pwc-archive/papers-with-abstracts huggingface dataset:
Comparative analysis of unsupervised clustering techniques using validation metrics: Study on cognitive features from the Canadian Longitudinal Study on Aging (CLSA)
Authors: ChenNingZhi Sheng, Rafal Kustra, Davide Chicco
Date: 2025-04-07 00:00:00
Tasks: Clustering

Purpose: The primary goal of this study is to explore the application of evaluation metrics to different clustering algorithms using the data provided from the Canadian Longitudinal Study (CLSA), focusing on cognitive features. The objective of our work is to discover potential clinically relevant clusters that contribute to the development of dementia over time-based on cognitive changes. Method: The CLSA dataset includes 18,891 participants with data available at both baseline and follow-up assessments, to which clustering algorithms were applied. The clustering methodologies employed in this analysis are K-means (KM) clustering, Hierarchical Clustering (HC) and Partitioning Around Medoids (PAM). We use multiple evaluation metrics to assess our analysis. For internal evaluation metrics, we use: Average silhouette Width, Within and Between the sum of square Ratio (WB.Ratio), Entropy, Calinski-Harabasz Index (CH Index), and Separation Index. For clustering comparison metrics, we used: Homogeneity, Completeness, Adjusted Rand Index (ARI), Rand Index (RI), and Variation Information. Results: Using evaluation metrics to compare the results of the three clustering techniques, K-means and Partitioning Around Medoids (PAM) produced similar results. In contrast, there are significant differences between K-means clustering and Hierarchical Clustering. Our study highlights the importance of the two internal evaluation metrics: entropy and separation index. In between clustering comparison metrics, the Adjusted Rand Index is a key tool. Conclusion: The study results have the potential to contribute to understanding dementia. Researchers can also benefit by applying the suggested evaluation metrics to other areas of healthcare research. Overall, our study improves the understanding of using clustering techniques and evaluation metrics to reveal complex patterns in medical data.
Predicting BVD Re-emergence in Irish Cattle From Highly Imbalanced Herd-Level Data Using Machine Learning Algorithms
Authors: Niamh Mimnagh, Andrew Parnell, Conor McAloon, Jaden Carlson, Maria Guelbenzu, Jonas Brock, Damien Barrett, Guy McGrath, Jamie Tratalos, Rafael Moral
Date: 2025-04-17 00:00:00
Tasks: Anomaly Detection, Binary Classification, Sensitivity

Bovine Viral Diarrhoea (BVD) has been the focus of a successful eradication programme in Ireland, with the herd-level prevalence declining from 11.3% in 2013 to just 0.2% in 2023. As the country moves toward BVD freedom, the development of predictive models for targeted surveillance becomes increasingly important to mitigate the risk of disease re-emergence. In this study, we evaluate the performance of a range of machine learning algorithms, including binary classification and anomaly detection techniques, for predicting BVD-positive herds using highly imbalanced herd-level data. We conduct an extensive simulation study to assess model performance across varying sample sizes and class imbalance ratios, incorporating resampling, class weighting, and appropriate evaluation metrics (sensitivity, positive predictive value, F1-score and AUC values). Random forests and XGBoost models consistently outperformed other methods, with the random forest model achieving the highest sensitivity and AUC across scenarios, including real-world prediction of 2023 herd status, correctly identifying 219 of 250 positive herds while halving the number of herds that require compared to a blanket-testing strategy.
Cluster weighted models with multivariate skewed distributions for functional data
Authors: Cristina Anton, Roy Shivam Ram Shreshtth
Date: 2025-04-17 00:00:00
Tasks: Clustering

We propose a clustering method, funWeightClustSkew, based on mixtures of functional linear regression models and three skewed multivariate distributions: the variance-gamma distribution, the skew-t distribution, and the normal-inverse Gaussian distribution. Our approach follows the framework of the functional high dimensional data clustering (funHDDC) method, and we extend to functional data the cluster weighted models based on skewed distributions used for finite dimensional multivariate data. We consider several parsimonious models, and to estimate the parameters we construct an expectation maximization (EM) algorithm. We illustrate the performance of funWeightClustSkew for simulated data and for the Air Quality dataset.
Robust and Scalable Variational Bayes
Authors: Carlos Misael Madrid Padilla, Shitao Fan, Lizhen Lin
Date: 2025-04-16 00:00:00
Tasks: Bayesian Inference

We propose a robust and scalable framework for variational Bayes (VB) that effectively handles outliers and contamination of arbitrary nature in large datasets. Our approach divides the dataset into disjoint subsets, computes the posterior for each subset, and applies VB approximation independently to these posteriors. The resulting variational posteriors with respect to the subsets are then aggregated using the geometric median of probability measures, computed with respect to the Wasserstein distance. This novel aggregation method yields the Variational Median Posterior (VM-Posterior) distribution. We rigorously demonstrate that the VM-Posterior preserves contraction properties akin to those of the true posterior, while accounting for approximation errors or the variational gap inherent in VB methods. We also provide provable robustness guarantee of the VM-Posterior. Furthermore, we establish a variational Bernstein-von Mises theorem for both multivariate Gaussian distributions with general covariance structures and the mean-field variational family. To facilitate practical implementation, we adapt existing algorithms for computing the VM-Posterior and evaluate its performance through extensive numerical experiments. The results highlight its robustness and scalability, making it a reliable tool for Bayesian inference in the presence of complex, contaminated datasets.
A Survey on Archetypal Analysis
Authors: Aleix Alcacer, Irene Epifanio, Sebastian Mair, Morten Mørup
Date: 2025-04-16 00:00:00
Tasks: Dimensionality Reduction, Survey

Archetypal analysis (AA) was originally proposed in 1994 by Adele Cutler and Leo Breiman as a computational procedure to extract the distinct aspects called archetypes in observations with each observational record approximated as a mixture (i.e., convex combination) of these archetypes. AA thereby provides straightforward, interpretable, and explainable representations for feature extraction and dimensionality reduction, facilitating the understanding of the structure of high-dimensional data with wide applications throughout the sciences. However, AA also faces challenges, particularly as the associated optimization problem is non-convex. This survey provides researchers and data mining practitioners an overview of methodologies and opportunities that AA has to offer surveying the many applications of AA across disparate fields of science, as well as best practices for modeling data using AA and limitations. The survey concludes by explaining important future research directions concerning AA.
Towards Interpretable Deep Generative Models via Causal Representation Learning
Authors: Gemma E. Moran, Bryon Aragam
Date: 2025-04-15 00:00:00
Tasks: Representation Learning

Recent developments in generative artificial intelligence (AI) rely on machine learning techniques such as deep learning and generative modeling to achieve state-of-the-art performance across wide-ranging domains. These methods' surprising performance is due in part to their ability to learn implicit "representations'' of complex, multi-modal data. Unfortunately, deep neural networks are notoriously black boxes that obscure these representations, making them difficult to interpret or analyze. To resolve these difficulties, one approach is to build new interpretable neural network models from the ground up. This is the goal of the emerging field of causal representation learning (CRL) that uses causality as a vector for building flexible, interpretable, and transferable generative AI. CRL can be seen as a culmination of three intrinsically statistical problems: (i) latent variable models such as factor analysis; (ii) causal graphical models with latent variables; and (iii) nonparametric statistics and deep learning. This paper reviews recent progress in CRL from a statistical perspective, focusing on connections to classical models and statistical and causal identifiablity results. This review also highlights key application areas, implementation strategies, and open statistical questions in CRL.
Learning Optimal Prompt Ensemble for Multi-source Visual Prompt Transfer
Authors: Enming Zhang, Liwen Cao, Yanru Wu, Zijie Zhao, Guan Wang, Yang Li
Date: 2025-04-09 00:00:00
Tasks: Transfer Learning

Prompt tuning has emerged as a lightweight adaptation strategy for adapting foundation models to downstream tasks, particularly in resource-constrained systems. As pre-trained prompts have become valuable intellectual assets, combining multiple source prompts offers a promising approach to enhance generalization to new tasks by leveraging complementary knowledge from diverse sources. However, naive aggregation of these prompts often leads to representation collapse due to mutual interference, undermining their collective potential. To address these challenges, we propose HGPrompt, an adaptive framework for multi-source prompt transfer that learns optimal ensemble weights by jointly optimizing dual objectives: transferability and stability. Specifically, we first introduce an information-theoretic metric to evaluate the transferability of prompt-induced features on the target task, capturing the intrinsic alignment between the feature representations. Additionally, we propose a novel Gradient Alignment Regularization to mitigate gradient conflicts among prompts, enabling stable and coherent knowledge transfer from multiple sources while suppressing interference. Extensive experiments on the large-scale VTAB benchmark demonstrate that HGPrompt achieves state-of-the-art performance, validating its effectiveness in multi-source prompt transfer.
Socrates or Smartypants: Testing Logic Reasoning Capabilities of Large Language Models with Logic Programming-based Test Oracles
Authors: Zihao Xu, Junchen Ding, Yiling Lou, Kun Zhang, Dong Gong, Yuekang Li
Date: 2025-04-09 00:00:00
Tasks: Logical Fallacies, Logical Reasoning

Large Language Models (LLMs) have achieved significant progress in language understanding and reasoning. Evaluating and analyzing their logical reasoning abilities has therefore become essential. However, existing datasets and benchmarks are often limited to overly simplistic, unnatural, or contextually constrained examples. In response to the growing demand, we introduce SmartyPat-Bench, a challenging, naturally expressed, and systematically labeled benchmark derived from real-world high-quality Reddit posts containing subtle logical fallacies. Unlike existing datasets and benchmarks, it provides more detailed annotations of logical fallacies and features more diverse data. To further scale up the study and address the limitations of manual data collection and labeling - such as fallacy-type imbalance and labor-intensive annotation - we introduce SmartyPat, an automated framework powered by logic programming-based oracles. SmartyPat utilizes Prolog rules to systematically generate logically fallacious statements, which are then refined into fluent natural-language sentences by LLMs, ensuring precise fallacy representation. Extensive evaluation demonstrates that SmartyPat produces fallacies comparable in subtlety and quality to human-generated content and significantly outperforms baseline methods. Finally, experiments reveal nuanced insights into LLM capabilities, highlighting that while excessive reasoning steps hinder fallacy detection accuracy, structured reasoning enhances fallacy categorization performance.
How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension
Authors: Hao Li, Liuzhenghao Lv, He Cao, Zijing Liu, Zhiyuan Yan, Yu Wang, Yonghong Tian, Yu Li, Li Yuan
Date: 2025-04-10 00:00:00
Tasks: Computational Efficiency, Decoder, Drug Design, Hallucination

Large language models are increasingly used in scientific domains, especially for molecular understanding and analysis. However, existing models are affected by hallucination issues, resulting in errors in drug design and utilization. In this paper, we first analyze the sources of hallucination in LLMs for molecular comprehension tasks, specifically the knowledge shortcut phenomenon observed in the PubChem dataset. To evaluate hallucination in molecular comprehension tasks with computational efficiency, we introduce \textbf{Mol-Hallu}, a novel free-form evaluation metric that quantifies the degree of hallucination based on the scientific entailment relationship between generated text and actual molecular properties. Utilizing the Mol-Hallu metric, we reassess and analyze the extent of hallucination in various LLMs performing molecular comprehension tasks. Furthermore, the Hallucination Reduction Post-processing stage~(HRPP) is proposed to alleviate molecular hallucinations, Experiments show the effectiveness of HRPP on decoder-only and encoder-decoder molecular LLMs. Our findings provide critical insights into mitigating hallucination and improving the reliability of LLMs in scientific applications.
Capybara-OMNI: An Efficient Paradigm for Building Omni-Modal Language Models
Authors: Xingguang Ji, Jiakang Wang, Hongzhi Zhang, Jingyuan Zhang, Haonan Zhou, Chenxi Sun, Yahui Liu, Qi Wang, Fuzheng Zhang
Date: 2025-04-10 00:00:00
Tasks: Instruction Following

With the development of Multimodal Large Language Models (MLLMs), numerous outstanding accomplishments have emerged within the open-source community. Due to the complexity of creating and training multimodal data pairs, it is still a computational and time-consuming process to build powerful MLLMs. In this work, we introduce Capybara-OMNI, an MLLM that trains in a lightweight and efficient manner and supports understanding text, image, video, and audio modalities. We present in detail the framework design, the data construction, and the training recipe, to develop an MLLM step-by-step to obtain competitive performance. We also provide exclusive benchmarks utilized in our experiments to show how to properly verify understanding capabilities across different modalities. Results show that by following our guidance, we can efficiently build an MLLM that achieves competitive performance among models of the same scale on various multimodal benchmarks. Additionally, to enhance the multimodal instruction following and conversational capabilities of the model, we further discuss how to train the chat version upon an MLLM understanding model, which is more in line with user habits for tasks like real-time interaction with humans. We publicly disclose the Capybara-OMNI model, along with its chat-based version. The disclosure includes both the model weights, a portion of the training data, and the inference codes, which are made available on GitHub.
Data Metabolism: An Efficient Data Design Schema For Vision Language Model
Authors: Jingyuan Zhang, Hongzhi Zhang, Zhou Haonan, Chenxi Sun, Xingguang Ji, Jiakang Wang, Fanheng Kong, Yahui Liu, Qi Wang, Fuzheng Zhang
Date: 2025-04-10 00:00:00
Tasks: Language Modeling, Language Modelling, Question Answering, Visual Question Answering

Data curation plays a crucial role in training powerful Visual Language Models (VLMs). In this work, we introduce the concept of Data Metabolism and present our data-centric framework to build VLMs throughout the development lifecycle. Starting from a standard model architecture, we discuss and provide insights into two crucial development steps: data curation and iteration, forming a closed-loop system that continuously improves model performance. We show a detailed codebook on how to process existing massive datasets and build user-specific data flywheel. As a demonstration, we release a VLM, named Capybara-VL, which excels in typical multimodal tasks (e.g. , visual question answering, scientific reasoning, and text-rich tasks). Despite its relatively compact size, Capybara-VL surpasses several open-source models that are up to 10 times larger in size. Moreover, it achieves results that are on par with those of several leading proprietary models, demonstrating its remarkable competitiveness. These results highlight the power of our data-centric framework and the potential of training smaller and more efficient VLMs.
ChatGPT as Linguistic Equalizer? Quantifying LLM-Driven Lexical Shifts in Academic Writing
Authors: Dingkang Lin, Naixuan Zhao, Dan Tian, Jiang Li
Date: 2025-04-10 00:00:00
Tasks: Articles, Diversity

The advent of ChatGPT has profoundly reshaped scientific research practices, particularly in academic writing, where non-native English-speakers (NNES) historically face linguistic barriers. This study investigates whether ChatGPT mitigates these barriers and fosters equity by analyzing lexical complexity shifts across 2.8 million articles from OpenAlex (2020-2024). Using the Measure of Textual Lexical Diversity (MTLD) to quantify vocabulary sophistication and a difference-in-differences (DID) design to identify causal effects, we demonstrate that ChatGPT significantly enhances lexical complexity in NNES-authored abstracts, even after controlling for article-level controls, authorship patterns, and venue norms. Notably, the impact is most pronounced in preprint papers, technology- and biology-related fields and lower-tier journals. These findings provide causal evidence that ChatGPT reduces linguistic disparities and promotes equity in global academia.
AttentionDefense: Leveraging System Prompt Attention for Explainable Defense Against Novel Jailbreaks
Authors: Charlotte Siska, Anush Sankaran
Date: 2025-04-10 00:00:00

In the past few years, Language Models (LMs) have shown par-human capabilities in several domains. Despite their practical applications and exceeding user consumption, they are susceptible to jailbreaks when malicious input exploits the LM's weaknesses, causing it to deviate from its intended behavior. Current defensive strategies either classify the input prompt as adversarial or prevent LMs from generating harmful outputs. However, it is challenging to explain the reason behind the malicious nature of the jailbreak, which results in a wide variety of closed-box approaches. In this research, we propose and demonstrate that system-prompt attention from Small Language Models (SLMs) can be used to characterize adversarial prompts, providing a novel, explainable, and cheaper defense approach called AttentionDefense. Our research suggests that the attention mechanism is an integral component in understanding and explaining how LMs respond to malicious input that is not captured in the semantic meaning of text embeddings. The proposed AttentionDefense is evaluated against existing jailbreak benchmark datasets. Ablation studies show that SLM-based AttentionDefense has equivalent or better jailbreak detection performance compared to text embedding-based classifiers and GPT-4 zero-shot detectors.To further validate the efficacy of the proposed approach, we generate a dataset of novel jailbreak variants of the existing benchmark dataset using a closed-loop LLM-based multi-agent system. We demonstrate that the proposed AttentionDefense approach performs robustly on this novel jailbreak dataset while existing approaches suffer in performance. Additionally, for practical purposes AttentionDefense is an ideal solution as it has the computation requirements of a small LM but the performance of a LLM detector.
A Strategic Coordination Framework of Small LLMs Matches Large LLMs in Data Synthesis
Authors: Xin Gao, Qizhi Pei, Zinan Tang, Yu Li, Honglin Lin, Jiang Wu, Lijun Wu, Conghui He
Date: 2025-04-11 00:00:00

While data synthesis and distillation are promising strategies to enhance small language models, current approaches heavily rely on Large Language Models (LLMs), which suffer from high computational costs, environmental inefficiency, and potential biases inherited from monolithic architectures. In contrast, smaller LLMs are more accessible and sustainable, but their individual capabilities often fall short in generating high-quality, diverse, and reliable data. Inspired by collaborative human processes (e.g., peer review), we propose a multiple small LLMs involved framework, GRA, that aggregates specialized roles across small LLMs to iterative refinement and quality control typically achieved by a single large LLM. In this collaborative framework, multiple small LLMs assume distinct roles-Generator, Reviewer, and Adjudicator-to simulate a peer-review-inspired data synthesis pipeline. The Generator proposes initial data samples, the Reviewer critiques their quality and diversity, and the Adjudicator resolves conflicts to finalize the output. By decomposing the synthesis process into specialized sub-tasks, collaborative small LLMs can achieve data-level parity with large LLM-based distillation. Through experiments across multiple benchmarks, we demonstrate that GRA-produced data matches or exceeds the quality of single large LLM outputs, e.g., Qwen-2.5-72B-Instruct. Our results challenge the necessity of monolithic large models for high-quality data synthesis, advocating instead for strategic coordination of smaller agents. Our datasets, models, and code are publicly available at https://github.com/GX-XinGao/GRA.
The Other Side of the Coin: Exploring Fairness in Retrieval-Augmented Generation
Authors: Zheng Zhang, Ning li, Qi Liu, Rui Li, Weibo Gao, Qingyang Mao, Zhenya Huang, Baosheng Yu, DaCheng Tao
Date: 2025-04-11 00:00:00
Tasks: Fairness, Hallucination, RAG, Retrieval, Retrieval-augmented Generation

Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by retrieving relevant document from external knowledge sources. By referencing this external knowledge, RAG effectively reduces the generation of factually incorrect content and addresses hallucination issues within LLMs. Recently, there has been growing attention to improving the performance and efficiency of RAG systems from various perspectives. While these advancements have yielded significant results, the application of RAG in domains with considerable societal implications raises a critical question about fairness: What impact does the introduction of the RAG paradigm have on the fairness of LLMs? To address this question, we conduct extensive experiments by varying the LLMs, retrievers, and retrieval sources. Our experimental analysis reveals that the scale of the LLMs plays a significant role in influencing fairness outcomes within the RAG framework. When the model scale is smaller than 8B, the integration of retrieval mechanisms often exacerbates unfairness in small-scale LLMs (e.g., LLaMA3.2-1B, Mistral-7B, and LLaMA3-8B). To mitigate the fairness issues introduced by RAG for small-scale LLMs, we propose two approaches, FairFT and FairFilter. Specifically, in FairFT, we align the retriever with the LLM in terms of fairness, enabling it to retrieve documents that facilitate fairer model outputs. In FairFilter, we propose a fairness filtering mechanism to filter out biased content after retrieval. Finally, we validate our proposed approaches on real-world datasets, demonstrating their effectiveness in improving fairness while maintaining performance.