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Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a triennial, community-driven initiative that provides an…

Quantitative Methods · Quantitative Biology 2026-04-23 An Phan , Yanli Wang , Frimpong Boadu , Maxat Kulmanov , Robert Hoehndorf , Jianlin Cheng , Predrag Radivojac , Iddo Friedberg

With the pervasive deployment of Machine Learning (ML) models in real-world applications, verifying and auditing properties of ML models have become a central concern. In this work, we focus on three properties: robustness, individual…

Machine Learning · Computer Science 2024-10-11 Ayoub Ajarra , Bishwamittra Ghosh , Debabrota Basu

Affordance knowledge is a fundamental aspect of commonsense knowledge. Recent findings indicate that world knowledge emerges through large-scale self-supervised pretraining, motivating our exploration of acquiring affordance knowledge from…

Computation and Language · Computer Science 2023-12-19 Hsiu-Yu Yang , Carina Silberer

Biased data can lead to unfair machine learning models, highlighting the importance of embedding fairness at the beginning of data analysis, particularly during dataset curation and labeling. In response, we propose Falcon, a scalable fair…

Machine Learning · Computer Science 2024-01-25 Ki Hyun Tae , Hantian Zhang , Jaeyoung Park , Kexin Rong , Steven Euijong Whang

In this paper, we propose a novel Reinforcement Learning approach for solving the Active Information Acquisition problem, which requires an agent to choose a sequence of actions in order to acquire information about a process of interest…

Machine Learning · Computer Science 2019-10-25 Heejin Jeong , Brent Schlotfeldt , Hamed Hassani , Manfred Morari , Daniel D. Lee , George J. Pappas

Auto Feature Engineering (AFE) plays a crucial role in developing practical machine learning pipelines by automating the transformation of raw data into meaningful features that enhance model performance. By generating features in a…

Machine Learning · Statistics 2024-10-29 Tatsuya Matsukawa , Tomohiro Shiraishi , Shuichi Nishino , Teruyuki Katsuoka , Ichiro Takeuchi

Few-shot Continual Event Detection (FCED) poses the dual challenges of learning from limited data and mitigating catastrophic forgetting across sequential tasks. Existing approaches often suffer from severe forgetting due to the full…

Machine Learning · Computer Science 2025-09-30 Bao-Ngoc Dao , Quang Nguyen , Luyen Ngo Dinh , Minh Le , Linh Ngo Van

The costly human effort required to prepare the training data of machine learning (ML) models hinders their practical development and usage in software engineering (ML4Code), especially for those with limited budgets. Therefore, efficiently…

Software Engineering · Computer Science 2023-06-05 Qiang Hu , Yuejun Guo , Xiaofei Xie , Maxime Cordy , Lei Ma , Mike Papadakis , Yves Le Traon

We study the problem of feature selection in general machine learning (ML) context, which is one of the most critical subjects in the field. Although, there exist many feature selection methods, however, these methods face challenges such…

Machine Learning · Computer Science 2024-06-18 Mehmet Y. Turali , Mehmet E. Lorasdagi , Ali T. Koc , Suleyman S. Kozat

Deep learning models continue to advance in accuracy, yet they remain vulnerable to adversarial attacks, which often lead to the misclassification of adversarial examples. Adversarial training is used to mitigate this problem by increasing…

Computer Vision and Pattern Recognition · Computer Science 2024-02-20 Leo Hyun Park , Jaeuk Kim , Myung Gyo Oh , Jaewoo Park , Taekyoung Kwon

Federated learning is a decentralized and privacy-preserving technique that enables multiple clients to collaborate with a server to learn a global model without exposing their private data. However, the presence of statistical…

Machine Learning · Computer Science 2023-07-06 Shiyu Liu , Shaogao Lv , Dun Zeng , Zenglin Xu , Hui Wang , Yue Yu

The pursuit of fairness in machine learning (ML), ensuring that the models do not exhibit biases toward protected demographic groups, typically results in a compromise scenario. This compromise can be explained by a Pareto frontier where…

Machine Learning · Computer Science 2024-11-11 Jinlong Pang , Jialu Wang , Zhaowei Zhu , Yuanshun Yao , Chen Qian , Yang Liu

The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…

Genomics · Quantitative Biology 2024-06-06 Zicheng Liu , Jiahui Li , Siyuan Li , Zelin Zang , Cheng Tan , Yufei Huang , Yajing Bai , Stan Z. Li

It is not an exaggeration to say that the recent progress in artificial intelligence technology depends on large-scale and high-quality data. Simultaneously, a prevalent issue exists everywhere: the budget for data labeling is constrained.…

Machine Learning · Computer Science 2023-08-22 Yujin Hwang , Won Jo , Juyoung Hong , Yukyung Choi

Foundation models (FMs) are large neural networks trained on broad datasets, excelling in downstream tasks with minimal fine-tuning. Human activity recognition in video has advanced with FMs, driven by competition among different…

Computer Vision and Pattern Recognition · Computer Science 2024-07-23 Thinesh Thiyakesan Ponbagavathi , Kunyu Peng , Alina Roitberg

Facial affective behavior analysis (FABA) is crucial for understanding human mental states from images. However, traditional approaches primarily deploy models to discriminate among discrete emotion categories, and lack the fine granularity…

Computer Vision and Pattern Recognition · Computer Science 2024-07-15 Yifan Li , Anh Dao , Wentao Bao , Zhen Tan , Tianlong Chen , Huan Liu , Yu Kong

Entity Matching (EM) is a core data cleaning task, aiming to identify different mentions of the same real-world entity. Active learning is one way to address the challenge of scarce labeled data in practice, by dynamically collecting the…

Databases · Computer Science 2020-03-31 Venkata Vamsikrishna Meduri , Lucian Popa , Prithviraj Sen , Mohamed Sarwat

Varying annotation costs among data points and budget constraints can hinder the adoption of active learning strategies in real-world applications. This work introduces two Bayesian active learning strategies for batch acquisition under…

Machine Learning · Computer Science 2025-07-08 Pablo G. Morato , Charalampos P. Andriotis , Seyran Khademi

A critical yet frequently overlooked challenge in the field of deepfake detection is the lack of a standardized, unified, comprehensive benchmark. This issue leads to unfair performance comparisons and potentially misleading results.…

Computer Vision and Pattern Recognition · Computer Science 2023-10-31 Zhiyuan Yan , Yong Zhang , Xinhang Yuan , Siwei Lyu , Baoyuan Wu

In this paper, we present a new multi-branch neural network that simultaneously performs soft biometric (SB) prediction as an auxiliary modality and face recognition (FR) as the main task. Our proposed network named AAFace utilizes SB…

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