arXiv subjects

Ling Luo

Publications and source records attributed to Ling Luo.

At least 19 recordsLinked to original sources

arXiv2026

Overview of CHIP 2026 Shared Task 1: Patient-Specific Phenotype Concept Recognition in Full-Text Biomedical Literature

Automatic phenotype information extraction plays an important role in rare disease diagnosis, genotype-phenotype analysis, and precision medicine. However, accurately identifying phenotype concepts and determining their associations with specific patients remain challenging, particularly in full-text biomedical articles involving multiple patients and complex clinical descriptions. This paper presents an overview of CHIP 2026 Shared Task 1, which aims to promote the development of methods for patient-specific phenotype concept recognition from full-text biomedical literature. The task consists of two subtasks: full-text phenotype concept recognition and patient-specific phenotype association. For this evaluation, we used 200 annotated full-text biomedical articles from the PatientPheX dataset, containing 506 patients, 15,193 phenotype mentions, and 5,656 patient-phenotype associations. A total of 455 teams registered for the competition, with 189 and 103 valid submissions received on the Phase A and Phase B leaderboards, respectively. The best-performing system achieved an overall score of 0.7389 on the final test set, outperforming the baseline by 8.37 percentage points. The top-performing teams explored diverse approaches combining biomedical language models, large language models (LLMs), and ensemble strategies. The evaluation results highlight both the potential of these approaches and the remaining challenges in patient attribution and phenotype normalization from full-text biomedical literature. The post-evaluation phase remains open at https://tianchi.aliyun.com/competition/entrance/532512.

cs.CL↗

arXiv2026

Dynamic Dual-Feedback Conformal Inference for Time Series Forecasting

Quantifying uncertainty in time series forecasting is particularly demanding because sequential data exhibit temporal dependence and are prone to distributional changes. Conformal inference has emerged as a powerful uncertainty quantification approach through the construction of prediction sets. Recent advances have introduced online conformal methods that adaptively adjust prediction thresholds through feedback mechanisms. However, the existing feedback mechanism typically relies solely on miscoverage indicators (actual feedback), whether the true label falls within the interval at each time step, while overlooking the empirical prediction threshold (estimated feedback) that is derived from the oracle conformal method. In this paper, we propose Dynamic Dual-feedback Conformal Inference (DDCI), which incorporates a dual-feedback mechanism consisting of actual feedback and estimated feedback. The former drives the primary adjustment of the intervals based on true observations, while the latter dampens excessive expansions or contractions by leveraging empirical thresholds from conformal inference during updates. By balancing these two signals, DDCI achieves more stable and narrower prediction intervals in sequential settings while maintaining near-nominal coverage in practice.

stat.ML↗

arXiv2026

Tool-Augmented Large Language Models for Reliable Medical Calculation from Patient Notes

Medical calculators translate raw patient observations into clinically actionable values and scores. However, applying these calculators directly to free-form patient notes requires precise variable extraction combined with the exact execution of complex formulas, scoring rules, and output conventions. Relying solely on direct large language model (LLM) prompting is unreliable in this context, as rule recall, parameter extraction, arithmetic reasoning, and formatting become entangled within a single generative step. To address these limitations, we propose a tool-augmented LLM framework for reliable medical calculation from patient notes. The framework retrieves and structures calculator specifications, generates reusable executable tools, and uses a constrained extractor to map each patient note to calculator-ready inputs. The tools then perform deterministic calculation, separating clinical language understanding from rule execution and arithmetic. Evaluated on the MedCalc-Bench dataset, our method achieves 86.73% final-answer accuracy, outperforming the one-shot prompting and supervised fine tuning-only baselines by 24.0 and 17.27 percentage points. Ablation and error analyses show that these performance gains are primarily driven by rule-grounded tool synthesis and schema-constrained extraction, whereas remaining failures are concentrated in clinical-semantic extraction and benchmark-specific output contracts. By grounding calculator logic in executable tools, the proposed approach alleviates arithmetic hallucinations and improves the computational reliability of the final clinical outputs.

cs.AI↗

arXiv2026

Specialized Decision Models vs. General-Purpose LLMs: Benchmarking Jev Across Knowledge, Reasoning, and Multilingual Tasks

Jev is a "System One" model that returns a choice among given options instead of generating text. We study how such a specialized decision model compares with general-purpose large language models (LLMs). We evaluate Jev on 13 multiple-choice benchmarks covering knowledge, reasoning, and multilingual understanding, and compare it with 19 LLMs in three tiers: frontier, representative, and small. Jev is competitive with frontier LLMs on knowledge and commonsense benchmarks and obtains the best score on MMLU-Redux and ARC-Challenge. Outside mathematics, it also outperforms most representative LLMs and all small LLMs. However, it falls behind on mathematical word problems: on MathQA, it is 17.7 points below the frontier median and scores lower than all 19 LLMs. These results indicate that a specialized decision model can match general-purpose LLMs on decisions that rely mainly on knowledge, but not on decisions that require multi-step calculation.

cs.CL↗

arXiv2026

RexDrug: Reliable Multi-Drug Combination Extraction through Reasoning-Enhanced LLMs

Automated Drug Combination Extraction (DCE) from large-scale biomedical literature is crucial for advancing precision medicine and pharmacological research. However, existing relation extraction methods primarily focus on binary interactions and struggle to model variable-length n-ary drug combinations, where complex compatibility logic and distributed evidence need to be considered. To address these limitations, we propose RexDrug, an end-to-end reasoning-enhanced relation extraction framework for n-ary drug combination extraction based on large language models. RexDrug adopts a two-stage training strategy. First, a multi-agent collaborative mechanism is utilized to automatically generate high-quality expert-like reasoning traces for supervised fine-tuning. Second, reinforcement learning with a multi-dimensional reward function specifically tailored for DCE is applied to further refine reasoning quality and extraction accuracy. Extensive experiments on the DrugComb dataset show that RexDrug consistently outperforms state-of-the-art baselines for n-ary extraction. Additional evaluation on the DDI13 corpus confirms its generalizability to binary drugdrug interaction tasks. Human expert assessment and automatic reasoning metrics further indicates that RexDrug produces coherent medical reasoning while accurately identifying complex therapeutic regimens. These results establish RexDrug as a scalable and reliable solution for complex biomedical relation extraction from unstructured text. The source code and data are available at https://github.com/DUTIR-BioNLP/RexDrug

cs.CL↗

arXiv2026

Efficient Test-Time Scaling for LLM-based Time Series Forecasting

Long-term time series forecasting benefits from preserving global structure such as trends and seasonality. Recent LLM-based forecasters often improve accuracy through test-time scaling (e.g., iterative refinement), but these methods are computationally expensive and increasingly prone to global-shape mismatch as the prediction horizon extends. We propose SCALER, a coarse-to-fine forecasting framework that first employs a lightweight Transformer tailored to long-term shape modeling to predict a coarse representation of future dynamics. This predicted shape then serves as a compact guide for an LLM to perform test-time scaling via iterative coarse-to-fine residual token refinement, while processing substantially fewer tokens at each step. By guiding refinement with an explicit future-shape prediction, SCALER reduces reliance on long description prompts, and its fixed-step refinement avoids costly reward-model-based selection, further lowering computational overhead. Experimental results demonstrate that SCALER outperforms strong forecasting baselines in long-term, short-term and zero-shot forecasting while significantly reducing the inference cost associated with scaled LLM for time series forecasting. Code: https://github.com/xuanmay2701/SCALER.

cs.LG↗

arXiv2026

MediRec: Enhancing Chinese Medication Recommendation with Explainable Clinical Reasoning

Large language models (LLMs) have shown strong potential for clinical decision support through their advanced language understanding and reasoning capabilities. However, their application to Chinese clinical medication recommendation remains largely unexplored. Existing approaches are primarily developed on English electronic health record datasets and focus on coarse-grained medication code prediction, offering limited support for interpretable clinical decision-making. In this work, we propose MediRec, an explainable LLM-based framework for Chinese medication recommendation from electronic health records. MediRec combines clinically grounded reasoning-chain distillation with reinforcement learning to improve both recommendation accuracy and interpretability. Comprehensive experiments on a Chinese medication recommendation benchmark show that MediRec achieves strong performance, with an F1 score of 0.5813 and a Jaccard score of 0.4626. Further analyses indicate that MediRec generates clinically plausible recommendations with transparent reasoning, demonstrating its effectiveness for explainable medication decision support in Chinese healthcare settings.

cs.CL↗

arXiv2026

SeekBrain: An Autonomous Multi-Agent System for Accelerating Neuroscience Discovery

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

cs.MA↗

arXiv2026

AFD-INSTRUCTION: A Comprehensive Antibody Instruction Dataset with Functional Annotations for LLM-Based Understanding and Design

Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present AFD-Instruction, the first large-scale instruction dataset with functional annotations tailored to antibodies. This dataset encompasses two key components: antibody understanding, which infers functional attributes directly from sequences, and antibody design, which enables de novo sequence generation under functional constraints. These components provide explicit sequence-function alignment and support antibody design guided by natural language instructions. Extensive instruction-tuning experiments on general-purpose LLMs demonstrate that AFD-Instruction consistently improves performance across diverse antibody-related tasks. By linking antibody sequences with textual descriptions of function, AFD-Instruction establishes a new foundation for advancing antibody modeling and accelerating therapeutic discovery.

q-bio.QM↗

arXiv2026

RAGNav: A Retrieval-Augmented Topological Reasoning Framework for Multi-Goal Visual-Language Navigation

Vision-Language Navigation (VLN) is evolving from single-point pathfinding toward the more challenging Multi-Goal VLN. This task requires agents to accurately identify multiple entities while collaboratively reasoning over their spatial-physical constraints and sequential execution order. However, generic Retrieval-Augmented Generation (RAG) paradigms often suffer from spatial hallucinations and planning drift when handling multi-object associations due to the lack of explicit spatial modeling.To address these challenges, we propose RAGNav, a framework that bridges the gap between semantic reasoning and physical structure. The core of RAGNav is a Dual-Basis Memory system, which integrates a low-level topological map for maintaining physical connectivity with a high-level semantic forest for hierarchical environment abstraction. Building on this representation, the framework introduces an anchor-guided conditional retrieval and a topological neighbor score propagation mechanism. This approach facilitates the rapid screening of candidate targets and the elimination of semantic noise, while performing semantic calibration by leveraging the physical associations inherent in the topological neighborhood.This mechanism significantly enhances the capability of inter-target reachability reasoning and the efficiency of sequential planning. Experimental results demonstrate that RAGNav achieves state-of-the-art (SOTA) performance in complex multi-goal navigation tasks.

cs.AI↗

arXiv2026

MA-CoNav: A Master-Slave Multi-Agent Framework with Hierarchical Collaboration and Dual-Level Reflection for Long-Horizon Embodied VLN

Vision-Language Navigation (VLN) aims to empower robots with the ability to perform long-horizon navigation in unfamiliar environments based on complex linguistic instructions. Its success critically hinges on establishing an efficient ``language-understanding -- visual-perception -- embodied-execution'' closed loop. Existing methods often suffer from perceptual distortion and decision drift in complex, long-distance tasks due to the cognitive overload of a single agent. Inspired by distributed cognition theory, this paper proposes MA-CoNav, a Multi-Agent Collaborative Navigation framework. This framework adopts a ``Master-Slave'' hierarchical agent collaboration architecture, decoupling and distributing the perception, planning, execution, and memory functions required for navigation tasks to specialized agents. Specifically, the Master Agent is responsible for global orchestration, while the Subordinate Agent group collaborates through a clear division of labor: an Observation Agent generates environment descriptions, a Planning Agent performs task decomposition and dynamic verification, an Execution Agent handles simultaneous mapping and action, and a Memory Agent manages structured experiences. Furthermore, the framework introduces a ``Local-Global'' dual-stage reflection mechanism to dynamically optimize the entire navigation pipeline. Empirical experiments were conducted using a real-world indoor dataset collected by a Limo Pro robot, with no scene-specific fine-tuning performed on the models throughout the process. The results demonstrate that MA-CoNav comprehensively outperforms existing mainstream VLN methods across multiple metrics.

cs.RO↗

arXiv2026

Endowing Embodied Agents with Spatial Reasoning Capabilities for Vision-and-Language Navigation

Enhancing the spatial perception capabilities of mobile robots is crucial for achieving embodied Vision-and-Language Navigation (VLN). Although significant progress has been made in simulated environments, directly transferring these capabilities to real-world scenarios often results in severe hallucination phenomena, causing robots to lose effective spatial awareness. To address this issue, we propose BrainNav, a bio-inspired spatial cognitive navigation framework inspired by biological spatial cognition theories and cognitive map theory. BrainNav integrates dual-map (coordinate map and topological map) and dual-orientation (relative orientation and absolute orientation) strategies, enabling real-time navigation through dynamic scene capture and path planning. Its five core modules-Hippocampal Memory Hub, Visual Cortex Perception Engine, Parietal Spatial Constructor, Prefrontal Decision Center, and Cerebellar Motion Execution Unit-mimic biological cognitive functions to reduce spatial hallucinations and enhance adaptability. Validated in a zero-shot real-world lab environment using the Limo Pro robot, BrainNav, compatible with GPT-4, outperforms existing State-of-the-Art (SOTA) Vision-and-Language Navigation in Continuous Environments (VLN-CE) methods without fine-tuning.

cs.AI↗

arXiv2026

Softmax is not Enough (for Adaptive Conformal Classification)

The merit of Conformal Prediction (CP), as a distribution-free framework for uncertainty quantification, depends on generating prediction sets that are efficient, reflected in small average set sizes, while adaptive, meaning they signal uncertainty by varying in size according to input difficulty. A central limitation for deep conformal classifiers is that the nonconformity scores are derived from softmax outputs, which can be unreliable indicators of how certain the model truly is about a given input, sometimes leading to overconfident misclassifications or undue hesitation. In this work, we argue that this unreliability can be inherited by the prediction sets generated by CP, limiting their capacity for adaptiveness. We propose a new approach that leverages information from the pre-softmax logit space, using the Helmholtz Free Energy as a measure of model uncertainty and sample difficulty. By reweighting nonconformity scores with a monotonic transformation of the energy score of each sample, we improve their sensitivity to input difficulty. Our experiments with four state-of-the-art score functions on multiple datasets and deep architectures show that this energy-based enhancement improves the adaptiveness of the prediction sets, leading to a notable increase in both efficiency and adaptiveness compared to baseline nonconformity scores, without introducing any post-hoc complexity.

cs.LG↗

arXiv2026

Stability as a Liability:Systematic Breakdown of Linguistic Structure in LLMs

Training stability is typically regarded as a prerequisite for reliable optimization in large language models. In this work, we analyze how stabilizing training dynamics affects the induced generation distribution. We show that under standard maximum likelihood training, stable parameter trajectories lead stationary solutions to approximately minimize the forward KL divergence to the empirical distribution, while implicitly reducing generative entropy. As a consequence, the learned model can concentrate probability mass on a limited subset of empirical modes, exhibiting systematic degeneration despite smooth loss convergence. We empirically validate this effect using a controlled feedback-based training framework that stabilizes internal generation statistics, observing consistent low-entropy outputs and repetitive behavior across architectures and random seeds. It indicates that optimization stability and generative expressivity are not inherently aligned, and that stability alone is an insufficient indicator of generative quality.

cs.AI↗

arXiv2025

Overview of CHIP 2025 Shared Task 2: Discharge Medication Recommendation for Metabolic Diseases Based on Chinese Electronic Health Records

Discharge medication recommendation plays a critical role in ensuring treatment continuity, preventing readmission, and improving long-term management for patients with chronic metabolic diseases. This paper present an overview of the CHIP 2025 Shared Task 2 competition, which aimed to develop state-of-the-art approaches for automatically recommending appro-priate discharge medications using real-world Chinese EHR data. For this task, we constructed CDrugRed, a high-quality dataset consisting of 5,894 de-identified hospitalization records from 3,190 patients in China. This task is challenging due to multi-label nature of medication recommendation, het-erogeneous clinical text, and patient-specific variability in treatment plans. A total of 526 teams registered, with 167 and 95 teams submitting valid results to the Phase A and Phase B leaderboards, respectively. The top-performing team achieved the highest overall performance on the final test set, with a Jaccard score of 0.5102, F1 score of 0.6267, demonstrating the potential of advanced large language model (LLM)-based ensemble systems. These re-sults highlight both the promise and remaining challenges of applying LLMs to medication recommendation in Chinese EHRs. The post-evaluation phase remains open at https://tianchi.aliyun.com/competition/entrance/532411/.

cs.CL↗

arXiv2025

MedTrust-RAG: Evidence Verification and Trust Alignment for Biomedical Question Answering

Biomedical question answering (QA) requires accurate interpretation of complex medical knowledge. Large language models (LLMs) have shown promising capabilities in this domain, with retrieval-augmented generation (RAG) systems enhancing performance by incorporating external medical literature. However, RAG-based approaches in biomedical QA suffer from hallucinations due to post-retrieval noise and insufficient verification of retrieved evidence, undermining response reliability. We propose MedTrust-Guided Iterative RAG, a framework designed to enhance factual consistency and mitigate hallucinations in medical QA. Our method introduces three key innovations. First, it enforces citation-aware reasoning by requiring all generated content to be explicitly grounded in retrieved medical documents, with structured Negative Knowledge Assertions used when evidence is insufficient. Second, it employs an iterative retrieval-verification process, where a verification agent assesses evidence adequacy and refines queries through Medical Gap Analysis until reliable information is obtained. Third, it integrates the MedTrust-Align Module (MTAM) that combines verified positive examples with hallucination-aware negative samples, leveraging Direct Preference Optimization to reinforce citation-grounded reasoning while penalizing hallucination-prone response patterns.

cs.CL↗

arXiv2025

A Unified Biomedical Named Entity Recognition Framework with Large Language Models

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual generalization. In this paper, we propose a unified Biomedical Named Entity Recognition (BioNER) framework based on Large Language Models (LLMs). We first reformulate BioNER as a text generation task and design a symbolic tagging strategy to jointly handle both flat and nested entities with explicit boundary annotation. To enhance multilingual and multi-task generalization, we perform bilingual joint fine-tuning across multiple Chinese and English datasets. Additionally, we introduce a contrastive learning-based entity selector that filters incorrect or spurious predictions by leveraging boundary-sensitive positive and negative samples. Experimental results on four benchmark datasets and two unseen corpora show that our method achieves state-of-the-art performance and robust zero-shot generalization across languages. The source codes are freely available at https://github.com/dreamer-tx/LLMNER.

cs.CL↗

arXiv2025

FocusMed: A Large Language Model-based Framework for Enhancing Medical Question Summarization with Focus Identification

With the rapid development of online medical platforms, consumer health questions (CHQs) are inefficient in diagnosis due to redundant information and frequent non-professional terms. The medical question summary (MQS) task aims to transform CHQs into streamlined doctors' frequently asked questions (FAQs), but existing methods still face challenges such as poor identification of question focus and model hallucination. This paper explores the potential of large language models (LLMs) in the MQS task and finds that direct fine-tuning is prone to focus identification bias and generates unfaithful content. To this end, we propose an optimization framework based on core focus guidance. First, a prompt template is designed to drive the LLMs to extract the core focus from the CHQs that is faithful to the original text. Then, a fine-tuning dataset is constructed in combination with the original CHQ-FAQ pairs to improve the ability to identify the focus of the question. Finally, a multi-dimensional quality evaluation and selection mechanism is proposed to comprehensively improve the quality of the summary from multiple dimensions. We conduct comprehensive experiments on two widely-adopted MQS datasets using three established evaluation metrics. The proposed framework achieves state-of-the-art performance across all measures, demonstrating a significant boost in the model's ability to identify critical focus of questions and a notable mitigation of hallucinations. The source codes are freely available at https://github.com/DUT-LiuChao/FocusMed.

cs.CL↗