arXiv subjects

Yang Xie

Publications and source records attributed to Yang Xie.

At least 19 recordsLinked to original sources

arXiv2026

SAIN: Structure-Aware Interactive Navigation with Active Dialogue Grounding for Mobile Robot

Most existing vision-language navigation tasks assume that instructions are complete and unambiguous. However, real-world robots often encounter natural human instructions that are ambiguous, underspecified, or incomplete, requiring them to resolve such uncertainties through active questioning. Interactive Instance Goal Navigation (IIGN) requires an embodied agent to find the specific instance under an ambiguous category-level instruction through active dialogue. However, existing dialogue-enabled methods often consume oracle answers as transient textual context for immediate decisions, rather than persistent spatial or object-centric structured state. We present SAIN, a zero-shot framework that turns active dialogue into persistent navigation state. Instead of consuming oracle answers as one-step text hints, SAIN compiles them into target evidence, route-level corridor memory, and object-candidate labels. These states are stored in structured value, room, graph, and object memories, then consumed by a unified policy for frontier ranking and final target approach. On the VL-LN IIGN benchmark, SAIN improves SR from 20.2 to 25.4 and SPL from 13.07 to 14.17 over the strongest reported dialogue-enabled baseline, while requiring no task-specific policy training. The results support dialogue-to-state conversion as an effective zero-shot mechanism for long-horizon interactive instance navigation. Project website: https://zorattc.github.io/SAIN/

cs.RO↗

arXiv2026

Traceable LLM Reasoning for Fake-Order Fraud Detection

Detecting fake-order fraud at scale remains a critical challenge for large online-to-offline (O2O) service platforms, as existing approaches often rely on expert-designed features, produce black-box decisions, and provide limited interpretability. To address these limitations, we propose DeepScrub, a reinforcement learning framework built upon large language models (LLMs) for fake-order fraud detection with traceable reasoning. DeepScrub introduces three innovations. First, a semantic unification module converts heterogeneous risk signals into textual descriptions that LLMs can understand. Second, continued pre-training on risk-control corpora injects domain knowledge, and task rewards jointly evaluate prediction correctness and reasoning quality. Third, the SUggest-REflect (SURE) mechanism incorporates expert feedback and model self-checking to iteratively refine reasoning paths. On a real-world fake-order fraud detection dataset, DeepScrub achieves a macro-F1 score of 85.3%, outperforming the best baseline by 2.7 percentage points. Our task-optimized 8B model further surpasses a 32B model, showing that domain adaptation can matter more than model scale in this setting. In a four-week live pilot, DeepScrub achieved 91.8% precision and 88.5% recall, improving over first-stage human reviewers by 16.6 and 38.8 percentage points. It reduced first-stage manual review workload by 94% and saved nearly one million RMB annually. These results show that DeepScrub improves fraud review accuracy, reduces first-stage review workload, and provides traceable evidence for production risk-review workflows.

cs.CR↗

arXiv2026

GlaKG: A Biomarker-Centric Fundus Knowledge Graph for Explainable Glaucoma Diagnosis and Risk Assessment

Glaucoma is a leading cause of irreversible blindness worldwide, yet most automated diagnosis systems rely on opaque deep-learning models that offer little clinical interpretability. We present GlaKG, a biomarker-centric fundus knowledge graph that integrates structural biomarkers, clinically grounded rules, and image features to produce traceable reasoning for glaucoma diagnosis and risk stratification. GlaKG encodes six entity types (Fundus Image, Optic Disc, Neural Rim, Pathology, Diagnosis, Risk Level), eight relation types, and 11 clinically validated rules into a unified graph, so that every prediction is accompanied by an explicit reasoning chain linking biomarker evidence to activated clinical rules. To keep knowledge-based reasoning strictly separate from label information, we adopt a post-processing fusion framework that combines ResNet50 image embeddings with a normalized KG reasoning-chain score via a tunable weight alpha, with all fitting confined to the training split. On a publicly available, AI-annotated fundus dataset, GlaKG reaches F1 = 0.9953 for binary glaucoma classification and 0.930 accuracy with 0.922 weighted F1 for four-class risk stratification; we report openly that the dataset's biomarker annotations are highly label-correlated, and therefore frame these figures as an upper bound attainable with clean structured biomarkers rather than as leakage-free image-only performance. Feature-importance analysis shows KG-derived and biomarker features contributing near-equally (51.1% vs. 48.9%), and the reasoning chain flags borderline cases by exposing low chain scores rather than failing silently. GlaKG's central contribution is therefore a clinically auditable reasoning framework that complements raw predictive performance by explicitly exposing the biomarker evidence and rule activations behind each decision.

cs.CV↗

arXiv2026

GRAFT: Gain-Recalibrated Adapters for Transformer-Based Neural Population Activity Modeling

Neural population activity models can recover rich temporal structure from binned spikes, but their read-in and readout layers often remain tied to a fixed set of recorded neurons. This coupling limits reuse in long-term brain-computer interfaces, where recorded neuron identities, counts, and response statistics can change across days. We introduce GRAFT, a Transformer-based neural population activity model that separates reusable temporal dynamics from a recalibratable neuron interface. The neuron interface controls how recorded neurons enter and leave the shared backbone, and auxiliary gain and positional mechanisms support neural activity modeling inside the Transformer. On MC Maze under the standard NLB'21 protocol, GRAFT reaches 0.3866 co-bps as an ensemble, setting a new state of the art on the primary co-bps metric among public and reported NLB'21 results. In a cross-day protocol constructed from the NLB'21 MC Maze dataset series, GRAFT recalibrates from MC Maze to the scaled MC Maze datasets (Large/Medium/Small) by updating only 9.21% of parameters, reaching 0.3749, 0.3112, and 0.3152 co-bps with restricted target-day support sets. These results show that the same interface-backbone separation supports both strong Transformer-based neural population activity modeling and data-efficient cross-day recalibration.

cs.LG↗

arXiv2026

EgoAERO: Learning Dexterous Manipulation from a Single Egocentric Video without Object Assets

Egocentric RGB-D videos offer a natural source of human dexterous manipulation demonstrations, but existing data is difficult to use for robot learning because object pose, geometry, and contact information are often missing or require pre-scanned object assets. We present EgoAERO, the first framework that learns dexterous manipulation from a single egocentric RGB-D human demonstration without object assets. EgoAERO reconstructs contact-consistent hand-object trajectories through asset-free object tracking and reconstruction, ego motion compensation, and adaptive contact optimization, then converts them into robot policies using two-stage residual learning. We further introduce an online quality assessment mechanism and construct EgoDex-R, a large-scale egocentric dataset with 4.3M RGB-D frames for dexterous policy learning. Simulation and real-world experiments show that EgoAERO enables single-demonstration dexterous manipulation and achieves downstream performance close to CAD-based reconstructions on HOI4D.

cs.RO↗

arXiv2026

Software as Content: Dynamic Applications as the Human-Agent Interaction Layer

Chat-based natural language interfaces have emerged as the dominant paradigm for human-agent interaction, yet they fundamentally constrain engagement with structured information and complex tasks. We identify three inherent limitations: the mismatch between structured data and linear text, the high entropy of unconstrained natural language input, and the lack of persistent, evolving interaction state. We introduce Software as Content (SaC), a paradigm in which dynamically generated agentic applications serve as the primary medium of human-agent interaction. Rather than communicating through sequential text exchange, this medium renders task-specific interfaces that present structured information and expose actionable affordances through which users iteratively guide agent behavior without relying solely on language. These interfaces persist and evolve across interaction cycles, transforming from transient responses into a shared, stateful interaction layer that progressively converges toward personalized, task-specific software. We formalize SaC through a human-agent-environment interaction model, derive design principles for generating and evolving agentic applications, and present a system architecture that operationalizes the paradigm. We evaluate across representative tasks of selection, exploration, and execution, demonstrating technical viability and expressive range, while identifying boundary conditions under which natural language remains preferable. By reframing interfaces as dynamically generated software artifacts, SaC opens a new design space for human-AI interaction, positioning dynamic software as a concrete and tractable research object.

cs.HC↗

arXiv2026

Deep reflective reasoning in interdependence constrained structured data extraction from clinical notes for digital health

Extracting structured information from clinical notes requires navigating a dense web of interdependent variables where the value of one attribute logically constrains others. Existing Large Language Model (LLM)-based extraction pipelines often struggle to capture these dependencies, leading to clinically inconsistent outputs. We propose deep reflective reasoning, a large language model agent framework that iteratively self-critiques and revises structured outputs by checking consistency among variables, the input text, and retrieved domain knowledge, stopping when outputs converge. We extensively evaluate the proposed method in three diverse oncology applications: (1) On colorectal cancer synoptic reporting from gross descriptions (n=217), reflective reasoning improved average F1 across eight categorical synoptic variables from 0.828 to 0.911 and increased mean correct rate across four numeric variables from 0.806 to 0.895; (2) On Ewing sarcoma CD99 immunostaining pattern identification (n=200), the accuracy improved from 0.870 to 0.927; (3) On lung cancer tumor staging (n=100), tumor stage accuracy improved from 0.680 to 0.833 (pT: 0.842 -> 0.884; pN: 0.885 -> 0.948). The results demonstrate that deep reflective reasoning can systematically improve the reliability of LLM-based structured data extraction under interdependence constraints, enabling more consistent machine-operable clinical datasets and facilitating knowledge discovery with machine learning and data science towards digital health.

cs.AI↗

arXiv2026

MEDVISTAGYM: A Scalable Training Environment for Thinking with Medical Images via Tool-Integrated Reinforcement Learning

Vision language models (VLMs) achieve strong performance on general image understanding but struggle to think with medical images, especially when performing multi-step reasoning through iterative visual interaction. Medical VLMs often rely on static visual embeddings and single-pass inference, preventing models from re-examining, verifying, or refining visual evidence during reasoning. While tool-integrated reasoning offers a promising path forward, open-source VLMs lack the training infrastructure to learn effective tool selection, invocation, and coordination in multi-modal medical reasoning. We introduce MedVistaGym, a scalable and interactive training environment that incentivizes tool-integrated visual reasoning for medical image analysis. MedVistaGym equips VLMs to determine when and which tools to invoke, localize task-relevant image regions, and integrate single or multiple sub-image evidence into interleaved multimodal reasoning within a unified, executable interface for agentic training. Using MedVistaGym, we train MedVistaGym-R1 to interleave tool use with agentic reasoning through trajectory sampling and end-to-end reinforcement learning. Across six medical VQA benchmarks, MedVistaGym-R1-8B exceeds comparably sized tool-augmented baselines by 19.10% to 24.21%, demonstrating that structured agentic training--not tool access alone--unlocks effective tool-integrated reasoning for medical image analysis.

cs.CV↗

arXiv2025

Scaling Agentic Reinforcement Learning for Tool-Integrated Reasoning in VLMs

While recent vision-language models (VLMs) demonstrate strong image understanding, their ability to "think with images", i.e., to reason through multi-step visual interactions, remains limited. We introduce VISTA-Gym, a scalable training environment for incentivizing tool-integrated visual reasoning capabilities in VLMs. VISTA-Gym unifies diverse real-world multimodal reasoning tasks (7 tasks from 13 datasets in total) with a standardized interface for visual tools (e.g., grounding, parsing), executable interaction loops, verifiable feedback signals, and efficient trajectory logging, enabling visual agentic reinforcement learning at scale. While recent VLMs exhibit strong text-only reasoning, both proprietary and open-source models still struggle with tool selection, invocation, and coordination. With VISTA-Gym, we train VISTA-R1 to interleave tool-use with agentic reasoning via multi-turn trajectory sampling and end-to-end reinforcement learning. Extensive experiments across 11 public reasoning-intensive VQA benchmarks show that VISTA-R1-8B outperforms state-of-the-art baselines with similar sizes by 9.51%-18.72%, demonstrating VISTA-Gym as an effective training ground to unlock the tool-integrated reasoning capabilities for VLMs.

cs.AI↗

arXiv2025

Central limit theorem for high temperature spin models via martingale embedding

We use martingale embeddings to prove a central limit theorem (CLT) for one-dimensional projections of high-dimensional random vectors in $\{-1,1\}^n$ satisfying a Poincar\'e inequality. We obtain a non-asymptotic error bound involving two-point and three-point functions for the CLT in 2-Wasserstein distance. We present three illustrative applications: Ising model with finite-range interactions, ferromagnetic Ising model under the Dobrushin condition, and the Sherrington-Kirkpatrick spin glass model at sufficiently high temperature. In all the examples, we allow heterogeneous external fields.

math.PR↗

arXiv2025

GAS-MIL: Group-Aggregative Selection Multi-Instance Learning for Ensemble of Foundation Models in Digital Pathology Image Analysis

Foundation models (FMs) have transformed computational pathology by providing powerful, general-purpose feature extractors. However, adapting and benchmarking individual FMs for specific diagnostic tasks is often time-consuming and resource-intensive, especially given their scale and diversity. To address this challenge, we introduce Group-Aggregative Selection Multi-Instance Learning (GAS-MIL), a flexible ensemble framework that seamlessly integrates features from multiple FMs, preserving their complementary strengths without requiring manual feature selection or extensive task-specific fine-tuning. Across classification tasks in three cancer datasets-prostate (PANDA), ovarian (UBC-OCEAN), and breast (TCGA-BrCa)-GAS-MIL consistently achieves superior or on-par performance relative to individual FMs and established MIL methods, demonstrating its robustness and generalizability. By enabling efficient integration of heterogeneous FMs, GAS-MIL streamlines model deployment for pathology and provides a scalable foundation for future multimodal and precision oncology applications.

cs.CV↗

arXiv2025

MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

cs.CL↗

arXiv2024

Large Language Models Powered Multiagent Ensemble for Mitigating Hallucination and Efficient Atrial Fibrillation Annotation of ECG Reports

This study introduces a LLMs powered multiagent ensemble method to address challenges in hallucination and data labeling, particularly in large-scale EHR datasets. Manual labeling of such datasets requires domain expertise and is labor-intensive, time-consuming, expensive, and error-prone. To overcome this bottleneck, we developed an ensemble LLMs method and demonstrated its effectiveness in two real-world tasks: (1) labeling a large-scale unlabeled ECG dataset in MIMIC-IV; (2) identifying social determinants of health (SDOH) from the clinical notes of EHR. Trading off benefits and cost, we selected a pool of diverse open source LLMs with satisfactory performance. We treat each LLM's prediction as a vote and apply a mechanism of majority voting with minimal winning threshold for ensemble. We implemented an ensemble LLMs application for EHR data labeling tasks. By using the ensemble LLMs and natural language processing, we labeled MIMIC-IV ECG dataset of 623,566 ECG reports with an estimated accuracy of 98.2%. We applied the ensemble LLMs method to identify SDOH from social history sections of 1,405 EHR clinical notes, also achieving competitive performance. Our experiments show that the ensemble LLMs can outperform individual LLM even the best commercial one, and the method reduces hallucination errors. From the research, we found that (1) the ensemble LLMs method significantly reduces the time and effort required for labeling large-scale EHR data, automating the process with high accuracy and quality; (2) the method generalizes well to other text data labeling tasks, as shown by its application to SDOH identification; (3) the ensemble of a group of diverse LLMs can outperform or match the performance of the best individual LLM; and (4) the ensemble method substantially reduces hallucination errors. This approach provides a scalable and efficient solution to data-labeling challenges.

cs.AI↗

arXiv2024

Causal Effect Estimation using identifiable Variational AutoEncoder with Latent Confounders and Post-Treatment Variables

Estimating causal effects from observational data is challenging, especially in the presence of latent confounders. Much work has been done on addressing this challenge, but most of the existing research ignores the bias introduced by the post-treatment variables. In this paper, we propose a novel method of joint Variational AutoEncoder (VAE) and identifiable Variational AutoEncoder (iVAE) for learning the representations of latent confounders and latent post-treatment variables from their proxy variables, termed CPTiVAE, to achieve unbiased causal effect estimation from observational data. We further prove the identifiability in terms of the representation of latent post-treatment variables. Extensive experiments on synthetic and semi-synthetic datasets demonstrate that the CPTiVAE outperforms the state-of-the-art methods in the presence of latent confounders and post-treatment variables. We further apply CPTiVAE to a real-world dataset to show its potential application.

cs.LG↗

arXiv2024

A Systematic Literature Review on Large Language Models for Automated Program Repair

Automated Program Repair (APR) attempts to patch software bugs and reduce manual debugging efforts. Very recently, with the advances in Large Language Models (LLMs), an increasing number of APR techniques have been proposed, facilitating software development and maintenance and demonstrating remarkable performance. However, due to ongoing explorations in the LLM-based APR field, it is challenging for researchers to understand the current achievements, challenges, and potential opportunities. This work provides the first systematic literature review to summarize the applications of LLMs in APR between 2020 and 2025. We analyze 189 relevant papers from LLMs, APR and their integration perspectives. First, we categorize existing popular LLMs that are applied to support APR and outline four types of utilization strategies for their deployment. Besides, we detail some specific repair scenarios that benefit from LLMs, e.g., semantic bugs and security vulnerabilities. Furthermore, we discuss several critical aspects of integrating LLMs into APR research, e.g., input forms and open science. Finally, we highlight a set of challenges remaining to be investigated and the potential guidelines for future research. Overall, our paper provides a systematic overview of the research landscape to the APR community, helping researchers gain a comprehensive understanding of achievements and promote future research.

cs.SE↗

arXiv2023

A Survey on Large Language Models for Software Engineering

Software Engineering (SE) is the systematic design, development, maintenance, and management of software applications underpinning the digital infrastructure of our modern world. Very recently, the SE community has seen a rapidly increasing number of techniques employing Large Language Models (LLMs) to automate a broad range of SE tasks. Nevertheless, existing information of the applications, effects, and possible limitations of LLMs within SE is still not well-studied. In this paper, we provide a systematic survey to summarize the current state-of-the-art research in the LLM-based SE community. We summarize 62 representative LLMs of Code across three model architectures, 15 pre-training objectives across four categories, and 16 downstream tasks across five categories. We then present a detailed summarization of the recent SE studies for which LLMs are commonly utilized, including 947 studies for 112 specific code-related tasks across five crucial phases within the SE workflow. We also discuss several critical aspects during the integration of LLMs into SE, such as empirical evaluation, benchmarking, security and reliability, domain tuning, compressing and distillation. Finally, we highlight several challenges and potential opportunities on applying LLMs for future SE studies, such as exploring domain LLMs and constructing clean evaluation datasets. Overall, our work can help researchers gain a comprehensive understanding about the achievements of the existing LLM-based SE studies and promote the practical application of these techniques. Our artifacts are publicly available and will be continuously updated at the living repository: https://github.com/iSEngLab/AwesomeLLM4SE.

cs.SE↗

arXiv2023

Bayesian Nonparametric Clustering with Feature Selection for Spatially Resolved Transcriptomics Data

The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context. Nevertheless, there are inherent challenges associated with these new high-dimensional spatial data, such as zero-inflation, over-dispersion, and heterogeneity. These challenges pose obstacles to effective clustering, which is a fundamental problem in SRT data analysis. Current computational approaches often rely on heuristic data preprocessing and arbitrary cluster number prespecification, leading to considerable information loss and consequently, suboptimal downstream analysis. In response to these challenges, we introduce BNPSpace, a novel Bayesian nonparametric spatial clustering framework that directly models SRT count data. BNPSpace facilitates the partitioning of the whole spatial domain, which is characterized by substantial heterogeneity, into homogeneous spatial domains with similar molecular characteristics while identifying a parsimonious set of discriminating genes among different spatial domains. Moreover, BNPSpace incorporates spatial information through a Markov random field prior model, encouraging a smooth and biologically meaningful partition pattern.

stat.AP↗

arXiv2023

Disentangled Latent Representation Learning for Tackling the Confounding M-Bias Problem in Causal Inference

In causal inference, it is a fundamental task to estimate the causal effect from observational data. However, latent confounders pose major challenges in causal inference in observational data, for example, confounding bias and M-bias. Recent data-driven causal effect estimators tackle the confounding bias problem via balanced representation learning, but assume no M-bias in the system, thus they fail to handle the M-bias. In this paper, we identify a challenging and unsolved problem caused by a variable that leads to confounding bias and M-bias simultaneously. To address this problem with co-occurring M-bias and confounding bias, we propose a novel Disentangled Latent Representation learning framework for learning latent representations from proxy variables for unbiased Causal effect Estimation (DLRCE) from observational data. Specifically, DLRCE learns three sets of latent representations from the measured proxy variables to adjust for the confounding bias and M-bias. Extensive experiments on both synthetic and three real-world datasets demonstrate that DLRCE significantly outperforms the state-of-the-art estimators in the case of the presence of both confounding bias and M-bias.

cs.LG↗