Xin Lian

Tianxiang Xu, Xiaoyan Zhu, Xin Lai et al.

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.

Tianxiang Xu, Xiaoyan Zhu, Xin Lai et al.

Ensuring consistency between research papers and their corresponding software implementations is fundamental to software reliability and scientific reproducibility. However, this problem remains underexplored, particularly in the domain of bioinformatics, where discrepancies between methodological descriptions in papers and their actual code implementations are prevalent. To address this gap, this paper introduces a new task, namely paper-code consistency detection, and curates a collection of 48 bioinformatics software projects along with their associated publications. We systematically align sentence-level algorithmic descriptions from papers with function-level code snippets. Combined with expert annotations and a hybrid negative sampling strategy, we construct the first benchmark dataset in the bioinformatics domain tailored to this task, termed BioCon. Based on this benchmark, we further propose a cross-modal consistency detection framework designed to model the semantic relationships between natural language descriptions and code implementations. The framework adopts a unified input representation and leverages pre-trained models to capture deep semantic alignment between papers and code. To mitigate the effects of class imbalance and hard samples, we incorporate a weighted focal loss to enhance model robustness. Experimental results demonstrate that our framework effectively identifies consistency between papers and code in bioinformatics, achieving an accuracy of 0.9056 and an F1 score of 0.8011. Overall, this study opens a new research direction for paper-code consistency analysis and lays the foundation for automated reproducibility assessment and cross-modal understanding in scientific software.

Xin Lian, Nishant Baglodi, Christopher J. MacLellan

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.

Xin Lian

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.

Nicki Barari, Xin Lian, Christopher J. MacLellan

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.

Xin Lian, Sashank Varma, Christopher J. MacLellan

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.

Christophe J. MacLellan, Karthik Singaravadivelan, Xin Lian et al.

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 at least as well (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).

Xin Lian, Kenneth D. Forbus

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.

Xin Lian, Kshitij Jain, Jakub Truszkowski et al.

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.