arXiv subjects

Xin Lian

Publications and source records attributed to Xin Lian.

10 recordsLinked to original sources

arXiv2026

BioDefect: The First Dataset for Defect Detection in Bioinformatics Software

Software defect detection is a critical task in software engineering. However, no prior studies have specifically addressed defect detection in bioinformatics software. Given that the performance of defect detection tasks is primarily influenced by both models and datasets, our experiments controlled for model-related factors and confirmed the limitations of existing datasets in bioinformatics software. To address this issue, we introduce BioDefect, the first dataset specifically designed for defect detection in bioinformatics software, aiming to overcome the limitations of existing datasets in this context. Unlike prior datasets, BioDefect includes complete source code repositories, preserving the actual contextual information of defective code, thereby more accurately reflecting real-world defect scenarios in bioinformatics software. Additionally, BioDefect mitigates issues related to label inconsistency and data leakage, ensuring high data quality and experimental reliability. To evaluate the effectiveness of BioDefect, we conduct a systematic assessment on nine language models (LMs), including DeepSeek-R1. The results demonstrate that BioDefect significantly enhances defect detection performance for bioinformatics software. Compared to existing datasets, BioDefect achieves an average F1-score improvement of 29.61% to 38.04% across all models, highlighting its superior advantages. This study fills a critical research gap in bioinformatics software defect detection, laying a foundation for future studies in this field and offering new insights for improving bioinformatics software quality assurance.

cs.SE↗

arXiv2026

Do Papers Tell the Whole Story? A Benchmark and Framework for Uncovering Hidden Implementation Gaps in Bioinformatics

Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However, this issue has received limited attention to date, particularly in the field of bioinformatics, where inconsistencies between methodological descriptions in papers and their actual code implementations are prevalent. To address this gap, we introduce a novel research task, namely paper-code consistency detection, which aims to characterize the cross-modal semantic alignment between methodological descriptions in papers and their corresponding code implementations. At the data level, we construct the first benchmark dataset for this task in the bioinformatics domain, termed BioCon, comprising 48 bioinformatics software projects and their associated publications. BioCon is built by fine-grained alignment between sentence-level methodological descriptions in papers and function-level code snippets, combined with expert annotation and hard negative sampling strategies, resulting in a high-quality sentence-code paired dataset. At the methodological level, we propose a unified cross-modal consistency detection framework that leverages pre-trained models to jointly encode paper sentences and code functions. We conduct a systematic analysis from three perspectives: sentence-level classification, cross-modal retrieval, and project-level consistency assessment. Experimental results demonstrate that the proposed approach achieves strong performance in both consistency discrimination and semantic alignment. Overall, this work establishes the first systematic benchmark and framework for paper-code consistency analysis, opening a new research direction and providing a foundation for improving reproducibility and reliability in bioinformatics software.

cs.LG↗

arXiv2026

A Rational Account of Categorization Based on Information Theory

We present a new theory of categorization based on an information-theoretic rational analysis. To evaluate this theory, we investigate how well it can account for key findings from classic categorization experiments conducted by Hayes-Roth and Hayes-Roth (1977), Medin and Schaffer (1978), and Smith and Minda (1998). We find that it explains the human categorization behavior as well as (or better) than the independent cue and context models (Medin & Schaffer, 1978), the rational model of categorization (Anderson, 1991), and a hierarchical Dirichlet process model (Griffiths et al., 2007).

cs.AI↗

arXiv2025

LLM-Augmented Symbolic NLU System for More Reliable Continuous Causal Statement Interpretation

Despite the broad applicability of large language models (LLMs), their reliance on probabilistic inference makes them vulnerable to errors such as hallucination in generated facts and inconsistent output structure in natural language understanding (NLU) tasks. By contrast, symbolic NLU systems provide interpretable understanding grounded in curated lexicons, semantic resources, and syntactic & semantic interpretation rules. They produce relational representations that can be used for accurate reasoning and planning, as well as incremental debuggable learning. However, symbolic NLU systems tend to be more limited in coverage than LLMs and require scarce knowledge representation and linguistics skills to extend and maintain. This paper explores a hybrid approach that integrates the broad-coverage language processing of LLMs with the symbolic NLU capabilities of producing structured relational representations to hopefully get the best of both approaches. We use LLMs for rephrasing and text simplification, to provide broad coverage, and as a source of information to fill in knowledge gaps more automatically. We use symbolic NLU to produce representations that can be used for reasoning and for incremental learning. We evaluate this approach on the task of extracting and interpreting quantities and causal laws from commonsense science texts, along with symbolic- and LLM-only pipelines. Our results suggest that our hybrid method works significantly better than the symbolic-only pipeline.

cs.CL↗

arXiv2025

Proton-neutron pairing correlations in N=Z nuclei with Deformed Skyrme+pnBCS model

We investigate the effects of neutron-neutron (nn), proton-proton (pp) and proton-neutron (pn) pairing correlations on the ground-states of $N = Z$ even-even $pf$-shell nuclei by using an axially symmetric deformed Hartree-Fock (HF)+pnBardeen-Cooper-Schrieffer (BCS) model. We adopt a Skyrme energy density functional (EDF) SGII, together with contact volume- and surface-type pairing interactions, whose strengths are adjusted to reproduce empirical pairing gaps of each nucleus. It is shown that the strength of the IS pairing is correlated to the nuclear deformation: for oblate deformation with $-0.3<β_2<0.0$, a stronger IS pairing is required to reproduce the empirical pairing gap, while for prolate deformation a weaker one is enough. Among the eight $N=Z$ nuclei, we found that $^{64}$Ge, $^{68}$Se and $^{72}$Kr show the dominance of isovector (IV) spin-singlet superfluidity, while lighter 5 nuclei $^{44}$Ti, $^{48}$Cr, $^{52}$Fe, $^{56}$Ni and $^{60}$Zn exhibit the coexistence of IV spin-singlet and isoscalar (IS) spin-triplet superfluidities. We found also that the IS abnormal density always exhibits the oblate deformation, regardless of whether the normal density is prolate, spherical or oblate.

nucl-th↗

arXiv2024

Incremental Concept Formation over Visual Images Without Catastrophic Forgetting

Deep neural networks have excelled in machine learning, particularly in vision tasks, however, they often suffer from catastrophic forgetting when learning new tasks sequentially. In this work, we introduce Cobweb4V, an alternative to traditional neural network approaches. Cobweb4V is a novel visual classification method that builds on Cobweb, a human like learning system that is inspired by the way humans incrementally learn new concepts over time. In this research, we conduct a comprehensive evaluation, showcasing Cobweb4Vs proficiency in learning visual concepts, requiring less data to achieve effective learning outcomes compared to traditional methods, maintaining stable performance over time, and achieving commendable asymptotic behavior, without catastrophic forgetting effects. These characteristics align with learning strategies in human cognition, positioning Cobweb4V as a promising alternative to neural network approaches.

cs.LG↗

arXiv2024

Incremental and Data-Efficient Concept Formation to Support Masked Word Prediction

This paper introduces Cobweb4L, a novel approach for efficient language model learning that supports masked word prediction. The approach builds on Cobweb, an incremental system that learns a hierarchy of probabilistic concepts. Each concept stores the frequencies of words that appear in instances tagged with that concept label. The system utilizes an attribute value representation to encode words and their surrounding context into instances. Cobweb4L uses the information theoretic variant of category utility and a new performance mechanism that leverages multiple concepts to generate predictions. We demonstrate that with these extensions it significantly outperforms prior Cobweb performance mechanisms that use only a single node to generate predictions. Further, we demonstrate that Cobweb4L learns rapidly and achieves performance comparable to and even superior to Word2Vec. Next, we show that Cobweb4L and Word2Vec outperform BERT in the same task with less training data. Finally, we discuss future work to make our conclusions more robust and inclusive.

cs.CL↗

arXiv2024

Cobweb: An Incremental and Hierarchical Model of Human-Like Category Learning

Cobweb, a human-like category learning system, differs from most cognitive science models in incrementally constructing hierarchically organized tree-like structures guided by the category utility measure. Prior studies have shown that Cobweb can capture psychological effects such as basic-level, typicality, and fan effects. However, a broader evaluation of Cobweb as a model of human categorization remains lacking. The current study addresses this gap. It establishes Cobweb's alignment with classical human category learning effects. It also explores Cobweb's flexibility to exhibit both exemplar- and prototype-like learning within a single framework. These findings set the stage for further research on Cobweb as a robust model of human category learning.

cs.LG↗

arXiv2022

Speech Detection Task Against Asian Hate: BERT the Central, While Data-Centric Studies the Crucial

With the COVID-19 pandemic continuing, hatred against Asians is intensifying in countries outside Asia, especially among the Chinese. There is an urgent need to detect and prevent hate speech towards Asians effectively. In this work, we first create COVID-HATE-2022, an annotated dataset including 2,025 annotated tweets fetched in early February 2022, which are labeled based on specific criteria, and we present the comprehensive collection of scenarios of hate and non-hate tweets in the dataset. Second, we fine-tune the BERT model based on the relevant datasets and demonstrate several strategies related to the "cleaning" of the tweets. Third, we investigate the performance of advanced fine-tuning strategies with various model-centric and data-centric approaches, and we show that both strategies generally improve the performance, while data-centric ones outperform the others, and it demonstrates the feasibility and effectiveness of the data-centric approaches in the associated tasks.

cs.CL↗

arXiv2020

Unsupervised Multilingual Alignment using Wasserstein Barycenter

We study unsupervised multilingual alignment, the problem of finding word-to-word translations between multiple languages without using any parallel data. One popular strategy is to reduce multilingual alignment to the much simplified bilingual setting, by picking one of the input languages as the pivot language that we transit through. However, it is well-known that transiting through a poorly chosen pivot language (such as English) may severely degrade the translation quality, since the assumed transitive relations among all pairs of languages may not be enforced in the training process. Instead of going through a rather arbitrarily chosen pivot language, we propose to use the Wasserstein barycenter as a more informative "mean" language: it encapsulates information from all languages and minimizes all pairwise transportation costs. We evaluate our method on standard benchmarks and demonstrate state-of-the-art performances.

cs.CL↗