arXiv subjects

Lin Xu

Publications and source records attributed to Lin Xu.

At least 37 records · Page 2Linked to original sources

arXiv2025

GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences

Exploring how genetic sequences shape phenotypes is a fundamental challenge in biology and a key step toward scalable, hypothesis-driven experimentation. The task is complicated by the large modality gap between sequences and phenotypes, as well as the pleiotropic nature of gene-phenotype relationships. Existing sequence-based efforts focus on the degree to which variants of specific genes alter a limited set of phenotypes, while general gene knockout induced phenotype abnormality prediction methods heavily rely on curated genetic information as inputs, which limits scalability and generalizability. As a result, the task of broadly predicting the presence of multiple phenotype abnormalities under gene knockout directly from gene sequences remains underexplored. We introduce GenePheno, the first interpretable multi-label prediction framework that predicts knockout induced phenotypic abnormalities from gene sequences. GenePheno employs a contrastive multi-label learning objective that captures inter-phenotype correlations, complemented by an exclusive regularization that enforces biological consistency. It further incorporates a gene function bottleneck layer, offering human interpretable concepts that reflect functional mechanisms behind phenotype formation. To support progress in this area, we curate four datasets with canonical gene sequences as input and multi-label phenotypic abnormalities induced by gene knockouts as targets. Across these datasets, GenePheno achieves state-of-the-art gene-centric $F_{\text{max}}$ and phenotype-centric AUC, and case studies demonstrate its ability to reveal gene functional mechanisms.

cs.LG↗

arXiv2025

Aeolus: A Multi-structural Flight Delay Dataset

We introduce Aeolus, a large-scale Multi-modal Flight Delay Dataset designed to advance research on flight delay prediction and support the development of foundation models for tabular data. Existing datasets in this domain are typically limited to flat tabular structures and fail to capture the spatiotemporal dynamics inherent in delay propagation. Aeolus addresses this limitation by providing three aligned modalities: (i) a tabular dataset with rich operational, meteorological, and airportlevel features for over 50 million flights; (ii) a flight chain module that models delay propagation along sequential flight legs, capturing upstream and downstream dependencies; and (iii) a flight network graph that encodes shared aircraft, crew, and airport resource connections, enabling cross-flight relational reasoning. The dataset is carefully constructed with temporal splits, comprehensive features, and strict leakage prevention to support realistic and reproducible machine learning evaluation. Aeolus supports a broad range of tasks, including regression, classification, temporal structure modeling, and graph learning, serving as a unified benchmark across tabular, sequential, and graph modalities. We release baseline experiments and preprocessing tools to facilitate adoption. Aeolus fills a key gap for both domain-specific modeling and general-purpose structured data research.Our source code and data can be accessed at https://github.com/Flnny/Delay-data

cs.LG↗

arXiv2025

TianHui: A Domain-Specific Large Language Model for Diverse Traditional Chinese Medicine Scenarios

Domain-specific LLMs in TCM face limitations in research settings due to constrained adaptability, insufficient evaluation datasets, and limited computational resources. This study presents TianHui, a specialized TCM LLM built through contextual data integration and domain knowledge fusion. We constructed a large-scale TCM corpus (0.97GB unsupervised data + 611,312 QA pairs) and employed a two-stage training strategy with QLoRA, DeepSpeed Stage 2, and Flash Attention 2. Evaluation on 12 benchmarks showed TianHui ranked top-three in all metrics for six datasets (APQ, TCMCD, HFR, HCCA, DHPE, TLAW) and achieved top results in the other six (TCMEE, APR, GCPMI, TCMKQA, TCMRC, ADTG). Optimal configuration was identified as LoRA rank=128, alpha=256, epoch=4, dropout=0.2, max length=2048. TianHui enables systematic preservation and scalable application of TCM knowledge. All resources are open-sourced.

cs.CL↗

arXiv2025

CLAP: Coreference-Linked Augmentation for Passage Retrieval

Large Language Model (LLM)-based passage expansion has shown promise for enhancing first-stage retrieval, but often underperforms with dense retrievers due to semantic drift and misalignment with their pretrained semantic space. Beyond this, only a portion of a passage is typically relevant to a query, while the rest introduces noise--an issue compounded by chunking techniques that break coreference continuity. We propose Coreference-Linked Augmentation for Passage Retrieval (CLAP), a lightweight LLM-based expansion framework that segments passages into coherent chunks, resolves coreference chains, and generates localized pseudo-queries aligned with dense retriever representations. A simple fusion of global topical signals and fine-grained subtopic signals achieves robust performance across domains. CLAP yields consistent gains even as retriever strength increases, enabling dense retrievers to match or surpass second-stage rankers such as BM25 + MonoT5-3B, with up to 20.68% absolute nDCG@10 improvement. These improvements are especially notable in out-of-domain settings, where conventional LLM-based expansion methods relying on domain knowledge often falter. CLAP instead adopts a logic-centric pipeline that enables robust, domain-agnostic generalization.

cs.IR↗

arXiv2025

Topological Layer-Spin Filter in Screw Dislocation

While the quantum spin Hall effect leverages two-dimensional topological states to manipulate spin without dissipation, layertonics extends this paradigm to three dimension by enabling control over the layer degree of freedom. Topological materials incorporating screw dislocations exhibit the capability for simultaneous manipulation of both electronic spin and layer degrees of freedom. In this work, the electronic transport properties of a multilayer Kane-Mele model with screw dislocations is studied theoretically. Numerical simulations of a screw dislocation reveal that dissipationless quantum spin Hall edge states propagate not only at the outer boundaries of the structure but also along the screw dislocation itself, working as layer-spin filter. In detail, 1) the spin-up and spin-down carriers starting from the same source layer flow to different drain layers along the topological channels, respectively. 2) The spin of carriers flowing into a given drain layer is determined by the input source layer. Moreover, we found that the transmission coefficient and spin polarization remain robust against Anderson disorder. Under magnetic disorder, spin flip and backscattering occur, suppressing the transmission coefficient while maintaining nearly unchanged spin polarization. Finally, the layer- and spin-resolved transport properties in a device with two screw dislocations are investigated as well. We have developed an innovative methodology to modulate electron transport with simultaneous layer and spin resolution.

cond-mat.mes-hall↗

arXiv2024

MAgIC: Investigation of Large Language Model Powered Multi-Agent in Cognition, Adaptability, Rationality and Collaboration

Large Language Models (LLMs) have significantly advanced natural language processing, demonstrating exceptional reasoning, tool usage, and memory capabilities. As their applications expand into multi-agent environments, there arises a need for a comprehensive evaluation framework that captures LLMs' reasoning, planning, collaboration, and other social abilities. This work introduces a novel competition-based benchmark framework specifically designed to assess LLMs within multi-agent settings, providing quantitative metrics to evaluate their judgment, reasoning, deception, self-awareness, cooperation, coordination, and rationality. We utilize two social deduction games alongside three game-theory scenarios to create diverse environments. Our frame is fortified with the probabilistic graphic modeling (PGM) method, enhancing the LLMs' capabilities in navigating complex social and cognitive dimensions. We evaluate seven LLMs, quantitatively highlighting a significant capability gap of over threefold between the strongest, GPT o1, and the weakest, Llama-2-70B. It also confirms that our PGM enhancement boosts the abilities of all selected models by an average of 37%. Our data and code can be found here https://github.com/cathyxl/MAgIC.

cs.CL↗

arXiv2024

Ab Initio Device-Driven Screening of Sub-1-nm Thickness Oxide Semiconductors for Future CMOS Technology Nodes

Ultrathin oxide semiconductors with sub-1-nm thickness are promising building blocks for ultrascaled field-effect transistor (FET) applications due to their resilience against short-channel effects, high air stability, and potential for low-energy device operation. However, the n-type dominance of ultrathin oxide FET has hindered their integration into complementary metal-oxide-semiconductor (CMOS) technology, which requires both n-and p-type devices. Here we develop an ab initio device-driven computational screening workflow to identify sub-1-nm thickness oxide semiconductors for sub-5-nm FET applications. We demonstrate that ultrathin CaO2, CaO, and SrO are compatible with p-type device operations under both high-performance (HP) and low-power (LP) requirements specified by the International Technology Roadmap of Semiconductors (ITRS), thereby expanding the limited family of p-type oxide semiconductors. Notably, CaO and SrO emerge as the first-of-kind sub-1-nm thickness oxide semiconductors capable of simultaneously meeting the ITRS HP and LP criteria for both n-and p-type devices. CaO and SrO FETs outperform many existing low-dimensional semiconductors, exhibiting scalability below 5-nm gate length. Our findings offer a pioneering effort in the ab initio, device-driven screening of sub-1-nm thickness oxide semiconductors, significantly broadening the material candidate pool for future CMOS technology nodes.

cond-mat.mtrl-sci↗

arXiv2024

ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects

In silico methods evaluating the mutation effects of missense mutations are providing an important approach for understanding mutations in personal genomes and identifying disease-relevant biomarkers. However, existing methods, including deep learning methods, heavily rely on sequence-aware information, and do not fully leverage the potential of available 3D structural information. In addition, these methods may exhibit an inability to predict mutations in domains difficult to formulate sequence-based embeddings. In this study, we introduce a novel rationale-guided graph neural network AlphaGMut to evaluate mutation effects and to distinguish pathogenic mutations from neutral mutations. We compute the alpha shapes of protein structures to obtain atomic-resolution edge connectivities and map them to an accurate residue-level graph representation. We then compute structural-, topological-, biophysical-, and sequence properties of the mutation sites, which are assigned as node attributes in the graph. These node attributes could effectively guide the graph neural network to learn the difference between pathogenic and neutral mutations using k-hop message passing with a short training period. We demonstrate that AlphaGMut outperforms state-of-the-art methods, including DeepMind's AlphaMissense, in many performance metrics. In addition, AlphaGMut has the advantage of performing well in alignment-free settings, which provides broader prediction coverage and better generalization compared to current methods requiring deep sequence-aware information.

q-bio.QM↗

arXiv2024

Non-Euclidean conformal devices with continuously varying refractive index profiles based on bi-spheres

Either conformal transformation optics or geodesic mapping provides a design method to bend light rays in two-dimensional space with a nonuniform refractive index profile. In this paper, we combine both methods above to design a conformal invisible cloak based on bi-spheres with a refractive index profile varying from 0 to 10.7, smaller than 24.6 for the previous case of a single sphere. Moreover, we obtain an omnidirectional retro-reflector and a specular reflector by making position adjustments to mirrors, and achieve similar invisible effect by tuning sizes of the bi-spheres. Our work expands the toolkits for designing conformal devices with continuously-varying index profile.

physics.optics↗

arXiv2024

PLLaVA : Parameter-free LLaVA Extension from Images to Videos for Video Dense Captioning

Vision-language pre-training has significantly elevated performance across a wide range of image-language applications. Yet, the pre-training process for video-related tasks demands exceptionally large computational and data resources, which hinders the progress of video-language models. This paper investigates a straight-forward, highly efficient, and resource-light approach to adapting an existing image-language pre-trained model for dense video understanding. Our preliminary experiments reveal that directly fine-tuning pre-trained image-language models with multiple frames as inputs on video datasets leads to performance saturation or even a drop. Our further investigation reveals that it is largely attributed to the bias of learned high-norm visual features. Motivated by this finding, we propose a simple but effective pooling strategy to smooth the feature distribution along the temporal dimension and thus reduce the dominant impacts from the extreme features. The new model is termed Pooling LLaVA, or PLLaVA in short. PLLaVA achieves new state-of-the-art performance on modern benchmark datasets for both video question-answer and captioning tasks. Notably, on the recent popular VideoChatGPT benchmark, PLLaVA achieves a score of 3.48 out of 5 on average of five evaluated dimensions, exceeding the previous SOTA results from GPT4V (IG-VLM) by 9%. On the latest multi-choice benchmark MVBench, PLLaVA achieves 58.1% accuracy on average across 20 sub-tasks, 14.5% higher than GPT4V (IG-VLM). Code is available at https://pllava.github.io/

cs.CV↗

arXiv2024

Chain of Thought Explanation for Dialogue State Tracking

Dialogue state tracking (DST) aims to record user queries and goals during a conversational interaction achieved by maintaining a predefined set of slots and their corresponding values. Current approaches decide slot values opaquely, while humans usually adopt a more deliberate approach by collecting information from relevant dialogue turns and then reasoning the appropriate values. In this work, we focus on the steps needed to figure out slot values by proposing a model named Chain-of-Thought-Explanation (CoTE) for the DST task. CoTE, which is built on the generative DST framework, is designed to create detailed explanations step by step after determining the slot values. This process leads to more accurate and reliable slot values. More-over, to improve the reasoning ability of the CoTE, we further construct more fluent and high-quality explanations with automatic paraphrasing, leading the method CoTE-refined. Experimental results on three widely recognized DST benchmarks-MultiWOZ 2.2, WoZ 2.0, and M2M-demonstrate the remarkable effectiveness of the CoTE. Furthermore, through a meticulous fine-grained analysis, we observe significant benefits of our CoTE on samples characterized by longer dialogue turns, user responses, and reasoning steps.

cs.CL↗

arXiv2024

CET2: Modelling Topic Transitions for Coherent and Engaging Knowledge-Grounded Conversations

Knowledge-grounded dialogue systems aim to generate coherent and engaging responses based on the dialogue contexts and selected external knowledge. Previous knowledge selection methods tend to rely too heavily on the dialogue contexts or over-emphasize the new information in the selected knowledge, resulting in the selection of repetitious or incongruous knowledge and further generating repetitive or incoherent responses, as the generation of the response depends on the chosen knowledge. To address these shortcomings, we introduce a Coherent and Engaging Topic Transition (CET2) framework to model topic transitions for selecting knowledge that is coherent to the context of the conversations while providing adequate knowledge diversity for topic development. Our CET2 framework considers multiple factors for knowledge selection, including valid transition logic from dialogue contexts to the following topics and systematic comparisons between available knowledge candidates. Extensive experiments on two public benchmarks demonstrate the superiority and the better generalization ability of CET2 on knowledge selection. This is due to our well-designed transition features and comparative knowledge selection strategy, which are more transferable to conversations about unseen topics. Analysis of fine-grained knowledge selection accuracy also shows that CET2 can better balance topic entailment (contextual coherence) and development (knowledge diversity) in dialogue than existing approaches.

cs.CL↗

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

Hyp-UML: Hyperbolic Image Retrieval with Uncertainty-aware Metric Learning

Metric learning plays a critical role in training image retrieval and classification. It is also a key algorithm in representation learning, e.g., for feature learning and its alignment in metric space. Hyperbolic embedding has been recently developed. Compared to the conventional Euclidean embedding in most of the previously developed models, Hyperbolic embedding can be more effective in representing the hierarchical data structure. Second, uncertainty estimation/measurement is a long-lasting challenge in artificial intelligence. Successful uncertainty estimation can improve a machine learning model's performance, robustness, and security. In Hyperbolic space, uncertainty measurement is at least with equivalent, if not more, critical importance. In this paper, we develop a Hyperbolic image embedding with uncertainty-aware metric learning for image retrieval. We call our method Hyp-UML: Hyperbolic Uncertainty-aware Metric Learning. Our contribution are threefold: we propose an image embedding algorithm based on Hyperbolic space, with their corresponding uncertainty value; we propose two types of uncertainty-aware metric learning, for the popular Contrastive learning and conventional margin-based metric learning, respectively. We perform extensive experimental validations to prove that the proposed algorithm can achieve state-of-the-art results among related methods. The comprehensive ablation study validates the effectiveness of each component of the proposed algorithm.

cs.CV↗

arXiv2022

CorefDiffs: Co-referential and Differential Knowledge Flow in Document Grounded Conversations

Knowledge-grounded dialog systems need to incorporate smooth transitions among knowledge selected for generating responses, to ensure that dialog flows naturally. For document-grounded dialog systems, the inter- and intra-document knowledge relations can be used to model such conversational flows. We develop a novel Multi-Document Co-Referential Graph (Coref-MDG) to effectively capture the inter-document relationships based on commonsense and similarity and the intra-document co-referential structures of knowledge segments within the grounding documents. We propose CorefDiffs, a Co-referential and Differential flow management method, to linearize the static Coref-MDG into conversational sequence logic. CorefDiffs performs knowledge selection by accounting for contextual graph structures and the knowledge difference sequences. CorefDiffs significantly outperforms the state-of-the-art by 9.5\%, 7.4\%, and 8.2\% on three public benchmarks. This demonstrates that the effective modeling of co-reference and knowledge difference for dialog flows are critical for transitions in document-grounded conversation

cs.CL↗

arXiv2022

Premise-based Multimodal Reasoning: Conditional Inference on Joint Textual and Visual Clues

It is a common practice for recent works in vision language cross-modal reasoning to adopt a binary or multi-choice classification formulation taking as input a set of source image(s) and textual query. In this work, we take a sober look at such an unconditional formulation in the sense that no prior knowledge is specified with respect to the source image(s). Inspired by the designs of both visual commonsense reasoning and natural language inference tasks, we propose a new task termed Premise-based Multi-modal Reasoning(PMR) where a textual premise is the background presumption on each source image. The PMR dataset contains 15,360 manually annotated samples which are created by a multi-phase crowd-sourcing process. With selected high-quality movie screenshots and human-curated premise templates from 6 pre-defined categories, we ask crowd-source workers to write one true hypothesis and three distractors (4 choices) given the premise and image through a cross-check procedure. Besides, we generate adversarial samples to alleviate the annotation artifacts and double the size of PMR. We benchmark various state-of-the-art (pretrained) multi-modal inference models on PMR and conduct comprehensive experimental analyses to showcase the utility of our dataset.

cs.CL↗

arXiv2021

Social and behavioral determinants of health in the era of artificial intelligence with electronic health records: A scoping review

Background: There is growing evidence that social and behavioral determinants of health (SBDH) play a substantial effect in a wide range of health outcomes. Electronic health records (EHRs) have been widely employed to conduct observational studies in the age of artificial intelligence (AI). However, there has been little research into how to make the most of SBDH information from EHRs. Methods: A systematic search was conducted in six databases to find relevant peer-reviewed publications that had recently been published. Relevance was determined by screening and evaluating the articles. Based on selected relevant studies, a methodological analysis of AI algorithms leveraging SBDH information in EHR data was provided. Results: Our synthesis was driven by an analysis of SBDH categories, the relationship between SBDH and healthcare-related statuses, and several NLP approaches for extracting SDOH from clinical literature. Discussion: The associations between SBDH and health outcomes are complicated and diverse; several pathways may be involved. Using Natural Language Processing (NLP) technology to support the extraction of SBDH and other clinical ideas simplifies the identification and extraction of essential concepts from clinical data, efficiently unlocks unstructured data, and aids in the resolution of unstructured data-related issues. Conclusion: Despite known associations between SBDH and disease, SBDH factors are rarely investigated as interventions to improve patient outcomes. Gaining knowledge about SBDH and how SBDH data can be collected from EHRs using NLP approaches and predictive models improves the chances of influencing health policy change for patient wellness, and ultimately promoting health and health equity. Keywords: Social and Behavioral Determinants of Health, Artificial Intelligence, Electronic Health Records, Natural Language Processing, Predictive Model

cs.CY↗

arXiv2021

2nd Place Solution for IJCAI-PRICAI 2020 3D AI Challenge: 3D Object Reconstruction from A Single Image

In this paper, we present our solution for the {\it IJCAI--PRICAI--20 3D AI Challenge: 3D Object Reconstruction from A Single Image}. We develop a variant of AtlasNet that consumes single 2D images and generates 3D point clouds through 2D to 3D mapping. To push the performance to the limit and present guidance on crucial implementation choices, we conduct extensive experiments to analyze the influence of decoder design and different settings on the normalization, projection, and sampling methods. Our method achieves 2nd place in the final track with a score of $70.88$, a chamfer distance of $36.87$, and a mean f-score of $59.18$. The source code of our method will be available at https://github.com/em-data/Enhanced_AtlasNet_3DReconstruction.

cs.CV↗