arXiv subjects

Haoran Shi

Publications and source records attributed to Haoran Shi.

15 recordsLinked to original sources

arXiv2026

Prospects for probing dark matter with filamentary 21cm emission

The cosmic web contains most of the matter in the Universe, and its filamentary structure is closely related to the properties of dark matter. Compared with the cold dark matter (CDM) model, warm dark matter (WDM) suppresses the formation of low-mass halos and produces smoother cosmic filaments. In this work, we explore whether filamentary 21cm emission can be used to distinguish between these two dark matter models at $z=4$ and $2.5$. We generate intrinsic 21cm brightness temperature maps from cosmological hydrodynamical simulations and produce mock observations by convolving them with Gaussian beams of different angular resolutions. We then compare the predicted filament signals with the expected sensitivities of SKA1-Low and SKA2-Low. We find that the intrinsic 21cm emission clearly reflects the different filament morphologies in the CDM and WDM models, particularly at $z=4$. However, these differences rapidly disappear as the beam size increases, especially for beam sizes larger than 6 arcsec. Although larger beams improve the observational sensitivity, they also erase the small-scale structures that encode the dark matter information. As a result, neither SKA1-Low nor the planned SKA2-Low can directly resolve individual filaments with sufficient sensitivity to distinguish between the two models. We therefore conclude that direct imaging of cosmic filaments and constraining dark matter through their morphology are unlikely to be feasible with current and planned SKA-Low facilities.

astro-ph.CO↗

arXiv2026

PsyScore: A Psychometrically-Aware Framework for Trait-Adaptive Essay Scoring and ZPD-Scaffolded Feedback

Effective Automated Essay Scoring (AES) are expected to support both reliable assessment and actionable instructional feedback. However, existing approaches often treat scoring and feedback as separate components: neural scoring models provide limited interpretability, while Large Language Model (LLM)-based feedback is typically insensitive to learners proficiency levels. To address this fragmentation, this work proposes PsyScore, a psychometrically-aware framework that integrates diagnostic assessment with instructional scaffolding through a shared latent ability representation. PsyScore comprises three key modules: a Trait-Adaptive Neural IRT Scorer that incorporates the Graded Partial Credit Model (GPCM) into a neural architecture, enabling the precise estimation of student ability while maintaining psychometric interpretability, a ZPD-Scaffolded Feedback Generator, which conditions multi-agent feedback strategies on the diagnosed ability parameter to adapt instructional focus across different proficiency levels, and a Multi-Perspective Feedback Evaluation Strategy that assesses feedback quality via pairwise preference judgements and student revision simulations. Experiments on the ASAP++ dataset demonstrate that PsyScore achieves competitive scoring performance while providing more pedagogically aligned feedback.

cs.CL↗

arXiv2026

TeamLLM: A Human-Like Team-Oriented Collaboration Framework for Multi-Step Contextualized Tasks

Recently, multi-Large Language Model (LLM) frameworks have been proposed to solve contextualized tasks. However, these frameworks do not explicitly emulate human team role division, which may lead to a single perspective, thereby weakening performance on multi-step contextualized tasks. To address this issue, we propose TeamLLM, a human-like Team-Oriented Multi-LLM Collaboration Framework. TeamLLM adopts four team roles with distinct division and employs a three-phase multi-LLM collaboration for multi-step contextualized tasks. To evaluate the effectiveness of TeamLLM on multi-step contextualized tasks, we propose Contextually-Grounded and Procedurally-Structured tasks (CGPST) and construct the CGPST benchmark. This benchmark has four core features: contextual grounding, procedural structure, process-oriented evaluation and multi-dimensional assessment. We evaluate ten popular LLMs on CGPST at overall-level, step-level, and dimension-level. Results show that TeamLLM substantially improves performance on CGPST. We release the benchmark with scenarios, full-process responses and human scores from ten LLMs. The code and data are available at https://anonymous.4open.science/r/TeamLLM-anonymous-C50E/.

cs.CL↗

arXiv2026

AnomSeer: Reinforcing Multimodal LLMs to Reason for Time-Series Anomaly Detection

Time-series anomaly detection (TSAD) with multimodal large language models (MLLMs) is an emerging area, yet a persistent challenge remains: MLLMs rely on coarse time-series heuristics but struggle with multi-dimensional, detailed reasoning, which is vital for understanding complex time-series data. We present AnomSeer to address this by reinforcing the model to ground its reasoning in precise, structural details of time series, unifying anomaly classification, localization, and explanation. At its core, an expert chain-of-thought trace is generated to provide a verifiable, fine-grained reasoning from classical analyses (e.g., statistical measures, frequency transforms). Building on this, we propose a novel time-series grounded policy optimization (TimerPO) that incorporates two additional components beyond standard reinforcement learning: a time-series grounded advantage based on optimal transport and an orthogonal projection to ensure this auxiliary granular signal does not interfere with the primary detection objective. Across diverse anomaly scenarios, AnomSeer, with Qwen2.5-VL-3B/7B-Instruct, outperforms larger commercial baselines (e.g., GPT-4o) in classification and localization accuracy, particularly on point- and frequency-driven exceptions. Moreover, it produces plausible time-series reasoning traces that support its conclusions.

cs.LG↗

arXiv2025

Black-Box Guardrail Reverse-engineering Attack

Large language models (LLMs) increasingly employ guardrails to enforce ethical, legal, and application-specific constraints on their outputs. While effective at mitigating harmful responses, these guardrails introduce a new class of vulnerabilities by exposing observable decision patterns. In this work, we present the first study of black-box LLM guardrail reverse-engineering attacks. We propose Guardrail Reverse-engineering Attack (GRA), a reinforcement learning-based framework that leverages genetic algorithm-driven data augmentation to approximate the decision-making policy of victim guardrails. By iteratively collecting input-output pairs, prioritizing divergence cases, and applying targeted mutations and crossovers, our method incrementally converges toward a high-fidelity surrogate of the victim guardrail. We evaluate GRA on three widely deployed commercial systems, namely ChatGPT, DeepSeek, and Qwen3, and demonstrate that it achieves an rule matching rate exceeding 0.92 while requiring less than $85 in API costs. These findings underscore the practical feasibility of guardrail extraction and highlight significant security risks for current LLM safety mechanisms. Our findings expose critical vulnerabilities in current guardrail designs and highlight the urgent need for more robust defense mechanisms in LLM deployment.

cs.CR↗

arXiv2025

Quantifying Conversation Drift in MCP via Latent Polytope

The Model Context Protocol (MCP) enhances large language models (LLMs) by integrating external tools, enabling dynamic aggregation of real-time data to improve task execution. However, its non-isolated execution context introduces critical security and privacy risks. In particular, adversarially crafted content can induce tool poisoning or indirect prompt injection, leading to conversation hijacking, misinformation propagation, or data exfiltration. Existing defenses, such as rule-based filters or LLM-driven detection, remain inadequate due to their reliance on static signatures, computational inefficiency, and inability to quantify conversational hijacking. To address these limitations, we propose SecMCP, a secure framework that detects and quantifies conversation drift, deviations in latent space trajectories induced by adversarial external knowledge. By modeling LLM activation vectors within a latent polytope space, SecMCP identifies anomalous shifts in conversational dynamics, enabling proactive detection of hijacking, misleading, and data exfiltration. We evaluate SecMCP on three state-of-the-art LLMs (Llama3, Vicuna, Mistral) across benchmark datasets (MS MARCO, HotpotQA, FinQA), demonstrating robust detection with AUROC scores exceeding 0.915 while maintaining system usability. Our contributions include a systematic categorization of MCP security threats, a novel latent polytope-based methodology for quantifying conversation drift, and empirical validation of SecMCP's efficacy.

cs.CL↗

arXiv2025

A Forced-Choice Neural Cognitive Diagnostic Model of Personality Testing

In the smart era, psychometric tests are becoming increasingly important for personnel selection, career development, and mental health assessment. Forced-choice tests are common in personality assessments because they require participants to select from closely related options, lowering the risk of response distortion. This study presents a deep learning-based Forced-Choice Neural Cognitive Diagnostic Model (FCNCD) that overcomes the limitations of traditional models and is applicable to the three most common item block types found in forced-choice tests. To account for the unidimensionality of items in forced-choice tests, we create interpretable participant and item parameters. We model the interactions between participant and item features using multilayer neural networks after mining them using nonlinear mapping. In addition, we use the monotonicity assumption to improve the interpretability of the diagnostic results. The FCNCD's effectiveness is validated by experiments on real-world and simulated datasets that show its accuracy, interpretability, and robustness.

cs.AI↗

arXiv2025

ControlNET: A Firewall for RAG-based LLM System

Retrieval-Augmented Generation (RAG) has significantly enhanced the factual accuracy and domain adaptability of Large Language Models (LLMs). This advancement has enabled their widespread deployment across sensitive domains such as healthcare, finance, and enterprise applications. RAG mitigates hallucinations by integrating external knowledge, yet introduces privacy risk and security risk, notably data breaching risk and data poisoning risk. While recent studies have explored prompt injection and poisoning attacks, there remains a significant gap in comprehensive research on controlling inbound and outbound query flows to mitigate these threats. In this paper, we propose an AI firewall, ControlNET, designed to safeguard RAG-based LLM systems from these vulnerabilities. ControlNET controls query flows by leveraging activation shift phenomena to detect adversarial queries and mitigate their impact through semantic divergence. We conduct comprehensive experiments on four different benchmark datasets including Msmarco, HotpotQA, FinQA, and MedicalSys using state-of-the-art open source LLMs (Llama3, Vicuna, and Mistral). Our results demonstrate that ControlNET achieves over 0.909 AUROC in detecting and mitigating security threats while preserving system harmlessness. Overall, ControlNET offers an effective, robust, harmless defense mechanism, marking a significant advancement toward the secure deployment of RAG-based LLM systems.

cs.CR↗

arXiv2025

Microbial correlation: a semi-parametric model for investigating microbial co-metabolism

The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired microbiome-metabolome studies (PM2S), provide valuable insights into gut metabolism as a key mediator of these interactions. Our preliminary data reveal strong correlations among certain gut metabolites, suggesting shared metabolic pathways and microbial co-metabolism. However, these findings are confounded by various factors, underscoring the need for a more rigorous statistical approach. Thus, we introduce microbial correlation, a novel metric that quantifies how two metabolites are co-regulated by the same gut microbes while accounting for confounders. Statistically, it is based on a partially linear model that isolates microbial-driven associations, and a consistent estimator is established based on semi-parametric theory. To improve efficiency, we develop a calibrated estimator with a parametric rate, maximizing the use of large external metagenomic datasets without paired metabolomic profiles. This calibrated estimator also enables efficient p-value calculation for identifying significant microbial co-metabolism signals. Through extensive numerical analysis, our method identifies important microbial co-metabolism patterns for healthy individuals, serving as a benchmark for future studies in diseased populations.

stat.ME↗

arXiv2024

Direct estimation and inference of higher-level correlations from lower-level measurements with applications in gene-pathway and proteomics studies

This paper tackles the challenge of estimating correlations between higher-level biological variables (e.g., proteins and gene pathways) when only lower-level measurements are directly observed (e.g., peptides and individual genes). Existing methods typically aggregate lower-level data into higher-level variables and then estimate correlations based on the aggregated data. However, different data aggregation methods can yield varying correlation estimates as they target different higher-level quantities. Our solution is a latent factor model that directly estimates these higher-level correlations from lower-level data without the need for data aggregation. We further introduce a shrinkage estimator to ensure the positive definiteness and improve the accuracy of the estimated correlation matrix. Furthermore, we establish the asymptotic normality of our estimator, enabling efficient computation of p-values for the identification of significant correlations. The effectiveness of our approach is demonstrated through comprehensive simulations and the analysis of proteomics and gene expression datasets. We develop the R package highcor for implementing our method.

stat.ME↗

arXiv2023

Imitator Learning: Achieve Out-of-the-Box Imitation Ability in Variable Environments

Imitation learning (IL) enables agents to mimic expert behaviors. Most previous IL techniques focus on precisely imitating one policy through mass demonstrations. However, in many applications, what humans require is the ability to perform various tasks directly through a few demonstrations of corresponding tasks, where the agent would meet many unexpected changes when deployed. In this scenario, the agent is expected to not only imitate the demonstration but also adapt to unforeseen environmental changes. This motivates us to propose a new topic called imitator learning (ItorL), which aims to derive an imitator module that can on-the-fly reconstruct the imitation policies based on very limited expert demonstrations for different unseen tasks, without any extra adjustment. In this work, we focus on imitator learning based on only one expert demonstration. To solve ItorL, we propose Demo-Attention Actor-Critic (DAAC), which integrates IL into a reinforcement-learning paradigm that can regularize policies' behaviors in unexpected situations. Besides, for autonomous imitation policy building, we design a demonstration-based attention architecture for imitator policy that can effectively output imitated actions by adaptively tracing the suitable states in demonstrations. We develop a new navigation benchmark and a robot environment for \topic~and show that DAAC~outperforms previous imitation methods \textit{with large margins} both on seen and unseen tasks.

cs.LG↗

arXiv2021

A Data-Centric Framework for Composable NLP Workflows

Empirical natural language processing (NLP) systems in application domains (e.g., healthcare, finance, education) involve interoperation among multiple components, ranging from data ingestion, human annotation, to text retrieval, analysis, generation, and visualization. We establish a unified open-source framework to support fast development of such sophisticated NLP workflows in a composable manner. The framework introduces a uniform data representation to encode heterogeneous results by a wide range of NLP tasks. It offers a large repository of processors for NLP tasks, visualization, and annotation, which can be easily assembled with full interoperability under the unified representation. The highly extensible framework allows plugging in custom processors from external off-the-shelf NLP and deep learning libraries. The whole framework is delivered through two modularized yet integratable open-source projects, namely Forte (for workflow infrastructure and NLP function processors) and Stave (for user interaction, visualization, and annotation).

cs.CL↗

arXiv2019

Learning Hierarchical Representations of Electronic Health Records for Clinical Outcome Prediction

Clinical outcome prediction based on the Electronic Health Record (EHR) plays a crucial role in improving the quality of healthcare. Conventional deep sequential models fail to capture the rich temporal patterns encoded in the longand irregular clinical event sequences. We make the observation that clinical events at a long time scale exhibit strongtemporal patterns, while events within a short time period tend to be disordered co-occurrence. We thus propose differentiated mechanisms to model clinical events at different time scales. Our model learns hierarchical representationsof event sequences, to adaptively distinguish between short-range and long-range events, and accurately capture coretemporal dependencies. Experimental results on real clinical data show that our model greatly improves over previous state-of-the-art models, achieving AUC scores of 0.94 and 0.90 for predicting death and ICU admission respectively, Our model also successfully identifies important events for different clinical outcome prediction tasks

cs.LG↗

arXiv2019

Texar: A Modularized, Versatile, and Extensible Toolkit for Text Generation

We introduce Texar, an open-source toolkit aiming to support the broad set of text generation tasks that transform any inputs into natural language, such as machine translation, summarization, dialog, content manipulation, and so forth. With the design goals of modularity, versatility, and extensibility in mind, Texar extracts common patterns underlying the diverse tasks and methodologies, creates a library of highly reusable modules, and allows arbitrary model architectures and algorithmic paradigms. In Texar, model architecture, inference, and learning processes are properly decomposed. Modules at a high concept level can be freely assembled and plugged in/swapped out. The toolkit also supports a rich set of large-scale pretrained models. Texar is thus particularly suitable for researchers and practitioners to do fast prototyping and experimentation. The versatile toolkit also fosters technique sharing across different text generation tasks. Texar supports both TensorFlow and PyTorch, and is released under Apache License 2.0 at https://www.texar.io.

cs.CL↗

arXiv2017

Towards Automated ICD Coding Using Deep Learning

International Classification of Diseases(ICD) is an authoritative health care classification system of different diseases and conditions for clinical and management purposes. Considering the complicated and dedicated process to assign correct codes to each patient admission based on overall diagnosis, we propose a hierarchical deep learning model with attention mechanism which can automatically assign ICD diagnostic codes given written diagnosis. We utilize character-aware neural language models to generate hidden representations of written diagnosis descriptions and ICD codes, and design an attention mechanism to address the mismatch between the numbers of descriptions and corresponding codes. Our experimental results show the strong potential of automated ICD coding from diagnosis descriptions. Our best model achieves 0.53 and 0.90 of F1 score and area under curve of receiver operating characteristic respectively. The result outperforms those achieved using character-unaware encoding method or without attention mechanism. It indicates that our proposed deep learning model can code automatically in a reasonable way and provide a framework for computer-auxiliary ICD coding.

cs.CL↗