Glaucoma causes irreversible blindness. In 2020, about 80 million people worldwide had glaucoma. Existing machine learning (ML) models are limited to glaucoma prediction, where clinicians, patients, and medical experts are unaware of how data analysis and decision-making are handled. Explainable artificial intelligence (XAI) and interpretable ML (IML) create opportunities to increase user confidence in the decision-making process. This article proposes XAI and IML models for analyzing glaucoma predictions/results. XAI primarily uses adaptive neuro-fuzzy inference system (ANFIS) and pixel density analysis (PDA) to provide trustworthy explanations for glaucoma predictions from infected and healthy images. IML uses sub-modular pick local interpretable model-agonistic explanation (SP-LIME) to explain results coherently. SP-LIME interprets spike neural network (SNN) results. Using two different publicly available datasets, namely fundus images, i.e., coherence tomography images of the eyes and clinical medical records of glaucoma patients, our experimental results show that XAI and IML models provide convincing and coherent decisions for clinicians/medical experts and patients.

Explainable AI for Glaucoma Prediction Analysis to Understand Risk Factors in Treatment Planning

Natural disaster impact assessment is of the utmost significance for post-disaster recovery, environmental protection, and hazard mitigation plans. With their recent usage in landslide susceptibility mapping, deep learning (DL) architectures have proven their efficiency in many scientific studies. However, some restrictions, including insufficient model variance and limited generalization capabilities, have been reported in the literature. To overcome these restrictions, ensembling DL models has often been preferred as a practical solution. In this study, an ensemble DL architecture, based on shared blocks, was proposed to improve the prediction capability of individual DL models. For this purpose, three DL models, namely Convolutional Neural Network (CNN), Recurrent Neural Network (RNN), and Long Short-Term Memory (LSTM), together with their ensemble form (CNN–RNN–LSTM) were utilized to model landslide susceptibility in Trabzon province, Turkey. The proposed DL architecture produced the highest modeling performance of 0.93, followed by CNN (0.92), RNN (0.91), and LSTM (0.86). Findings proved that the proposed model excelled the performance of the DL models by up to 7% in terms of overall accuracy, which was also confirmed by the Wilcoxon signed-rank test. The area under curve analysis also showed a significant improvement (~4%) in susceptibility map accuracy by the proposed strategy.

Shared Blocks-Based Ensemble Deep Learning for Shallow Landslide Susceptibility Mapping

High-throughput technologies such as next-generation sequencing allow biologists to observe cell function with unprecedented resolution, but the resulting datasets are too large and complicated for humans to understand without the aid of advanced statistical methods. Machine learning (ML) algorithms, which are designed to automatically find patterns in data, are well suited to this task. Yet these models are often so complex as to be opaque, leaving researchers with few clues about underlying mechanisms. Interpretable machine learning (iML) is a burgeoning subdiscipline of computational statistics devoted to making the predictions of ML models more intelligible to end users. This article is a gentle and critical introduction to iML, with an emphasis on genomic applications. I define relevant concepts, motivate leading methodologies, and provide a simple typology of existing approaches. I survey recent examples of iML in genomics, demonstrating how such techniques are increasingly integrated into research workflows. I argue that iML solutions are required to realize the promise of precision medicine. However, several open challenges remain. I examine the limitations of current state-of-the-art tools and propose a number of directions for future research. While the horizon for iML in genomics is wide and bright, continued progress requires close collaboration across disciplines.

/pdf/interpretable-machine-learning-for-genomics-4bhh49f7pb.pdf

Interpretable machine learning for genomics.

Conventional methods of estimating pressure coefficients of buildings retain time and cost constraints. Recently, machine learning (ML) has been successfully established to predict wind pressure coefficients. However, regardless of the accuracy, ML models are incompetent in providing end-users’ confidence as a result of the black-box nature of predictions. In this study, we employed tree-based regression models (Decision Tree, XGBoost, Extra-tree, LightGBM) to predict surface-averaged mean pressure coefficient (Cp,mean), fluctuation pressure coefficient (Cp, rms), and peak pressure coefficient (Cp,peak) of low-rise gable-roofed buildings. The accuracy of models was verified using Tokyo Polytechnic University (TPU) wind tunnel data. Subsequently, we used Shapley Additive Explanations (SHAP) to explain the black-box nature of the ML predictions. The comparison revealed that tree-based models are efficient and accurate in wind-predicting pressure coefficients. Interestingly, SHAP provided human-comprehensible explanations for the interaction of variables, the importance of features towards the outcome, and the underlying reasoning behind the predictions. Moreover, SHAP confirmed that tree-based predictions adhere to the flow physics of wind engineering, advancing the fidelity of ML-based predictions.

/pdf/interpretation-of-machine-learning-based-black-box-wind-11ud3vb0.pdf

Interpretation of Machine-Learning-Based (Black-box) Wind Pressure Predictions for Low-Rise Gable-Roofed Buildings Using Shapley Additive Explanations (SHAP)

Cells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumour purities and cell lineages, to compare the performance of nine TME deconvolution methods (BayesPrism, Scaden, CIBERSORTx, MuSiC, DWLS, hspe, CPM, Bisque, and EPIC). Some methods are more robust in deconvolving mixtures with high tumour purity levels. Most methods tend to mis-predict normal epithelial for cancer epithelial as tumour purity increases, a finding that is validated in two independent datasets. The breast cancer molecular subtype influences this mis-prediction. BayesPrism and DWLS have the lowest combined numbers of false positives and false negatives, and have the best performance when deconvolving granular immune lineages. Our findings highlight the need for more single-cell characterisation of rarer cell types, and suggest that tumour cell compositions should be considered when deconvolving the TME. 

Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures

For complex machine learning (ML) algorithms to gain widespread acceptance in decision making, we must be able to identify the features driving the predictions. Explainability models allow transparency of ML algorithms, however their reliability within high-dimensional data is unclear. To test the reliability of the explainability model SHapley Additive exPlanations (SHAP), we developed a convolutional neural network to predict tissue classification from Genotype-Tissue Expression (GTEx) RNA-seq data representing 16,651 samples from 47 tissues. Our classifier achieved an average F1 score of 96.1% on held-out GTEx samples. Using SHAP values, we identified the 2423 most discriminatory genes, of which 98.6% were also identified by differential expression analysis across all tissues. The SHAP genes reflected expected biological processes involved in tissue differentiation and function. Moreover, SHAP genes clustered tissue types with superior performance when compared to all genes, genes detected by differential expression analysis, or random genes. We demonstrate the utility and reliability of SHAP to explain a deep learning model and highlight the strengths of applying ML to transcriptome data.

/pdf/verifying-explainability-of-a-deep-learning-tissue-4jzimke67n.pdf

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data.

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Verifying explainability of a deep learning tissue classifier trained on RNA-seq data.