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While deep learning has achieved great success in many fields, one common criticism about deep learning is its lack of interpretability. In most cases, the hidden units in a deep neural network do not have a clear semantic meaning or…

Genomics · Quantitative Biology 2019-06-04 Tianle Ma , Aidong Zhang

This paper proposes an architecture for deep neural networks with hidden layer branches that learn targets of lower hierarchy than final layer targets. The branches provide a channel for enforcing useful information in hidden layer which…

Neural and Evolutionary Computing · Computer Science 2016-09-27 Abhinav Tushar

To understand how well a large language model captures certain semantic or syntactic features, researchers typically apply probing classifiers. However, the accuracy of these classifiers is critical for the correct interpretation of the…

Computation and Language · Computer Science 2023-12-19 Sergey A. Saltykov

Tree-like structures, such as blood vessels, often express complexity at very fine scales, requiring high-resolution grids to adequately describe their shape. Such sparse morphology can alternately be represented by locations of centreline…

Computer Vision and Pattern Recognition · Computer Science 2018-11-09 Kerry Halupka , Rahil Garnavi , Stephen Moore

Monumental advances in deep learning have led to unprecedented achievements across various domains. While the performance of deep neural networks is indubitable, the architectural design and interpretability of such models are nontrivial.…

Machine Learning · Computer Science 2023-07-06 Zachariah Carmichael , Tim Moon , Sam Ade Jacobs

Interpretable machine learning has emerged as central in leveraging artificial intelligence within high-stakes domains such as healthcare, where understanding the rationale behind model predictions is as critical as achieving high…

Machine Learning · Computer Science 2024-04-30 Christel Sirocchi , Martin Urschler , Bastian Pfeifer

The lack of interpretability remains a barrier to the adoption of deep neural networks. Recently, tree regularization has been proposed to encourage deep neural networks to resemble compact, axis-aligned decision trees without significant…

Machine Learning · Computer Science 2020-03-17 Mike Wu , Sonali Parbhoo , Michael Hughes , Ryan Kindle , Leo Celi , Maurizio Zazzi , Volker Roth , Finale Doshi-Velez

Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…

Genomics · Quantitative Biology 2024-10-10 Alex M. Tseng , Gokcen Eraslan , Tommaso Biancalani , Gabriele Scalia

We describe how hierarchical concepts can be represented in three types of layered neural networks. The aim is to support recognition of the concepts when partial information about the concepts is presented, and also when some of the…

Neural and Evolutionary Computing · Computer Science 2025-03-25 Nancy A. Lynch

The success of neural networks builds to a large extent on their ability to create internal knowledge representations from real-world high-dimensional data, such as images, sound, or text. Approaches to extract and present these…

Artificial Intelligence · Computer Science 2023-01-03 Lars Holmberg , Paul Davidsson , Per Linde

Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…

Data Analysis, Statistics and Probability · Physics 2021-01-04 Leonardo L. Portes , Michael Small

Deep learning-based AI models have been extensively applied in genomics, achieving remarkable success across diverse applications. As these models gain prominence, there exists an urgent need for interpretability methods to establish…

Genomics · Quantitative Biology 2025-05-16 Chenyu Wang , Chaoying Zuo , Zihan Su , Yuhang Xing , Lu Li , Maojun Wang , Zeyu Zhang

High-dimensional policies, such as those represented by neural networks, cannot be reasonably interpreted by humans. This lack of interpretability reduces the trust users have in policy behavior, limiting their use to low-impact tasks such…

Machine Learning · Computer Science 2021-09-20 John Mern , Sidhart Krishnan , Anil Yildiz , Kyle Hatch , Mykel J. Kochenderfer

Neural network models can now recognise images, understand text, translate languages, and play many human games at human or superhuman levels. These systems are highly abstracted, but are inspired by biological brains and use only…

Neurons and Cognition · Quantitative Biology 2019-03-06 Katherine R. Storrs , Nikolaus Kriegeskorte

In this work, we propose a simple but effective method to interpret black-box machine learning models globally. That is, we use a compact binary tree, the interpretation tree, to explicitly represent the most important decision rules that…

Machine Learning · Computer Science 2018-05-24 Chengliang Yang , Anand Rangarajan , Sanjay Ranka

Plant phenotyping is the assessment of a plant's traits and plant identification is the process of determining the category such as genus and species. In this paper we present an interpretable neural network trained on the UPWINS spectral…

Machine Learning · Computer Science 2024-07-16 William Basener , Abigail Basener , Michael Luegering

Artificial Neural Networks form the basis of very powerful learning methods. It has been observed that a naive application of fully connected neural networks to data with many irrelevant variables often leads to overfitting. In an attempt…

Machine Learning · Computer Science 2020-02-12 Gitesh Dawer , Yangzi Guo , Sida Liu , Adrian Barbu

Interpretability of machine learning is defined as the extent to which humans can comprehend the reason of a decision. However, a neural network is not considered interpretable due to the ambiguity in its decision-making process. Therefore,…

Machine Learning · Computer Science 2020-03-30 Yusuke Kubo , Yuto Komori , Toyonobu Okuyama , Hiroshi Tokieda

The thesis explores the role machine learning methods play in creating intuitive computational models of neural processing. Combined with interpretability techniques, machine learning could replace human modeler and shift the focus of human…

Neurons and Cognition · Quantitative Biology 2020-10-20 Ilya Kuzovkin

With the success of deep learning, recent efforts have been focused on analyzing how learned networks make their classifications. We are interested in analyzing the network output based on the network structure and information flow through…

Machine Learning · Computer Science 2018-02-13 Sandeep Konam , Ian Quah , Stephanie Rosenthal , Manuela Veloso