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Dongxu Zhang

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Artificial Intelligence Computation and Language Machine Learning Neural and Evolutionary Computing Information Retrieval

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preprint2026arXiv

Intern-Atlas: A Methodological Evolution Graph as Research Infrastructure for AI Scientists

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

preprint2026arXiv

MedFabric and EtHER: A Data-Centric Framework for Word-Level Fabrication Generation and Detection in Medical LLMs

Large Language Models exhibit strong reasoning and semantic understanding capabilities but often hallucinate in domains that require expert knowledge, among which fabrications, the generation of factually incorrect yet fluent statements, pose the greatest risk in medical contexts. Existing medical hallucination datasets inadequately capture fabrication phenomena due to limited fabrication coverage, stylistic disparities between human and LLM-authored texts, and distributional drift during hallucinated sample synthesis. To address this, we propose a data-centric pipeline to generate realistic and word-level fabrications that preserve syntactic and stylistic fidelity while introducing subtle factual deviations, resulting in MedFabric. Building upon this dataset, we introduce ETHER, a modular word-level fabrication detector integrating Text2Table Decomposition, Word Masking and Filling and Hybrid Sentence Pair Evaluation to enhance factual alignment. Empirical results demonstrate that MedFabric outperforms state-of-the-art detectors by over 15% on word-level fabrication benchmarks while maintaining consistent performance across structural similarities, offering a comprehensive framework for reliable and domain-specific factuality detection.

preprint2026arXiv

NanoResearch: Co-Evolving Skills, Memory, and Policy for Personalized Research Automation

LLM-powered multi-agent systems can now automate the full research pipeline from ideation to paper writing, but a fundamental question remains: automation for whom? Researchers operate under different resource configurations, hold different methodological preferences, and target different output formats. A system that produces uniform outputs regardless of these differences will systematically under-serve every individual user, making personalization a precondition for research automation to be genuinely usable. However, achieving it requires three capabilities that current systems lack: accumulating reusable procedural knowledge across projects, retaining user-specific experience across sessions, and internalizing implicit preferences that resist explicit formalization. We propose NanoResearch, a multi-agent framework that addresses these gaps through tri-level co-evolution. A skill bank distills recurring operations into compact procedural rules reusable across projects. A memory module maintains user- and project-specific experience that grounds planning decisions in each user's research history. A label-free policy learning converts free-form feedback into persistent parameter updates of the planner, reshaping subsequent coordination. These three layers co-evolve: reliable skills produce richer memory, richer memory informs better planning, and preference internalization continuously realigns the loop to each user. Extensive experiments demonstrate that NanoResearch delivers substantial gains over state-of-the-art AI research systems, and progressively refines itself to produce better research at lower cost over successive cycles.

preprint2026arXiv

Offline Policy Optimization with Posterior Sampling

A fundamental challenge in model-based offline reinforcement learning (RL) lies in the trade-off between generalization and robustness against exploitation errors in out-of-distribution (OOD) regions. While OOD samples may capture valid underlying physical dynamics, they also introduce the risk of model exploitation. Existing methods typically address this risk through excessive pessimistic regularization, which ensures robustness but often sacrifices generalization. To overcome this limitation, we propose Posterior Sampling-based Policy Optimization (PSPO), which formulates dynamics modeling as a Bayesian inference process to derive a posterior that explicitly quantifies model fidelity. Through the integration of posterior sampling and constrained policy optimization, our method leverages dynamics-consistent OOD transitions for generalization while ensuring robustness against model exploitation. Theoretically, we formulate Q-value estimation under posterior sampling as a stochastic approximation problem and establish its convergence. We decompose policy optimization into a sequence of constrained subproblems, demonstrating that solving these subproblems guarantees monotonic improvement until convergence. Experiments on standard benchmarks validate that PSPO achieves superior performance compared to state-of-the-art baselines.

preprint2022arXiv

A Distant Supervision Corpus for Extracting Biomedical Relationships Between Chemicals, Diseases and Genes

We introduce ChemDisGene, a new dataset for training and evaluating multi-class multi-label document-level biomedical relation extraction models. Our dataset contains 80k biomedical research abstracts labeled with mentions of chemicals, diseases, and genes, portions of which human experts labeled with 18 types of biomedical relationships between these entities (intended for evaluation), and the remainder of which (intended for training) has been distantly labeled via the CTD database with approximately 78\% accuracy. In comparison to similar preexisting datasets, ours is both substantially larger and cleaner; it also includes annotations linking mentions to their entities. We also provide three baseline deep neural network relation extraction models trained and evaluated on our new dataset.

preprint2015arXiv

Learning from LDA using Deep Neural Networks

Latent Dirichlet Allocation (LDA) is a three-level hierarchical Bayesian model for topic inference. In spite of its great success, inferring the latent topic distribution with LDA is time-consuming. Motivated by the transfer learning approach proposed by~\newcite{hinton2015distilling}, we present a novel method that uses LDA to supervise the training of a deep neural network (DNN), so that the DNN can approximate the costly LDA inference with less computation. Our experiments on a document classification task show that a simple DNN can learn the LDA behavior pretty well, while the inference is speeded up tens or hundreds of times.

preprint2015arXiv

Relation Classification via Recurrent Neural Network

Deep learning has gained much success in sentence-level relation classification. For example, convolutional neural networks (CNN) have delivered competitive performance without much effort on feature engineering as the conventional pattern-based methods. Thus a lot of works have been produced based on CNN structures. However, a key issue that has not been well addressed by the CNN-based method is the lack of capability to learn temporal features, especially long-distance dependency between nominal pairs. In this paper, we propose a simple framework based on recurrent neural networks (RNN) and compare it with CNN-based model. To show the limitation of popular used SemEval-2010 Task 8 dataset, we introduce another dataset refined from MIMLRE(Angeli et al., 2014). Experiments on two different datasets strongly indicates that the RNN-based model can deliver better performance on relation classification, and it is particularly capable of learning long-distance relation patterns. This makes it suitable for real-world applications where complicated expressions are often involved.

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