Codes and supplementary materials for our paper "Explainable AI for Bioinformatics: Importance, Methods, Tools, and Applications", submitted to Briefings in Bioinformatics journal. This repo will be updated periodically.
We provided several interactive Jupyter notebooks showing how interpretable ML techniques can be used to improve the interpretability for bioinformatics research use cases. Please note that some notebooks don't accompany the datasets, mainly due to NDA agreements.
We categorize the papers and books based on interpretable ML methods
- A Guide for Making Black Box Models Explainable. Molnar 2019 pdf
- A Survey on Explainable Artificial Intelligence (XAI): Toward Medical XAI. Tjao et al. 2020 pdf
- Opportunities and Challenges in Explainable Artificial Intelligence (XAI): A Survey. Das et al. 2020 pdf
- Interpretable machine learning: definitions, methods, and applications. Murdoch et al. 2019 pdf
- A brief survey of visualization methods for deep learning models from the perspective of Explainable AI. Chalkiadakis 2018 pdf
- A Survey Of Methods For Explaining Black Box Models. Guidotti et al. 2018 pdf
- Explaining Explanations: An Overview of Interpretability of Machine Learning. Gilpin et al. 2019 pdf
- Explainable Artificial Intelligence: a Systematic Review. Vilone at al. 2020 pdf
DTCAV: Automating Interpretability: Discovering and Testing Visual Concepts Learned by Neural Networks. Ghorbani et al. 2019 pdfAM: Visualizing higher-layer features of a deep network. Erhan et al. 2009 pdf- Deep inside convolutional networks: Visualising image classification models and saliency maps. Simonyan et al. 2013 pdf
DeepVis: Understanding Neural Networks through Deep Visualization. Yosinski et al. ICML workshop 2015 pdf- Visualizing and Understanding Recurrent Networks. Kaparthey et al. ICLR 2015 pdf
- Feature Removal Is A Unifying Principle For Model Explanation Methods. Covert et al. 2020 pdf
Gradient: Deep inside convolutional networks: Visualising image classification models and saliency maps. Simonyan et al. 2013 pdfGuided-backprop: Striving for simplicity: The all convolutional net. Springenberg et al. 2015 pdfSmoothGrad: removing noise by adding noise. Smilkov et al. 2017 pdfDeepLIFT: Learning important features through propagating activation differences. Shrikumar et al. 2017 pdfIG: Axiomatic Attribution for Deep Networks. Sundararajan et al. 2018 pdfEG: Learning Explainable Models Using Attribution Priors. Erion et al. 2019 pdfLRP: Beyond saliency: understanding convolutional neural networks from saliency prediction on layer-wise relevance propagation pdfDTD: Explaining NonLinear Classification Decisions With Deep Tayor Decomposition pdfCAM: Learning Deep Features for Discriminative Localization. Zhou et al. 2016 linkGrad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization. Selvaraju et al. 2017 pdfGrad-CAM++: Improved Visual Explanations for Deep Convolutional Networks. Chattopadhyay et al. 2017 pdfSmooth Grad-CAM++: An Enhanced Inference Level Visualization Technique for Deep Convolutional Neural Network Models. Omeiza et al. 2019 pdfNormGrad: There and Back Again: Revisiting Backpropagation Saliency Methods. Rebuffi et al. CVPR 2020 pdfScore-CAM: Score-Weighted Visual Explanations for Convolutional Neural Networks. Wang et al. CVPR 2020 workshop pdfRelevance-CAM: Your Model Already Knows Where to Look. Lee et al. CVPR 2021 pdfLIFT-CAM: Towards Better Explanations of Class Activation Mapping. Jung & Oh ICCV 2021 pdf.
- Generative causal explanations of black-box classifiers. O’Shaughnessy et al. 2020 pdf
- Removing input features via a generative model to explain their attributions to classifier's decisions. Agarwal et al. 2019 pdf
- Challenging common interpretability assumptions in feature attribution explanations? Dinu et al. NeurIPS workshop 2020 pdf
- The effectiveness of feature attribution methods and its correlation with automatic evaluation scores. Nguyen, Kim, Nguyen 2021 pdf
Deletion&Insertion: Randomized Input Sampling for Explanation of Black-box Models. Petsiuk et al. BMVC 2018 pdf- DiffROAR: Do Input Gradients Highlight Discriminative Features? Shah et al. NeurIPS 2021 pdf
RISE: Randomized Input Sampling for Explanation of Black-box Models. Petsiuk et al. BMVC 2018 pdfLIME: Why should i trust you?: Explaining the predictions of any classifier. Ribeiro et al. 2016 pdfLIME-G: Removing input features via a generative model to explain their attributions to classifier's decisions. Agarwal & Nguyen. ACCV 2020 pdfSHAP: A Unified Approach to Interpreting Model Predictions. Lundberg et al. 2017 pdfIM: Interpretation of NLP models through input marginalization. Kim et al. EMNLP 2020 pdf.
- Local Rule-based Explanations of Black Box Decision Systems. Guidotti et al. 2021 pdf
FIDO: Explaining image classifiers by counterfactual generation. Chang et al. ICLR 2019 pdfCEM: Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negatives. Dhurandhar & Chen et al. NeurIPS 2018 pdf- Counterfactual Explanations for Machine Learning: A Review. Verma et al. 2020 pdf
- Interpreting Neural Network Judgments via Minimal, Stable, and Symbolic Corrections. Zhang et al. 2018 pdf
- Counterfactual Visual Explanations. Goyal et al. 2019 pdf
- Generative Counterfactual Introspection for Explainable Deep Learning. Liu et al. 2019 pdf.
- ReasonChainQA: Text-based Complex Question Answering with Explainable Evidence Chains. Zhu et al. 2022 pdf
- Knowledge-graph-based explainable AI: A systematic review. Rajabi et al. 2022 link
- Knowledge-based XAI through CBR: There is more to explanations than models can tell. Weber et al. 2021 pdf
- The Role of Human Knowledge in Explainable AI. Tocchetti et al. 2022 link.
- Question-Driven Design Process for Explainable AI User Experiences Liao 2021 pdf
- Evaluating Explainable AI: Which Algorithmic Explanations Help Users Predict Model Behavior? Hase & Bansal ACL 2020 pdf
- Teach Me to Explain: A Review of Datasets for Explainable NLP. Wiegreffe & Marasović 2021 pdf
- Yang, S. C. H., & Shafto, P. Explainable Artificial Intelligence via Bayesian Teaching. NIPS 2017 pdf
- Explainable AI for Designers: A Human-Centered Perspective on Mixed-Initiative Co-Creation pdf
- ICADx: Interpretable computer aided diagnosis of breast masses. Kim et al. 2018 pdf
- Neural Network Interpretation via Fine Grained Textual Summarization. Guo et al. 2018 pdf
- LS-Tree: Model Interpretation When the Data Are Linguistic. Chen et al. 2019 pdf.
- Interpreting CNNs via Decision Trees pdf
- Distilling a Neural Network Into a Soft Decision Tree pdf
- Improving the Interpretability of Deep Neural Networks with Knowledge Distillation. Liu et al. 2018 pdf.
- Multimodal explanations: Justifying decisions and pointing to the evidence. Park et al. CVPR 2018 pdf
IA-RED2: Interpretability-Aware Redundancy Reduction for Vision Transformers. Pan et al. NeurIPS 2021 pdf- Transformer Interpretability Beyond Attention Visualization. Hila et al. CVPR 2021 pdf
Deletion_BERT: Double Trouble: How to not explain a text classifier’s decisions using counterfactuals synthesized by masked language models. Pham et al. 2022 pdf- Considering Likelihood in NLP Classification Explanations with Occlusion and Language Modeling. Harbecke et al. 2020 pdf.
DeepVis: Deep Visualization Toolbox. Yosinski et al. ICML 2015 codeSWAP: Generate adversarial poses of objects in a 3D space. Alcorn et al. CVPR 2019 codeAllenNLP: Query online NLP models with user-provided inputs and observe explanations (Gradient, Integrated Gradient, SmoothGrad). Last accessed 03/2020 demo3DB: A framework for analyzing computer vision models with simulated data code.
- CNN visualizations (feature visualization, PyTorch)
- iNNvestigate (attribution, Keras)
- DeepExplain (attribution, Keras)
- Lucid (feature visualization, attribution, Tensorflow)
- TorchRay (attribution, PyTorch)
- Captum (attribution, PyTorch)
- InterpretML (attribution, Python).
If you use the code of this repository in your research, please consider citing the folowing papers:
@article{karim_xai_bio_2022,
title={Explainable AI for Bioinformatics: Methods, Tools, and Applications},
author={Karim, Md Rezaul and Beyan, Oya and Zappa, Achille and Costa, Ivan G and Rebholz-Schuhmann, Dietrich and Cochez, Michael and Decker, Stefan},
journal={Briefings in bioinformatics},
volume={XXXX},
number={XXXX},
pages={XXXX},
year={2023},
publisher={Oxford University Press}
}
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