for quantitative measurement of generalization and is commonly adopted by meta-RL and multi-task RL benchmarks. In this setting, the training and test Markov Decision Processes (MDPs) only differ in certain properties, which we refer to as task parameters. We show that conditioning a decision transformer on these task parameters alone can enable zero-shot generalization on par with or better than its demonstration-conditioned counterpart. This suggests that task parameters are essential for the generalization and DT models are trying to recover it from the demonstration prompt. To extract the remaining generalizable information from the supervision, we introduce an additional learnable prompt which is demonstrated to further boost zero-shot generalization across a range of robotic control, manipulation, and navigation benchmark tasks.

cs.LG↗

arXiv2024

COMAE: COMprehensive Attribute Exploration for Zero-shot Hashing

Zero-shot hashing (ZSH) has shown excellent success owing to its efficiency and generalization in large-scale retrieval scenarios. While considerable success has been achieved, there still exist urgent limitations. Existing works ignore the locality relationships of representations and attributes, which have effective transferability between seeable classes and unseeable classes. Also, the continuous-value attributes are not fully harnessed. In response, we conduct a COMprehensive Attribute Exploration for ZSH, named COMAE, which depicts the relationships from seen classes to unseen ones through three meticulously designed explorations, i.e., point-wise, pair-wise and class-wise consistency constraints. By regressing attributes from the proposed attribute prototype network, COMAE learns the local features that are relevant to the visual attributes. Then COMAE utilizes contrastive learning to comprehensively depict the context of attributes, rather than instance-independent optimization. Finally, the class-wise constraint is designed to cohesively learn the hash code, image representation, and visual attributes more effectively. Experimental results on the popular ZSH datasets demonstrate that COMAE outperforms state-of-the-art hashing techniques, especially in scenarios with a larger number of unseen label classes.

cs.CV↗

arXiv2024

Dual-polarization huge photonic spin Hall shift and deep-subwavelength sensing based on topological singularities in one-dimensional photonic crystals

Although several efforts have been taken to enhance the photonic spin Hall shift in deep-subwavelength region, according to effective medium theory, the fundamental confliction between near-zero reflection coefficient and near-zero incident angle still hinders the further application. Here, we reveal a fundamental breakdown of effective medium theory due to the existing of topological singularity in deep-subwavelength region in one-dimensional photonic crystals. We find that near the topological singularity, huge photonic spin Hall shift can be achieved for s-polarization and p-polarization. At the topological singularity, the reflected filed is split as dipole-like distribution with zero photonic spin Hall shift for both-polarizations, which is resulted from the interfere of the spin-maintained normal light and spin-flipped abnormal light. Based on the theoretical research, dual-polarizations thickness and dielectric constant sensing devices can be designed in deep-subwavelength region. Further more, by applying more complicated layered structure, multi-channels dual-polarizations detection and broadband dual-polarizations huge spin Hall shift platform can be designed. This work paves the way to exploring the topological properties and polarization control of photonic crystals and provides a prospective method for the design of multi-channels sensitive detection spin optical devices.

physics.optics↗

arXiv2024

Chain-of-Thought Reasoning Without Prompting

In enhancing the reasoning capabilities of large language models (LLMs), prior research primarily focuses on specific prompting techniques such as few-shot or zero-shot chain-of-thought (CoT) prompting. These methods, while effective, often involve manually intensive prompt engineering. Our study takes a novel approach by asking: Can LLMs reason effectively without prompting? Our findings reveal that, intriguingly, CoT reasoning paths can be elicited from pre-trained LLMs by simply altering the \textit{decoding} process. Rather than conventional greedy decoding, we investigate the top-$k$ alternative tokens, uncovering that CoT paths are frequently inherent in these sequences. This approach not only bypasses the confounders of prompting but also allows us to assess the LLMs' \textit{intrinsic} reasoning abilities. Moreover, we observe that the presence of a CoT in the decoding path correlates with a higher confidence in the model's decoded answer. This confidence metric effectively differentiates between CoT and non-CoT paths. Extensive empirical studies on various reasoning benchmarks show that the proposed CoT-decoding effectively elicits reasoning capabilities from language models, which were previously obscured by standard greedy decoding.

cs.CL↗

arXiv2024

Premise Order Matters in Reasoning with Large Language Models

Large language models (LLMs) have accomplished remarkable reasoning performance in various domains. However, in the domain of reasoning tasks, we discover a frailty: LLMs are surprisingly brittle to the ordering of the premises, despite the fact that such ordering does not alter the underlying task. In particular, we observe that LLMs achieve the best performance when the premise order aligns with the context required in intermediate reasoning steps. For example, in deductive reasoning tasks, presenting the premises in the same order as the ground truth proof in the prompt (as opposed to random ordering) drastically increases the model's accuracy. We first examine the effect of premise ordering on deductive reasoning on a variety of LLMs, and our evaluation shows that permuting the premise order can cause a performance drop of over 30%. In addition, we release the benchmark R-GSM, based on GSM8K, to examine the ordering effect for mathematical problem-solving, and we again observe a significant drop in accuracy, relative to the original GSM8K benchmark.

cs.AI↗