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Honghan Wu

Honghan Wu contributes to research discovery and scholarly infrastructure.

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Machine Learning Artificial Intelligence Computation and Language Computer Vision Digital Libraries eess.IV Information Retrieval

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preprint2026arXiv

A Regime Theory of Controller Class Selection for LLM Action Decisions

Deployed language and vision-language models must decide, on each input, whether to answer directly, retrieve evidence, defer to a stronger model, or abstain. Contrary to the common monotonicity intuition, greater per-input expressivity is not uniformly beneficial in finite samples: under identical strict cross-validation, different benchmarks prefer different controller classes. This reflects a finite-sample limitation of instance-level uncertainty signals, which can be exhausted at a distribution-dependent scale. We organize controllers into a nested lattice of four classes: fixed actions, partition routers, instance-level controllers, and prior-gated controllers, ordered by complexity. We prove a regime theory that turns three data-estimable bottlenecks into a class choice: how much improvement is possible beyond the best fixed action, whether there are enough samples for instance-level controllers to make reliable decisions, and how much improvement a coarse partition router can recover when instance-level signal is unreliable. The resulting Bernstein-tight threshold has a matching information-theoretic lower bound, and strict nested cross-validation provably selects a near-best class. Across SMS-Spam, HallusionBench, A-OKVQA, and FOLIO, the predicted class matches the empirical winner; the prior-gated controller wins on TextVQA when OCR tokens supply a label-free prediction-time prior. Code is available at https://github.com/Anonymous-Awesome-Submissions/Regime-Theory.

preprint2026arXiv

BioMedArena: An Open-source Toolkit for Building and Evaluating Biomedical Deep Research Agents

Building a deep research agent today is an exercise in glue code: the same backbone evaluated on the same benchmark can report different accuracies in different papers because harness and tool registry all differ, and integrating a new foundation model into a comparable evaluation surface costs weeks of model-specific engineering. We call this the per-paper engineering tax and release BioMedArena, an open-source toolkit that not only alleviates it but also provides an arena for fair comparison of different foundation models when evaluating them as deep-research agents. BioMedArena decouples six layers of biomedical agent evaluation -- benchmark loading, tool exposure, tool selection, execution mode, context management, and scoring -- and exposes 147 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool reduces to registering a few-line provider adapter. We further provide 6 agent harnesses with 6 context-management strategies, which provide 12 backbones with competitive research capabilities and significantly improved performance, achieving state-of-the-art (SOTA) results on 8 representative biomedical benchmarks, with an average lift of +15.03 percentage points over prior SOTA. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena

preprint2026arXiv

HH-SAE: Discovering and Steering Hierarchical Knowledge of Complex Manifolds

Rare semantic innovations in high-dimensional, mission-critical domains are often obscured by dense background contexts, a challenge we define as \textit{feature density conflict}. We introduce the \textbf{Hybrid Hierarchical SAE (HH-SAE)} to resolve this by factorizing manifolds into a nested hierarchy of \textbf{Contextual} ($L_0$), \textbf{Atomic} ($f_1$), and \textbf{Compository} ($f_2$) tiers. Evaluating across disparate manifolds, HH-SAE demonstrates superior resolution by \textbf{``fracturing'' administrative clinical labels into physiological modes} and achieving a peak \textbf{cross-domain zero-shot AUC of 0.9156 in fraud detection}. Path ablation confirms the architecture's structural necessity, revealing a 13.46\% utility collapse when contextual subtraction is removed. Finally, knowledge-steered synthesis achieves a +9.9\% AUPRC lift over state-of-the-art generators, proving that HH-SAE effectively prioritizes high-order mechanistic innovation over environmental proxies to enable high-precision discovery in high-stakes environments.

preprint2026arXiv

Uncovering Latent Pathological Signatures in Pulmonary CT via Cross-Window Knowledge Distillation

Multi-window CT imaging captures complementary pathological information across anatomical structures of differing densities, yet existing deep learning methods fuse representations only at later stages, missing cross-density interactions. We propose a cross-window knowledge distillation framework in which student encoders learn latent clinical priors from a teacher trained on the most informative window. Evaluated retrospectively on three cohorts - COPD-CT-DF (n=719), RSNA PE (n=1,433), and an in-house CTEPD dataset (n=161) - distillation improved per-window AUC by 10.1-16.5 percentage points on COPD-CT-DF (0.75-0.81 to 0.90-0.94; all P<0.001), with ensemble AUC reaching 0.9960. Similar gains were observed on RSNA PE (0.80-0.83 to 0.90-0.92) and CTEPD (AUC 0.7481 vs. 0.6264). Cross-window distillation internalises pathological signatures invisible to supervised approaches, offering a generalisable solution for multi-window pulmonary CT analysis.

preprint2022arXiv

Adverse Childhood Experiences Identification from Clinical Notes with Ontologies and NLP

preprint2022arXiv

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

preprint2022arXiv

Ontology-Driven Self-Supervision for Adverse Childhood Experiences Identification Using Social Media Datasets

Adverse Childhood Experiences (ACEs) are defined as a collection of highly stressful, and potentially traumatic, events or circumstances that occur throughout childhood and/or adolescence. They have been shown to be associated with increased risks of mental health diseases or other abnormal behaviours in later lives. However, the identification of ACEs from textual data with Natural Language Processing (NLP) is challenging because (a) there are no NLP ready ACE ontologies; (b) there are few resources available for machine learning, necessitating the data annotation from clinical experts; (c) costly annotations by domain experts and large number of documents for supporting large machine learning models. In this paper, we present an ontology-driven self-supervised approach (derive concept embeddings using an auto-encoder from baseline NLP results) for producing a publicly available resource that would support large-scale machine learning (e.g., training transformer based large language models) on social media corpus. This resource as well as the proposed approach are aimed to facilitate the community in training transferable NLP models for effectively surfacing ACEs in low-resource scenarios like NLP on clinical notes within Electronic Health Records. The resource including a list of ACE ontology terms, ACE concept embeddings and the NLP annotated corpus is available at https://github.com/knowlab/ACE-NLP.

preprint2020arXiv

Identifying physical health comorbidities in a cohort of individuals with severe mental illness: An application of SemEHR

Multimorbidity research in mental health services requires data from physical health conditions which is traditionally limited in mental health care electronic health records. In this study, we aimed to extract data from physical health conditions from clinical notes using SemEHR. Data was extracted from Clinical Record Interactive Search (CRIS) system at South London and Maudsley Biomedical Research Centre (SLaM BRC) and the cohort consisted of all individuals who had received a primary or secondary diagnosis of severe mental illness between 2007 and 2018. Three pairs of annotators annotated 2403 documents with an average Cohen's Kappa of 0.757. Results show that the NLP performance varies across different diseases areas (F1 0.601 - 0.954) suggesting that the language patterns or terminologies of different condition groups entail different technical challenges to the same NLP task.

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