arXiv subjects

Nan Wang

Publications and source records attributed to Nan Wang.

At least 73 records · Page 4Linked to original sources

arXiv2025

MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available in huggingface.

cs.CV↗

arXiv2025

Deep holes of a class of twisted Reed-Solomon codes

The deep hole problem is a fundamental problem in coding theory, and it has many important applications in code constructions and cryptography. The deep hole problem of Reed-Solomon codes has gained a lot of attention. As a generalization of Reed-Solomon codes, we investigate the problem of deep holes of a class of twisted Reed-Solomon codes in this paper. Firstly, we provide the necessary and sufficient conditions for $\boldsymbol{a}=(a_{0},a_{1},\cdots,a_{n-k-1})\in\mathbb{F}_{q}^{n-k}$ to be the syndrome of some deep hole of $TRS_{k}(\mathcal{A},l,η)$. Next, we consider the problem of determining all deep holes of the twisted Reed-Solomon codes $TRS_{k}(\mathbb{F}_{q}^{*},k-1,η)$. Specifically, we prove that there are no other deep holes of $TRS_{k}(\mathbb{F}_{q}^{*},k-1,η)$ for $\frac{3q+2\sqrt{q}-8}{4}\leq k\leq q-5$ when q is even, and $\frac{3q+3\sqrt{q}-5}{4}\leq k\leq q-5$ when q is odd. We also completely determine their deep holes for $q-4\leq k\leq q-2$ when $q$ is even.

cs.IT↗

arXiv2025

One View, Many Worlds: Single-Image to 3D Object Meets Generative Domain Randomization for One-Shot 6D Pose Estimation

Estimating the 6D pose of arbitrary unseen objects from a single reference image is critical for robotics operating in the long-tail of real-world instances. However, this setting is notoriously challenging: 3D models are rarely available, single-view reconstructions lack metric scale, and domain gaps between generated models and real-world images undermine robustness. We propose OnePoseViaGen, a pipeline that tackles these challenges through two key components. First, a coarse-to-fine alignment module jointly refines scale and pose by combining multi-view feature matching with render-and-compare refinement. Second, a text-guided generative domain randomization strategy diversifies textures, enabling effective fine-tuning of pose estimators with synthetic data. Together, these steps allow high-fidelity single-view 3D generation to support reliable one-shot 6D pose estimation. On challenging benchmarks (YCBInEOAT, Toyota-Light, LM-O), OnePoseViaGen achieves state-of-the-art performance far surpassing prior approaches. We further demonstrate robust dexterous grasping with a real robot hand, validating the practicality of our method in real-world manipulation. Project page: https://gzwsama.github.io/OnePoseviaGen.github.io/

cs.CV↗

arXiv2025

SciGPT: A Large Language Model for Scientific Literature Understanding and Knowledge Discovery

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

cs.CL↗

arXiv2025

zkUnlearner: A Zero-Knowledge Framework for Verifiable Unlearning with Multi-Granularity and Forgery-Resistance

As the demand for exercising the "right to be forgotten" grows, the need for verifiable machine unlearning has become increasingly evident to ensure both transparency and accountability. We present {\em zkUnlearner}, the first zero-knowledge framework for verifiable machine unlearning, specifically designed to support {\em multi-granularity} and {\em forgery-resistance}. First, we propose a general computational model that employs a {\em bit-masking} technique to enable the {\em selectivity} of existing zero-knowledge proofs of training for gradient descent algorithms. This innovation enables not only traditional {\em sample-level} unlearning but also more advanced {\em feature-level} and {\em class-level} unlearning. Our model can be translated to arithmetic circuits, ensuring compatibility with a broad range of zero-knowledge proof systems. Furthermore, our approach overcomes key limitations of existing methods in both efficiency and privacy. Second, forging attacks present a serious threat to the reliability of unlearning. Specifically, in Stochastic Gradient Descent optimization, gradients from unlearned data, or from minibatches containing it, can be forged using alternative data samples or minibatches that exclude it. We propose the first effective strategies to resist state-of-the-art forging attacks. Finally, we benchmark a zkSNARK-based instantiation of our framework and perform comprehensive performance evaluations to validate its practicality.

cs.CR↗

arXiv2025

An Agentic Model Context Protocol Framework for Medical Concept Standardization

The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) provides a standardized representation of heterogeneous health data to support large-scale, multi-institutional research. One critical step in data standardization using OMOP CDM is the mapping of source medical terms to OMOP standard concepts, a procedure that is resource-intensive and error-prone. While large language models (LLMs) have the potential to facilitate this process, their tendency toward hallucination makes them unsuitable for clinical deployment without training and expert validation. Here, we developed a zero-training, hallucination-preventive mapping system based on the Model Context Protocol (MCP), a standardized and secure framework allowing LLMs to interact with external resources and tools. The system enables explainable mapping and significantly improves efficiency and accuracy with minimal effort. It provides real-time vocabulary lookups and structured reasoning outputs suitable for immediate use in both exploratory and production environments.

cs.AI↗

arXiv2025

Uni-AIMS: AI-Powered Microscopy Image Analysis

This paper presents a systematic solution for the intelligent recognition and automatic analysis of microscopy images. We developed a data engine that generates high-quality annotated datasets through a combination of the collection of diverse microscopy images from experiments, synthetic data generation and a human-in-the-loop annotation process. To address the unique challenges of microscopy images, we propose a segmentation model capable of robustly detecting both small and large objects. The model effectively identifies and separates thousands of closely situated targets, even in cluttered visual environments. Furthermore, our solution supports the precise automatic recognition of image scale bars, an essential feature in quantitative microscopic analysis. Building upon these components, we have constructed a comprehensive intelligent analysis platform and validated its effectiveness and practicality in real-world applications. This study not only advances automatic recognition in microscopy imaging but also ensures scalability and generalizability across multiple application domains, offering a powerful tool for automated microscopic analysis in interdisciplinary research. A online application is made available for researchers to access and evaluate the proposed automated analysis service.

eess.IV↗

arXiv2025

FFT-MoE: Efficient Federated Fine-Tuning for Foundation Models via Large-scale Sparse MoE under Heterogeneous Edge

As FMs drive progress toward Artificial General Intelligence (AGI), fine-tuning them under privacy and resource constraints has become increasingly critical particularly when highquality training data resides on distributed edge devices. Federated Learning (FL) offers a compelling solution through Federated Fine-Tuning (FFT), which enables collaborative model adaptation without sharing raw data. Recent approaches incorporate Parameter-Efficient Fine-Tuning (PEFT) techniques such as Low Rank Adaptation (LoRA) to reduce computational overhead. However, LoRA-based FFT faces two major limitations in heterogeneous FL environments: structural incompatibility across clients with varying LoRA configurations and limited adaptability to non-IID data distributions, which hinders convergence and generalization. To address these challenges, we propose FFT MoE, a novel FFT framework that replaces LoRA with sparse Mixture of Experts (MoE) adapters. Each client trains a lightweight gating network to selectively activate a personalized subset of experts, enabling fine-grained adaptation to local resource budgets while preserving aggregation compatibility. To further combat the expert load imbalance caused by device and data heterogeneity, we introduce a heterogeneity-aware auxiliary loss that dynamically regularizes the routing distribution to ensure expert diversity and balanced utilization. Extensive experiments spanning both IID and non-IID conditions demonstrate that FFT MoE consistently outperforms state of the art FFT baselines in generalization performance and training efficiency.

cs.LG↗

arXiv2025

KG-o1: Enhancing Multi-hop Question Answering in Large Language Models via Knowledge Graph Integration

Large Language Models (LLMs) face challenges in knowledge-intensive reasoning tasks like classic multi-hop question and answering, which involves reasoning across multiple facts. This difficulty arises because the chain of thoughts (CoTs) generated by LLMs in such tasks often deviate from real or a priori reasoning paths. In contrast, knowledge graphs (KGs) explicitly represent the logical connections between facts through entities and relationships. This reflects a significant gap. Meanwhile, large reasoning models (LRMs), such as o1, have demonstrated that long-step reasoning significantly enhances the performance of LLMs. Building on these insights, we propose KG-o1, a four-stage approach that integrates KGs to enhance the multi-hop reasoning abilities of LLMs. We first filter out initial entities and generate complex subgraphs. Secondly, we construct logical paths for subgraphs and then use knowledge graphs to build a dataset with a complex and extended brainstorming process, which trains LLMs to imitate long-term reasoning. Finally, we employ rejection sampling to generate a self-improving corpus for direct preference optimization (DPO), further refining the LLMs reasoning abilities. We conducted experiments on two simple and two complex datasets. The results show that KG-o1 models exhibit superior performance across all tasks compared to existing LRMs.

cs.CL↗

arXiv2025

AIR-Bench: Automated Heterogeneous Information Retrieval Benchmark

Evaluation plays a crucial role in the advancement of information retrieval (IR) models. However, current benchmarks, which are based on predefined domains and human-labeled data, face limitations in addressing evaluation needs for emerging domains both cost-effectively and efficiently. To address this challenge, we propose the Automated Heterogeneous Information Retrieval Benchmark (AIR-Bench). AIR-Bench is distinguished by three key features: 1) Automated. The testing data in AIR-Bench is automatically generated by large language models (LLMs) without human intervention. 2) Heterogeneous. The testing data in AIR-Bench is generated with respect to diverse tasks, domains and languages. 3) Dynamic. The domains and languages covered by AIR-Bench are constantly augmented to provide an increasingly comprehensive evaluation benchmark for community developers. We develop a reliable and robust data generation pipeline to automatically create diverse and high-quality evaluation datasets based on real-world corpora. Our findings demonstrate that the generated testing data in AIR-Bench aligns well with human-labeled testing data, making AIR-Bench a dependable benchmark for evaluating IR models. The resources in AIR-Bench are publicly available at https://github.com/AIR-Bench/AIR-Bench.

cs.IR↗

arXiv2025

Physics-Informed Implicit Neural Representations for Joint B0 Estimation and Echo Planar Imaging

Echo Planar Imaging (EPI) is widely used for its rapid acquisition but suffers from severe geometric distortions due to B0 inhomogeneities, particularly along the phase encoding direction. Existing methods follow a two-step process: reconstructing blip-up/down EPI images, then estimating B0, which can introduce error accumulation and reduce correction accuracy. This is especially problematic in high B0 regions, where distortions align along the same axis, making them harder to disentangle. In this work, we propose a novel approach that integrates Implicit Neural Representations (INRs) with a physics-informed correction model to jointly estimate B0 inhomogeneities and reconstruct distortion-free images from rotated-view EPI acquisitions. INRs offer a flexible, continuous representation that inherently captures complex spatial variations without requiring predefined grid-based field maps. By leveraging this property, our method dynamically adapts to subject-specific B0 variations and improves robustness across different imaging conditions. Experimental results on 180 slices of brain images from three subjects demonstrate that our approach outperforms traditional methods in terms of reconstruction quality and field estimation accuracy.

eess.IV↗

arXiv2025

TBDetector:Transformer-Based Detector for Advanced Persistent Threats with Provenance Graph

APT detection is difficult to detect due to the long-term latency, covert and slow multistage attack patterns of Advanced Persistent Threat (APT). To tackle these issues, we propose TBDetector, a transformer-based advanced persistent threat detection method for APT attack detection. Considering that provenance graphs provide rich historical information and have the powerful attacks historic correlation ability to identify anomalous activities, TBDetector employs provenance analysis for APT detection, which summarizes long-running system execution with space efficiency and utilizes transformer with self-attention based encoder-decoder to extract long-term contextual features of system states to detect slow-acting attacks. Furthermore, we further introduce anomaly scores to investigate the anomaly of different system states, where each state is calculated with an anomaly score corresponding to its similarity score and isolation score. To evaluate the effectiveness of the proposed method, we have conducted experiments on five public datasets, i.e., streamspot, cadets, shellshock, clearscope, and wget_baseline. Experimental results and comparisons with state-of-the-art methods have exhibited better performance of our proposed method.

cs.CR↗

arXiv2025

jina-embeddings-v4: Universal Embeddings for Multimodal Multilingual Retrieval

We introduce jina-embeddings-v4, a 3.8 billion parameter multimodal embedding model that unifies text and image representations through a novel architecture supporting both single-vector and multi-vector embeddings in the late interaction style. The model incorporates task-specific Low-Rank Adaptation (LoRA) adapters to optimize performance across diverse retrieval scenarios, including query-document retrieval, semantic text similarity, and code search. Comprehensive evaluations demonstrate that jina-embeddings-v4 achieves state-of-the-art performance on both single-modal and cross-modal retrieval tasks, with particular strength in processing visually rich content such as tables, charts, diagrams, and mixed-media formats. To facilitate evaluation of this capability, we also introduce Jina-VDR, a novel benchmark specifically designed for visually rich image retrieval.

cs.AI↗

arXiv2025

cHyRRT and cHySST: Two Motion Planning Tools for Hybrid Dynamical Systems

This paper presents two implementations of the recently developed motion planning algorithms HyRRT arXiv:2210.1508(2) and HySST arXiv:2305.1864(9). Specifically, cHyRRT, an implementation of the HyRRT algorithm, generates solutions to motion planning problems for hybrid systems with a probabilistic completeness guarantee, while cHySST, an implementation of the asymptotically near-optimal HySST algorithm, finds near-optimal trajectories based on a user-defined cost function. The implementations align with the theoretical foundations of hybrid system theory and are designed based on OMPL, ensuring compatibility with ROS while prioritizing computational efficiency. The structure, components, and usage of both tools are detailed. A modified pinball game and collision-resilient tensegrity multicopter example are provided to illustrate the tools' key capabilities.

cs.RO↗

arXiv2025

A$^2$ATS: Retrieval-Based KV Cache Reduction via Windowed Rotary Position Embedding and Query-Aware Vector Quantization

Long context large language models (LLMs) pose significant challenges for efficient serving due to the large memory footprint and high access overhead of KV cache. Retrieval-based KV cache reduction methods can mitigate these challenges, typically by offloading the complete KV cache to CPU and retrieving necessary tokens on demand during inference. However, these methods still suffer from unsatisfactory accuracy degradation and extra retrieval overhead. To address these limitations, this paper proposes A$^2$ATS, a novel retrieval-based KV cache reduction method. A$^2$ATS aims to obtain an accurate approximation of attention scores by applying the vector quantization technique to key states, thereby enabling efficient and precise retrieval of the top-K tokens. First, we propose Windowed Rotary Position Embedding, which decouples the positional dependency from query and key states after position embedding. Then, we propose query-aware vector quantization that optimizes the objective of attention score approximation directly. Finally, we design the heterogeneous inference architecture for KV cache offloading, enabling long context serving with larger batch sizes. Experimental results demonstrate that A$^2$ATS can achieve a lower performance degradation with similar or lower overhead compared to existing methods, thereby increasing long context serving throughput by up to $2.7 \times$.

cs.CL↗

arXiv2025

Nanoscale Ultrafast Lattice Modulation with Hard X-ray Free Electron Laser

Understanding and controlling microscopic dynamics across spatial and temporal scales has driven major progress in science and technology over the past several decades. While ultrafast laser-based techniques have enabled probing nanoscale dynamics at their intrinsic temporal scales down to femto- and attoseconds, the long wavelengths of optical lasers have prevented the interrogation and manipulation of such dynamics with nanoscale spatial specificity. With advances in hard X-ray free electron lasers (FELs), significant progress has been made developing X-ray transient grating (XTG) spectroscopy, aiming at the coherent control of elementary excitations with nanoscale X-ray standing waves. So far, XTGs have been probed only at optical wavelengths, thus intrinsically limiting the achievable periodicities to several hundreds of nm. By achieving sub-femtosecond synchronization of two hard X-ray pulses at a controlled crossing angle, we demonstrate the generation of an XTG with spatial periods of 10 nm. The XTG excitation drives a thermal grating that drives coherent monochromatic longitudinal acoustic phonons in the cubic perovskite, SrTiO3 (STO). With a third X-ray pulse with the same photon energy, time-and-momentum resolved measurement of the XTG-induced scattering intensity modulation provides evidence of ballistic thermal transport at nanometer scale in STO. These results highlight the great potential of XTG for studying high-wave-vector excitations and nanoscale transport in condensed matter, and establish XTG as a powerful platform for the coherent control and study of nanoscale dynamics.

physics.optics↗

arXiv2025

Improving Significant Wave Height Prediction Using Chronos Models

Accurate wave height prediction is critical for maritime safety and coastal resilience, yet conventional physics-based models and traditional machine learning methods face challenges in computational efficiency and nonlinear dynamics modeling. This study introduces Chronos, the first implementation of a large language model (LLM)-powered temporal architecture (Chronos) optimized for wave forecasting. Through advanced temporal pattern recognition applied to historical wave data from three strategically chosen marine zones in the Northwest Pacific basin, our framework achieves multimodal improvements: (1) 14.3% reduction in training time with 2.5x faster inference speed compared to PatchTST baselines, achieving 0.575 mean absolute scaled error (MASE) units; (2) superior short-term forecasting (1-24h) across comprehensive metrics; (3) sustained predictive leadership in extended-range forecasts (1-120h); and (4) demonstrated zero-shot capability maintaining median performance (rank 4/12) against specialized operational models. This LLM-enhanced temporal modeling paradigm establishes a new standard in wave prediction, offering both computationally efficient solutions and a transferable framework for complex geophysical systems modeling.

cs.LG↗

arXiv2025

jina-clip-v2: Multilingual Multimodal Embeddings for Text and Images

Contrastive Language-Image Pretraining (CLIP) has been widely used for crossmodal information retrieval and multimodal understanding tasks. However, CLIP models are mainly optimized for crossmodal vision-language tasks and underperform in single-mode text tasks. Moreover, these models are often trained on English datasets and therefore lack multilingual understanding. Additionally, from a visual understanding perspective, previous CLIP-based models exhibit insufficient understanding of visually rich documents. In this work, we propose jina-clip-v2, a contrastive vision-language model trained on text pairs, triplets and image-text pairs via a multi-task and multi-stage contrastive learning paradigm in order to support both text-only and crossmodal tasks. We employ a multilingual text encoder and expand the training dataset to include multilingual texts from 29 non-English languages, including Hindi, Chinese, German, French, and others, as well as images of visually rich documents. We evaluate the model's performance and show that jina-clip-v2 achieves notable improvements over state-of-the-art CLIP-based models in zero-shot text-only retrieval, semantic textual similarity, and crossmodal retrieval tasks in both English and multilingual settings. jina-clip-v2 also provides for flexibility in embedding dimensionality, enabling users to select the granularity of the representations. jina-clip-v2 is publicly available at https://huggingface.co/jinaai/jina-clip-v2.

cs.CL↗