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Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and…

Quantitative Methods · Quantitative Biology 2025-10-24 Tien Comlekoglu , J. Quetzalcoatl Toledo-Marín , Douglas W. DeSimone , Shayn M. Peirce , Geoffrey Fox , James A. Glazier

The artificial neural network shows powerful ability of inference, but it is still criticized for lack of interpretability and prerequisite needs of big dataset. This paper proposes the Rule-embedded Neural Network (ReNN) to overcome the…

Machine Learning · Computer Science 2018-09-03 Hu Wang

The nondeterminism of Deep Learning (DL) training algorithms and its influence on the explainability of neural network (NN) models are investigated in this work with the help of image classification examples. To discuss the issue, two…

Machine Learning · Computer Science 2022-03-03 A. -M. Leventi-Peetz , T. Östreich

Objective: To automatically create large labeled training datasets and reduce the efforts of feature engineering for training accurate machine learning models for clinical information extraction. Materials and Methods: We propose a distant…

Information Retrieval · Computer Science 2018-04-24 Yanshan Wang , Sunghwan Sohn , Sijia Liu , Feichen Shen , Liwei Wang , Elizabeth J. Atkinson , Shreyasee Amin , Hongfang Liu

The estimation of unknown values of parameters (or hidden variables, control variables) that characterise a physical system often relies on the comparison of measured data with synthetic data produced by some numerical simulator of the…

Machine Learning · Computer Science 2019-01-28 Xi Chen , Mike Hobson

The use of deep neural network (DNN) models as surrogates for linear and nonlinear structural dynamical systems is explored. The goal is to develop DNN based surrogates to predict structural response, i.e., displacements and accelerations,…

Machine Learning · Computer Science 2021-11-05 Nan Feng , Guodong Zhang , Kapil Khandelwal

We propose a novel model-level GNN explanation framework that shifts the explanation target from class-wise rule extraction to rule-based logit reconstruction. Our method recasts the graph-level readout of a pretrained GNN as a weighted…

Machine Learning · Computer Science 2026-05-13 Shengyao Lu , Jiuding Yang , Aedan J. DeFrates , Keith G. Mills , Baochun Li , Di Niu

Deep convolutional neural networks (DCNN) have enjoyed great successes in many signal processing applications because they can learn complex, non-linear causal relationships from input to output. In this light, DCNNs are well suited for the…

Image and Video Processing · Electrical Eng. & Systems 2018-10-31 Xi Zhang , Xiaolin Wu

Numerical simulation of multi-phase fluid dynamics in porous media is critical for many energy and environmental applications in Earth's subsurface. Data-driven surrogate modeling provides computationally inexpensive alternatives to…

Computational Physics · Physics 2024-04-16 Jiamin Jiang , Bo Guo

While machine learning techniques have been successfully applied in several fields, the black-box nature of the models presents challenges for interpreting and explaining the results. We develop a new framework called Adaptive Explainable…

Machine Learning · Statistics 2020-06-03 Jie Chen , Joel Vaughan , Vijayan N. Nair , Agus Sudjianto

The ubiquity of fluids in the physical world explains the need to accurately simulate their dynamics for many scientific and engineering applications. Traditionally, well established but resource intensive CFD solvers provide such…

Machine Learning · Computer Science 2021-12-21 Lucas Meyer , Louen Pottier , Alejandro Ribes , Bruno Raffin

We introduce Discovering Conceptual Network Explanations (DCNE), a new approach for generating human-comprehensible visual explanations to enhance the interpretability of deep neural image classifiers. Our method automatically finds visual…

Computer Vision and Pattern Recognition · Computer Science 2024-07-09 Neehar Kondapaneni , Markus Marks , Oisin Mac Aodha , Pietro Perona

Differential Diagnosis (DDx) is the process of identifying the most likely medical condition among the possible pathologies through the process of elimination based on evidence. An automated process that narrows a large set of pathologies…

Machine Learning · Computer Science 2023-12-05 Mohammad Mahmudul Alam , Edward Raff , Tim Oates , Cynthia Matuszek

Interpretability of deep neural networks (DNNs) is essential since it enables users to understand the overall strengths and weaknesses of the models, conveys an understanding of how the models will behave in the future, and how to diagnose…

Computer Vision and Pattern Recognition · Computer Science 2017-03-31 Yinpeng Dong , Hang Su , Jun Zhu , Bo Zhang

This paper investigates lung nodule classification by using deep neural networks (DNNs). Hyperparameter optimization in DNNs is a computationally expensive problem, where evaluating a hyperparameter configuration may take several hours or…

Machine Learning · Computer Science 2019-01-03 Miao Zhang , Huiqi Li , Juan Lyu , Sai Ho Ling , Steven Su

While machine-learning models are flourishing and transforming many aspects of everyday life, the inability of humans to understand complex models poses difficulties for these models to be fully trusted and embraced. Thus, interpretability…

Artificial Intelligence · Computer Science 2020-06-18 Guangyi Zhang , Aristides Gionis

Deep Generative Models (DGMs) have been shown to be powerful tools for generating tabular data, as they have been increasingly able to capture the complex distributions that characterize them. However, to generate realistic synthetic data,…

Machine Learning · Computer Science 2024-02-08 Mihaela Cătălina Stoian , Salijona Dyrmishi , Maxime Cordy , Thomas Lukasiewicz , Eleonora Giunchiglia

Numerically solving a large parametric nonlinear dynamical system is challenging due to its high complexity and the high computational costs. In recent years, machine-learning-aided surrogates are being actively researched. However, many…

Machine Learning · Computer Science 2024-10-18 Shuwen Sun , Lihong Feng , Peter Benner

Deep learning models are increasingly deployed in safety-critical tasks where predictions must satisfy hard constraints, such as physical laws, fairness requirements, or safety limits. However, standard architectures lack built-in…

Machine Learning · Computer Science 2025-11-26 Gonzalo E. Constante-Flores , Hao Chen , Can Li

We propose a deep learning-based surrogate model for stochastic simulators. The basic idea is to use generative neural network to approximate the stochastic response. The challenge with such a framework resides in designing the network…

Machine Learning · Computer Science 2021-10-27 Akshay Thakur , Souvik Chakraborty