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Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…

Computational Engineering, Finance, and Science · Computer Science 2012-05-10 Khalid Raza , Rafat Parveen

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

Machine Learning · Computer Science 2023-10-17 Adam Winnifrith , Carlos Outeiral , Brian Hie

This paper proposes a generic method to learn interpretable convolutional filters in a deep convolutional neural network (CNN) for object classification, where each interpretable filter encodes features of a specific object part. Our method…

Machine Learning · Computer Science 2020-03-13 Quanshi Zhang , Xin Wang , Ying Nian Wu , Huilin Zhou , Song-Chun Zhu

Despite their increasing popularity and success in a variety of supervised learning problems, deep neural networks are extremely hard to interpret and debug: Given and already trained Deep Neural Net, and a set of test inputs, how can we…

Machine Learning · Computer Science 2018-06-07 Uday Singh Saini , Evangelos E. Papalexakis

Mechanistic interpretability aims to reverse engineer the computation performed by a neural network in terms of its internal components. Although there is a growing body of research on mechanistic interpretation of neural networks, the…

Machine Learning · Computer Science 2025-06-24 Nils Palumbo , Ravi Mangal , Zifan Wang , Saranya Vijayakumar , Corina S. Pasareanu , Somesh Jha

This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed…

Machine Learning · Computer Science 2022-08-10 Yifei Wang , Shiyang Chen , Guobin Chen , Ethan Shurberg , Hang Liu , Pengyu Hong

To tackle interpretability in deep learning, we present a novel framework to jointly learn a predictive model and its associated interpretation model. The interpreter provides both local and global interpretability about the predictive…

Machine Learning · Computer Science 2022-02-24 Jayneel Parekh , Pavlo Mozharovskyi , Florence d'Alché-Buc

We consider the explanation problem of Graph Neural Networks (GNNs). Most existing GNN explanation methods identify the most important edges or nodes but fail to consider substructures, which are more important for graph data. The only…

Machine Learning · Computer Science 2023-02-28 Zhaoning Yu , Hongyang Gao

Decomposing a deep neural network's learned representations into interpretable features could greatly enhance its safety and reliability. To better understand features, we adopt a geometric perspective, viewing them as a learned coordinate…

Machine Learning · Computer Science 2025-04-30 Aryeh Brill

Alterations in the geometry and function of the heart define well-established causes of cardiovascular disease. However, current approaches to the diagnosis of cardiovascular diseases often rely on subjective human assessment as well as…

Computer Vision and Pattern Recognition · Computer Science 2018-07-19 Carlo Biffi , Ozan Oktay , Giacomo Tarroni , Wenjia Bai , Antonio De Marvao , Georgia Doumou , Martin Rajchl , Reem Bedair , Sanjay Prasad , Stuart Cook , Declan O'Regan , Daniel Rueckert

Deep learning and convolutional neural networks in particular are powerful and promising tools for cosmological analysis of large-scale structure surveys. They are already providing similar performance to classical analysis methods using…

Cosmology and Nongalactic Astrophysics · Physics 2026-05-06 Gaspard Aymerich , Tomasz Kacprzak , Alexandre Refregier

Mechanistic interpretability is an emerging diagnostic approach for neural models that has gained traction in broader natural language processing domains. This paradigm aims to provide attribution to components of neural systems where…

Information Retrieval · Computer Science 2025-01-20 Andrew Parry , Catherine Chen , Carsten Eickhoff , Sean MacAvaney

Network science can offer fundamental insights into the structural and functional properties of complex systems. For example, it is widely known that neuronal circuits tend to organize into basic functional topological modules, called…

Adaptation and Self-Organizing Systems · Physics 2022-08-03 Matteo Zambra , Alberto Testolin , Amos Maritan

Deep neural networks (DNNs) with high expressiveness have achieved state-of-the-art performance in many tasks. However, their distributed feature representations are difficult to interpret semantically. In this work, human-interpretable…

Computer Vision and Pattern Recognition · Computer Science 2019-10-22 Jindong Gu , Volker Tresp

Despite their impact on the society, deep neural networks are often regarded as black-box models due to their intricate structures and the absence of explanations for their decisions. This opacity poses a significant challenge to AI systems…

Machine Learning · Computer Science 2024-07-18 Biagio La Rosa

Model interpretability is a requirement in many applications in which crucial decisions are made by users relying on a model's outputs. The recent movement for "algorithmic fairness" also stipulates explainability, and therefore…

Machine Learning · Computer Science 2018-08-21 Xuan Liu , Xiaoguang Wang , Stan Matwin

Interpreting complex neural networks is crucial for understanding their decision-making processes, particularly in applications where transparency and accountability are essential. This proposed method addresses this need by focusing on…

Neural and Evolutionary Computing · Computer Science 2024-12-10 Deepshikha Bhati , Fnu Neha , Md Amiruzzaman , Angela Guercio , Deepak Kumar Shukla , Ben Ward

Can Machine Learning (ML) autonomously recover interpretable mathematical structure from raw numerical data? We aim to answer this question using the classification of real-root configurations of polynomials up to degree five as a…

Numerical Analysis · Mathematics 2026-03-02 Rohan Thomas , Majid Bani-Yaghoub

Despite the recent success of neural network models in mimicking animal performance on visual perceptual tasks, critics worry that these models fail to illuminate brain function. We take it that a central approach to explanation in systems…

Neurons and Cognition · Quantitative Biology 2021-04-13 Rosa Cao , Daniel Yamins

There is a growing concern about typically opaque decision-making with high-performance machine learning algorithms. Providing an explanation of the reasoning process in domain-specific terms can be crucial for adoption in risk-sensitive…

Computer Vision and Pattern Recognition · Computer Science 2022-11-28 Aditya Chattopadhyay , Stewart Slocum , Benjamin D. Haeffele , Rene Vidal , Donald Geman
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