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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

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA…

Machine Learning · Computer Science 2016-10-20 Jack Lanchantin , Ritambhara Singh , Beilun Wang , Yanjun Qi

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

With the advent of highly predictive but opaque deep learning models, it has become more important than ever to understand and explain the predictions of such models. Existing approaches define interpretability as the inverse of complexity…

Decision forests are widely used for classification and regression tasks. A lesser known property of tree-based methods is that one can construct a proximity matrix from the tree(s), and these proximity matrices are induced kernels. While…

Machine Learning · Statistics 2024-10-14 Sambit Panda , Cencheng Shen , Joshua T. Vogelstein

Decision trees are ubiquitous in machine learning for their ease of use and interpretability. Yet, these models are not typically employed in reinforcement learning as they cannot be updated online via stochastic gradient descent. We…

Machine Learning · Computer Science 2020-06-29 Andrew Silva , Taylor Killian , Ivan Dario Jimenez Rodriguez , Sung-Hyun Son , Matthew Gombolay

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

Recent years have witnessed the breakthrough success of deep convolutional neural networks (DCNNs) in image classification and other vision applications. Although freeing users from the troublesome handcrafted feature extraction by…

Computer Vision and Pattern Recognition · Computer Science 2018-07-03 Benteng Ma , Yong Xia

Dense retrievers have demonstrated significant potential for neural information retrieval; however, they exhibit a lack of robustness to domain shifts, thereby limiting their efficacy in zero-shot settings across diverse domains. Previous…

Information Retrieval · Computer Science 2025-01-27 Goksenin Yuksel , Jaap Kamps

The recent advances in deep learning predominantly construct models in their internal representations, and it is opaque to explain the rationale behind and decisions to human users. Such explainability is especially essential for domain…

Computer Vision and Pattern Recognition · Computer Science 2022-11-16 Yiheng Zhang , Ting Yao , Zhaofan Qiu , Tao Mei

The success of recent deep convolutional neural networks (CNNs) depends on learning hidden representations that can summarize the important factors of variation behind the data. However, CNNs often criticized as being black boxes that lack…

Computer Vision and Pattern Recognition · Computer Science 2018-06-27 Bolei Zhou , David Bau , Aude Oliva , Antonio Torralba

Deep learning continues to revolutionize an ever-growing number of critical application areas including healthcare, transportation, finance, and basic sciences. Despite their increased predictive power, model transparency and human…

Machine Learning · Computer Science 2020-04-28 Benjamin Shickel , Parisa Rashidi

Trustworthy Artificial Intelligence solutions are essential in today's data-driven applications, prioritizing principles such as robustness, safety, transparency, explainability, and privacy among others. This has led to the emergence of…

Machine Learning · Computer Science 2024-04-04 Alberto Argente-Garrido , Cristina Zuheros , M. Victoria Luzón , Francisco Herrera

Deep learning is currently playing a crucial role toward higher levels of artificial intelligence. This paradigm allows neural networks to learn complex and abstract representations, that are progressively obtained by combining simpler…

Audio and Speech Processing · Electrical Eng. & Systems 2019-08-12 Mirco Ravanelli , Yoshua Bengio

Interpretable Graph Neural Networks (GNNs) aim to reveal the underlying reasoning behind model predictions, attributing their decisions to specific subgraphs that are informative. However, existing subgraph-based interpretable methods…

Machine Learning · Computer Science 2025-05-02 Jie Yang , Yuwen Wang , Kaixuan Chen , Tongya Zheng , Yihe Zhou , Zhenbang Xiao , Ji Cao , Mingli Song , Shunyu Liu

The interpretation of reasoning by Deep Neural Networks (DNN) is still challenging due to their perceived black-box nature. Therefore, deploying DNNs in several real-world tasks is restricted by the lack of transparency of these models. We…

Computer Vision and Pattern Recognition · Computer Science 2024-03-12 Maddimsetti Srinivas , Debdoot Sheet

A variety of methods have been proposed for interpreting nodes in deep neural networks, which typically involve scoring nodes at lower layers with respect to their effects on the output of higher-layer nodes (where lower and higher layers…

Machine Learning · Computer Science 2018-12-04 Jonathan Warrell , Hussein Mohsen , Mark Gerstein

Deep neural networks (DNNs) and decision trees (DTs) are both state-of-the-art classifiers. DNNs perform well due to their representational learning capabilities, while DTs are computationally efficient as they perform inference along one…

Computer Vision and Pattern Recognition · Computer Science 2022-11-22 Noam Gottlieb , Michael Werman

Interpretability and effectiveness are two essential and indispensable requirements for adopting machine learning methods in reality. In this paper, we propose a knowledge distillation based decision trees extension, dubbed rectified…

Machine Learning · Computer Science 2020-08-24 Yiming Li , Jiawang Bai , Jiawei Li , Xue Yang , Yong Jiang , Shu-Tao Xia

Recent research towards understanding neural networks probes models in a top-down manner, but is only able to identify model tendencies that are known a priori. We propose Susceptibility Identification through Fine-Tuning (SIFT), a novel…

Computation and Language · Computer Science 2019-09-11 Jonas Pfeiffer , Aishwarya Kamath , Iryna Gurevych , Sebastian Ruder