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We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers three key benefits: i) Control: We can…

Learning-based surrogate models have become a practical alternative to high-fidelity CFD solvers, but their latent representations remain opaque and hinder adoption in safety-critical or regulation-bound settings. This work introduces a…

Computational Engineering, Finance, and Science · Computer Science 2025-07-23 Yeping Hu , Shusen Liu

Artificial intelligence (AI) is transforming scientific research, with explainable AI methods like concept-based models (CMs) showing promise for new discoveries. However, in molecular science, CMs are less common than black-box models like…

Artificial Intelligence · Computer Science 2024-12-17 Zimin Zhang , Qianli Wu , Botao Xia , Fang Sun , Ziniu Hu , Yizhou Sun , Shichang Zhang

We propose an automated genomic interpretation module that transforms raw DNA sequences into actionable, interpretable decisions suitable for integration into medical automation and robotic systems. Our framework combines Chaos Game…

Computer Vision and Pattern Recognition · Computer Science 2026-03-17 Zijun Li , Jinchang Zhang , Ming Zhang , Guoyu Lu

Concept Bottleneck Models (CBMs) map dense feature representations into human-interpretable concepts which are then combined linearly to make a prediction. However, modern CBMs rely on the CLIP model to obtain image-concept annotations, and…

Computer Vision and Pattern Recognition · Computer Science 2026-02-27 Fawaz Sammani , Jonas Fischer , Nikos Deligiannis

With the ever-increasing use of complex machine learning models in critical applications within the finance domain, explaining the decisions of the model has become a necessity. With applications spanning from credit scoring to credit…

Machine Learning · Computer Science 2020-09-14 Aditya Lahiri , Narayanan Unny Edakunni

Concept Bottleneck Models (CBM) map images to human-interpretable concepts before making class predictions. Recent approaches automate CBM construction by prompting Large Language Models (LLMs) to generate text concepts and employing Vision…

Computer Vision and Pattern Recognition · Computer Science 2024-08-27 Nithish Muthuchamy Selvaraj , Xiaobao Guo , Adams Wai-Kin Kong , Alex Kot

Local surrogate approaches for explaining machine learning model predictions have appealing properties, such as being model-agnostic and flexible in their modelling. Several methods exist that fit this description and share this goal.…

Machine Learning · Computer Science 2021-06-11 Rafael Poyiadzi , Xavier Renard , Thibault Laugel , Raul Santos-Rodriguez , Marcin Detyniecki

Recent breakthroughs in artificial intelligence (AI) are reshaping the way we construct computational counterparts of the brain, giving rise to a new class of ``surrogate brains''. In contrast to conventional hypothesis-driven biophysical…

Neurons and Cognition · Quantitative Biology 2025-10-14 Yinuo Zhang , Demao Liu , Zhichao Liang , Jiani Cheng , Kexin Lou , Jinqiao Duan , Ting Gao , Bin Hu , Quanying Liu

Deep learning models have achieved strong performance in medical image analysis, but their internal decision processes remain difficult to interpret. Concept Bottleneck Models (CBMs) partially address this limitation by structuring…

Computer Vision and Pattern Recognition · Computer Science 2026-03-24 Getamesay Dagnaw , Xuefei Yin , Muhammad Hassan Maqsood , Yanming Zhu , Alan Wee-Chung Liew

Rising usage of deep neural networks to perform decision making in critical applications like medical diagnosis and financial analysis have raised concerns regarding their reliability and trustworthiness. As automated systems become more…

Machine Learning · Computer Science 2022-11-30 Sanchit Sinha , Mengdi Huai , Jianhui Sun , Aidong Zhang

Despite the success of deep learning in dermoscopy image analysis, its inherent black-box nature hinders clinical trust, motivating the use of prototypical networks for case-based visual transparency. However, inevitable selection bias in…

Image and Video Processing · Electrical Eng. & Systems 2026-03-02 Junhao Jia , Yueyi Wu , Huangwei Chen , Haodong Jing , Haishuai Wang , Jiajun Bu , Lei Wu

Surrogate models play a crucial role in retrospectively interpreting complex and powerful black box machine learning models via model distillation. This paper focuses on using model-based trees as surrogate models which partition the…

Machine Learning · Statistics 2023-10-06 Julia Herbinger , Susanne Dandl , Fiona K. Ewald , Sofia Loibl , Giuseppe Casalicchio

Extreme ocean phenomena are challenging not only to predict but to diagnose, as accurate forecasts alone do not reveal the underlying physical drivers. While recent machine learning approaches achieve strong predictive skill, they remain…

Machine Learning · Computer Science 2026-05-14 Sanah Suri , Kieran Ringel , Maike Sonnewald

This paper provides empirical concerns about post-hoc explanations of black-box ML models, one of the major trends in AI explainability (XAI), by showing its lack of interpretability and societal consequences. Using a representative…

Human-Computer Interaction · Computer Science 2021-10-01 Jean-Marie John-Mathews

Existing deep learning-based surrogate models facilitate efficient data generation, but fall short in uncertainty quantification, efficient parameter space exploration, and reverse prediction. In our work, we introduce SurroFlow, a novel…

Machine Learning · Computer Science 2024-07-19 Jingyi Shen , Yuhan Duan , Han-Wei Shen

Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…

Quantitative Methods · Quantitative Biology 2025-04-17 Kerri-Ann Norton , Daniel Bergman , Harsh Vardhan Jain , Trachette Jackson

Several explainable AI methods allow a Machine Learning user to get insights on the classification process of a black-box model in the form of local linear explanations. With such information, the user can judge which features are locally…

Machine Learning · Computer Science 2023-02-16 Francesco Lomuscio , Paolo Bajardi , Alan Perotti , Elvio G. Amparore

Meta-learning is a field that aims at discovering how different machine learning algorithms perform on a wide range of predictive tasks. Such knowledge speeds up the hyperparameter tuning or feature engineering. With the use of surrogate…

Machine Learning · Statistics 2021-07-13 Katarzyna Woźnica , Przemysław Biecek

Post-hoc explanation methods for black-box models often struggle with faithfulness and human interpretability due to the lack of explainability in current neural architectures. Meanwhile, B-cos networks have been introduced to improve model…

Computation and Language · Computer Science 2025-12-10 Yifan Wang , Sukrut Rao , Ji-Ung Lee , Mayank Jobanputra , Vera Demberg