arXiv subjects

Jia Wu

Publications and source records attributed to Jia Wu.

At least 19 recordsLinked to original sources

arXiv2026

Beyond Solution-Centric Search: Adaptive Inquiry and Knowledge Revision for Autonomous ML Engineering

Long-horizon autonomous research tasks such as machine learning engineering require systems to make interdependent decisions under a limited budget. Existing LLM-based agents typically organize candidate-solution improvement through tree, graph, or chain structures, meaning that the search process determines how information is acquired and managed. We call this design solution-centric search and propose instead the information paradigm, in which an evolving information state represents the system's understanding of the task and guides solution improvement. We instantiate this paradigm in Iris, an inquiry-revision loop. For information acquisition, Iris generates local action plans from the current information state and uses epistemic actions to probe decision-critical unknowns without modifying the retained solution. For information management, Iris synthesizes observations across experiments into task knowledge composed of revisable claims with explicit scope and status. It updates this knowledge as new evidence arrives and constructs each decision context from raw evidence, structured summaries, or task knowledge at the required level of detail. On MLE-Bench, Iris attains a 64.9% any-medal rate under a 12-hour budget, the highest among compared systems. Across four tasks spanning harness engineering and model post-training, Iris also demonstrates cross-domain generalization.

cs.AI↗

arXiv2026

From Observation to Intervention: Memory in Brains and Large Language Models

Brains and large language models (LLMs) are fundamentally different memory systems, but they can be compared through shared functional questions: where memory-related information is represented, how partial cues recover broader associations, how new information is written or updated, and how memory-related states can be perturbed. In biological systems, these questions span synapses, neuronal ensembles, hippocampal-cortical interactions, and plasticity; in LLMs, they span weights, activations, context windows, retrieval systems, and external stores. The comparison is therefore functional and experimental rather than anatomical. Human studies reveal sparse concept responses, temporal binding, rapid association formation, episode-specific coding, and recall-related reactivation, but selective intervention remains limited. Rodent studies provide more selective causal access to learning-related ensembles, whereas human and macaque interventions usually affect broader circuits. LLMs lack lived episodic memory, yet they permit unusually direct and repeatable manipulation of internal states and stored information. We argue that this asymmetry creates a new opportunity. LLMs are not ahead in memory itself, but in experimental access. Their tools may help turn broad questions about retrieval, updating, persistence, reversibility, and unintended effects into sharper biological hypotheses. The productive bridge is to transfer experimental logic, not anatomical parts.

q-bio.NC↗

arXiv2026

Do Medical Vision Language Models Actually See? A Counterfactual Grounding Framework and Hard-Negative Contrastive Training for Visually-Reliant Medical VLMs

Large vision language models (VLMs) report strong accuracy on medical question-answering, yet it remains unclear whether they reason from visual evidence or exploit textual shortcuts. We introduce a counterfactual evaluation framework that decouples visual and textual contributions by substituting input images with controlled surrogates blank, pixel-shuffled, image-absent, and CLIP-retrieved hard negatives and derive a suite of grounding metrics including the Visual Reliance Score (VRS) and Visual Hallucination Rate (VHR). We further introduce CORAL (COntrastive Retrieval-Augmented Learning), a 7B-parameter LoRA fine-tune of Qwen2.5-VL-7B trained with a Contrastive Grounding Objective (CGO) that penalises answer invariance under hard-negative image swaps. On a paired controlled evaluation across four closed-form medical VQA benchmarks (PathVQA, PMC-VQA, SLAKE, VQA-RAD; n=400 total), CORAL improves macro accuracy by +6.7 pp (P(Delta>0)=0.988) and reduces VHR by 8.0 pp (P<0.001) over the matched Qwen2.5-VL-7B base; neither MedVLThinker RL variant achieves a significant gain on either metric. Cross-domain diagnostics further reveal that image substitution costs only <=6.5 pp on medical benchmarks versus 48-61 pp on general-domain tasks, situating the grounding gap that CGO targets. We discuss evaluation limitations openly including train/eval benchmark overlap and underpowered secondary metrics and release our framework, training code, and model weights to support reproducible grounding audits of medical VLMs.

cs.CV↗

arXiv2026

Efficient Serving for Dynamic Agent Workflows with Prediction-based KV-Cache Management

LLM-based workflows compose specialized agents to execute complex tasks, and these agents usually share substantial context, allowing KV-Cache reuse to save computation. Existing approaches either manage KV-Cache at agent level and fail to exploit the reuse opportunities within workflows, or manage cache at the workflow level but assume that each workflow calls a static sequence of agents. However, practical workflows are typically dynamic, where the sequence of invoked agents and thus induced cache reuse opportunities depend on the context of each task. To serve such dynamic workflows efficiently, we build a system dubbed PBKV (\textbf{P}rediction-\textbf{B}ased \textbf{KV}-Cache Management). For each workflow, PBKV predicts the agent invocations in several future steps by fusing the guidance from historical workflows and context of the target workflow. Based on the predictions, PBKV estimates the reuse potential of cache entries and keeps the high-potential entries in GPU memory. To be robust to prediction errors, PBKV utilizes the predictions conservatively during both cache eviction and prefetching. Experiments on three workflow benchmarks show that PBKV achieves up to $1.85\times$ speedup over LRU on dynamic workflows, and up to $1.26\times$ speedup over the SOTA baseline KVFlow on the static workflow.

cs.LG↗

arXiv2026

Projection Guided Personalized Federated Learning for Low Dose CT Denoising

Low-dose CT (LDCT) reduces radiation exposure but introduces protocol-dependent noise and artifacts that vary across institutions. While federated learning enables collaborative training without centralizing patient data, existing methods personalize in image space, making it difficult to separate scanner noise from patient anatomy. We propose ProFed (Projection Guided Personalized Federated Learning), a framework that complements the image space approach by performing dual-level personalization in the projection space, where noise originates during CT measurements before reconstruction combines protocol and anatomy effects. ProFed introduces: (i) anatomy-aware and protocol-aware networks that personalize CT reconstruction to patient and scanner-specific features, (ii) multi-constraint projection losses that enforce consistency with CT measurements, and (iii) uncertainty-guided selective aggregation that weights clients by prediction confidence. Extensive experiments on the Mayo Clinic 2016 dataset demonstrate that ProFed achieves 42.56 dB PSNR with CNN backbones and 44.83 dB with Transformers, outperforming 11 federated learning baselines, including the physics-informed SCAN-PhysFed by +1.42 dB.

eess.IV↗

arXiv2026

CARL-CXR: Continual Adapter-Based Routing for Task-Unknown Chest Radiograph Classification

Clinical deployment of chest radiograph classifiers requires models that can be updated as new datasets become available without retraining on previously observed data or degrading validated performance. We study a task-incremental continual learning setting for chest radiograph classification under task-unknown inference, where heterogeneous chest X-ray datasets arrive sequentially and task identity is unavailable at deployment time. We propose CARL-CXR, a continual adapter-based routing framework that maintains a fixed high-capacity backbone while incrementally introducing lightweight task-specific adapters and classifier heads. A latent task selector operates on adapter-conditioned features to dynamically route each input to the most relevant task pathway, leveraging compact task prototypes and feature-level experience replay to preserve task identity across sequential updates without storing raw images. Experiments on MIMIC-CXR and CheXpert two large-scale datasets with distinct patient populations, imaging devices, and annotation pipelines demonstrate that CARL-CXR achieves minimal catastrophic forgetting (0.012 AUROC drop), representing a 6X and 11X reduction over established continual learning baselines LwF and EWC respectively, while maintaining competitive diagnostic performance (AUROC 0.74). Under task unknown deployment, CARL-CXR outperforms joint training by 12.5 points in routing accuracy (75.0% vs. 62.5%): unlike LwF and EWC, which require explicit task identifiers at inference and provide no routing mechanism.

cs.CV↗

arXiv2026

Variational Bayesian Flow Network for Graph Generation

Graph generation aims to sample discrete node and edge attributes while satisfying coupled structural constraints. Diffusion models for graphs often adopt largely factorized forward-noising, and many flow-matching methods start from factorized reference noise and coordinate-wise interpolation, so node-edge coupling is not encoded by the generative geometry and must be recovered implicitly by the core network, which can be brittle after discrete decoding. Bayesian Flow Networks (BFNs) evolve distribution parameters and naturally support discrete generation. But classical BFNs typically rely on factorized beliefs and independent channels, which limit geometric evidence fusion. We propose Variational Bayesian Flow Network (VBFN), which performs a variational lifting to a tractable joint Gaussian variational belief family governed by structured precisions. Each Bayesian update reduces to solving a symmetric positive definite linear system, enabling coupled node and edge updates within a single fusion step. We construct sample-agnostic sparse precisions from a representation-induced dependency graph, thereby avoiding label leakage while enforcing node-edge consistency. On synthetic and molecular graph datasets, VBFN improves fidelity and diversity, and surpasses baseline methods.

cs.LG↗

arXiv2026

Modeling Endogenous Logic: Causal Neuro-Symbolic Reasoning Model for Explainable Multi-Behavior Recommendation

Existing multi-behavior recommendations tend to prioritize performance at the expense of explainability, while current explainable methods suffer from limited generalizability due to their reliance on external information. Neuro-Symbolic integration offers a promising avenue for explainability by combining neural networks with symbolic logic rule reasoning. Concurrently, we posit that user behavior chains inherently embody an endogenous logic suitable for explicit reasoning. However, these observational multiple behaviors are plagued by confounders, causing models to learn spurious correlations. By incorporating causal inference into this Neuro-Symbolic framework, we propose a novel Causal Neuro-Symbolic Reasoning model for Explainable Multi-Behavior Recommendation (CNRE). CNRE operationalizes the endogenous logic by simulating a human-like decision-making process. Specifically, CNRE first employs hierarchical preference propagation to capture heterogeneous cross-behavior dependencies. Subsequently, it models the endogenous logic rule implicit in the user's behavior chain based on preference strength, and adaptively dispatches to the corresponding neural-logic reasoning path (e.g., conjunction, disjunction). This process generates an explainable causal mediator that approximates an ideal state isolated from confounding effects. Extensive experiments on three large-scale datasets demonstrate CNRE's significant superiority over state-of-the-art baselines, offering multi-level explainability from model design and decision process to recommendation results.

cs.AI↗

arXiv2026

Multimodal Visual Surrogate Compression for Alzheimer's Disease Classification

High-dimensional structural MRI (sMRI) images are widely used for Alzheimer's Disease (AD) diagnosis. Most existing methods for sMRI representation learning rely on 3D architectures (e.g., 3D CNNs), slice-wise feature extraction with late aggregation, or apply training-free feature extractions using 2D foundation models (e.g., DINO). However, these three paradigms suffer from high computational cost, loss of cross-slice relations, and limited ability to extract discriminative features, respectively. To address these challenges, we propose Multimodal Visual Surrogate Compression (MVSC). It learns to compress and adapt large 3D sMRI volumes into compact 2D features, termed as visual surrogates, which are better aligned with frozen 2D foundation models to extract powerful representations for final AD classification. MVSC has two key components: a Volume Context Encoder that captures global cross-slice context under textual guidance, and an Adaptive Slice Fusion module that aggregates slice-level information in a text-enhanced, patch-wise manner. Extensive experiments on three large-scale Alzheimer's disease benchmarks demonstrate our MVSC performs favourably on both binary and multi-class classification tasks compared against state-of-the-art methods.

cs.CV↗

arXiv2026

PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.

q-bio.BM↗

arXiv2026

Contrast-X: A Multi-Modal Contrast Image Synthesis Benchmark and Universal Modality Flow Matching

Contrast-enhanced imaging is central to oncologic diagnosis, but contrast agents can be contraindicated for many of the patients who need them most. Synthesizing contrast scans from non-contrast inputs is the natural response. Two obstacles stand in the way: no benchmark provides paired contrast data with lesion-level evaluation, and no single model handles the arbitrary missing patterns seen in practice. We introduce Contrast-X, a benchmark of paired contrast-enhanced and non-contrast imaging spanning 10 organs in CT (1{,}526 patients) and multi-phase breast DCE-MRI (1116 patients). Every case carries radiologist-verified phase labels and tumor masks. We further propose FlowMI, a single model that handles arbitrary subsets of available modalities through a unified multi-modal latent space and flow matching. We benchmark a range of missing-modality configurations, reporting standard image-quality metrics, radiologist reader studies, and downstream lesion analysis on the synthesized scans. We further evaluate cross-organ generalization to test whether the model has learned a transferable contrast-enhancement operation. Dataset, code, and leaderboard will be released. Our code are available at https://github.com/YifanChen02/Contrast-X.

cs.CV↗

arXiv2025

Foundation Models in Biomedical Imaging: Turning Hype into Reality

Foundation models (FMs) are driving a prominent shift in biomedical imaging from task-specific models to unified backbone models for diverse tasks. This opens an avenue to integrate imaging, pathology, clinical records, and genomics data into a composite system. However, this vision contrasts sharply with modern medicine's trajectory toward more granular sub-specialization. This tension, coupled with data scarcity, domain heterogeneity, and limited interpretability, creates a gap between benchmark success and real-world clinical value. We argue that the immediate role of FMs lies in augmenting, not replacing, clinical expertise. To separate hype from reality, we introduce REAL-FM (Real-world Evaluation and Assessment of Foundation Models), a multi-dimensional framework for assessing data, technical readiness, clinical value, workflow integration, and responsible AI. Using REAL-FM, we find that while FMs excel in pattern recognition, they fall short in causal reasoning, domain robustness, and safety. Clinical translation is hindered by scarce representative data for model training, unverified generalization beyond oversimplified benchmark settings, and a lack of prospective outcome-based validation. We further examine FM reasoning paradigms, including sequential logic, spatial understanding, and symbolic domain knowledge. We envision that the path forward lies not in a monolithic medical oracle, but in coordinated subspecialist AI systems that are transparent, safe, and clinically grounded.

q-bio.QM↗

arXiv2025

Can We Go Beyond Visual Features? Neural Tissue Relation Modeling for Relational Graph Analysis in Non-Melanoma Skin Histology

Histopathology image segmentation is essential for delineating tissue structures in skin cancer diagnostics, but modeling spatial context and inter-tissue relationships remains a challenge, especially in regions with overlapping or morphologically similar tissues. Current convolutional neural network (CNN)-based approaches operate primarily on visual texture, often treating tissues as independent regions and failing to encode biological context. To this end, we introduce Neural Tissue Relation Modeling (NTRM), a novel segmentation framework that augments CNNs with a tissue-level graph neural network to model spatial and functional relationships across tissue types. NTRM constructs a graph over predicted regions, propagates contextual information via message passing, and refines segmentation through spatial projection. Unlike prior methods, NTRM explicitly encodes inter-tissue dependencies, enabling structurally coherent predictions in boundary-dense zones. On the benchmark Histopathology Non-Melanoma Skin Cancer Segmentation Dataset, NTRM outperforms state-of-the-art methods, achieving a robust Dice similarity coefficient that is 4.9\% to 31.25\% higher than the best-performing models among the evaluated approaches. Our experiments indicate that relational modeling offers a principled path toward more context-aware and interpretable histological segmentation, compared to local receptive-field architectures that lack tissue-level structural awareness. Our code is available at https://github.com/shravan-18/NTRM.

cs.CV↗

arXiv2025

When and What to Recommend: Joint Modeling of Timing and Content for Active Sequential Recommendation

Sequential recommendation models user preferences to predict the next target item. Most existing work is passive, where the system responds only when users open the application, missing chances after closure. We investigate active recommendation, which predicts the next interaction time and actively delivers items. Two challenges: accurately estimating the Time of Interest (ToI) and generating Item of Interest (IoI) conditioned on the predicted ToI. We propose PASRec, a diffusion-based framework that aligns ToI and IoI via a joint objective. Experiments on five benchmarks show superiority over eight state-of-the-art baselines under leave-one-out and temporal splits.

cs.IR↗

arXiv2025

FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation

Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 {\AA} when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.

cs.LG↗

arXiv2025

Transport-Coupled Bayesian Flows for Molecular Graph Generation

Molecular graph generation (MGG) is essentially a multi-class generative task, aimed at predicting categories of atoms and bonds under strict chemical and structural constraints. However, many prevailing diffusion paradigms learn to regress numerical embeddings and rely on a hard discretization rule during sampling to recover discrete labels. This introduces a fundamental discrepancy between training and sampling. While models are trained for point-wise numerical fidelity, the sampling process fundamentally relies on crossing categorical decision boundaries. This discrepancy forces the model to expend efforts on intra-class variations that become irrelevant after discretization, ultimately compromising diversity, structural statistics, and generalization performance. Therefore, we propose TopBF, a unified framework that (i) performs MGG directly in continuous parameter distributions, (ii) learns graph-topological understanding through a Quasi-Wasserstein optimal-transport coupling under geodesic costs, and (iii) supports controllable, property-conditioned generation during sampling without retraining the base model. TopBF innovatively employs cumulative distribution function (CDF) to compute category probabilities induced by the Gaussian channel, thereby unifying the training objective with the sampling discretization operation. Experiments on QM9 and ZINC250k demonstrate superior structural fidelity and efficient generation with improved performance.

cs.LG↗

arXiv2025

LLM-based Agents Suffer from Hallucinations: A Survey of Taxonomy, Methods, and Directions

Driven by the rapid advancements of Large Language Models (LLMs), LLM-based agents have emerged as powerful intelligent systems capable of human-like cognition, reasoning, and interaction. These agents are increasingly being deployed across diverse real-world applications, including student education, scientific research, and financial analysis. However, despite their remarkable potential, LLM-based agents remain vulnerable to hallucination issues, which can result in erroneous task execution and undermine the reliability of the overall system design. Addressing this critical challenge requires a deep understanding and a systematic consolidation of recent advances on LLM-based agents. To this end, we present the first comprehensive survey of hallucinations in LLM-based agents. By carefully analyzing the complete workflow of agents, we propose a new taxonomy that identifies different types of agent hallucinations occurring at different stages. Furthermore, we conduct an in-depth examination of eighteen triggering causes underlying the emergence of agent hallucinations. Through a detailed review of a large number of existing studies, we summarize approaches for hallucination mitigation and detection, and highlight promising directions for future research. We hope this survey will inspire further efforts toward addressing hallucinations in LLM-based agents, ultimately contributing to the development of more robust and reliable agent systems.

cs.AI↗

arXiv2025

Adversarial Attacks Against Automated Fact-Checking: A Survey

In an era where misinformation spreads freely, fact-checking (FC) plays a crucial role in verifying claims and promoting reliable information. While automated fact-checking (AFC) has advanced significantly, existing systems remain vulnerable to adversarial attacks that manipulate or generate claims, evidence, or claim-evidence pairs. These attacks can distort the truth, mislead decision-makers, and ultimately undermine the reliability of FC models. Despite growing research interest in adversarial attacks against AFC systems, a comprehensive, holistic overview of key challenges remains lacking. These challenges include understanding attack strategies, assessing the resilience of current models, and identifying ways to enhance robustness. This survey provides the first in-depth review of adversarial attacks targeting FC, categorizing existing attack methodologies and evaluating their impact on AFC systems. Additionally, we examine recent advancements in adversary-aware defenses and highlight open research questions that require further exploration. Our findings underscore the urgent need for resilient FC frameworks capable of withstanding adversarial manipulations in pursuit of preserving high verification accuracy.

cs.CL↗