SIMLR: Machine Learning inside the SIR Model for COVID-19 Forecasting

Accurate forecasts of the number of newly infected people during an epidemic are critical for making effective timely decisions. This paper addresses this challenge using the SIMLR model, which incorporates machine learning (ML) into the epidemiological SIR model. For each region, SIMLR tracks the changes in the policies implemented at the government level, which it uses to estimate the time-varying parameters of an SIR model for forecasting the number of new infections one to four weeks in advance. It also forecasts the probability of changes in those government policies at each of these future times, which is essential for the longer-range forecasts. We applied SIMLR to data from in Canada and the United States, and show that its mean average percentage error is as good as state-of-the-art forecasting models, with the added advantage of being an interpretable model. We expect that this approach will be useful not only for forecasting COVID-19 infections, but also in predicting the evolution of other infectious diseases.

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer

Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.

LIME-Based Data Selection Method for SAR Images Generation Using GAN

Deep learning has obtained remarkable achievements in computer vision, especially image and video processing. However, in synthetic aperture radar (SAR) image recognition, the application of DNNs is usually restricted due to data insufficiency. To augment datasets, generative adversarial networks (GANs) are usually used to generate numerous photo-realistic SAR images. Although there are many pixel-level metrics to measure GAN’s performance from the quality of generated SAR images, there are few measurements to evaluate whether the generated SAR images include the most representative features of the target. In this case, the classifier probably categorizes a SAR image into the corresponding class based on “wrong” criterion, i.e., “Clever Hans”. In this paper, local interpretable model-agnostic explanation (LIME) is innovatively utilized to evaluate whether a generated SAR image possessed the most representative features of a specific kind of target. Firstly, LIME is used to visualize positive contributions of the input SAR image to the correct prediction of the classifier. Subsequently, these representative SAR images can be selected handily by evaluating how much the positive contribution region matches the target. Experimental results demonstrate that the proposed method can ally “Clever Hans” phenomenon greatly caused by the spurious relationship between generated SAR images and the corresponding classes.

Explaining Deep Learning Models for Tabular Data Using Layer-Wise Relevance Propagation

Trust and credibility in machine learning models are bolstered by the ability of a model to explain its decisions. While explainability of deep learning models is a well-known challenge, a further challenge is clarity of the explanation itself for relevant stakeholders of the model. Layer-wise Relevance Propagation (LRP), an established explainability technique developed for deep models in computer vision, provides intuitive human-readable heat maps of input images. We present the novel application of LRP with tabular datasets containing mixed data (categorical and numerical) using a deep neural network (1D-CNN), for Credit Card Fraud detection and Telecom Customer Churn prediction use cases. We show how LRP is more effective than traditional explainability concepts of Local Interpretable Model-agnostic Explanations (LIME) and Shapley Additive Explanations (SHAP) for explainability. This effectiveness is both local to a sample level and holistic over the whole testing set. We also discuss the significant computational time advantage of LRP (1–2 s) over LIME (22 s) and SHAP (108 s) on the same laptop, and thus its potential for real time application scenarios. In addition, our validation of LRP has highlighted features for enhancing model performance, thus opening up a new area of research of using XAI as an approach for feature subset selection.

Wearable Devices, Smartphones, and Interpretable Artificial Intelligence in Combating COVID-19

Physiological measures, such as heart rate variability (HRV) and beats per minute (BPM), can be powerful health indicators of respiratory infections. HRV and BPM can be acquired through widely available wrist-worn biometric wearables and smartphones. Successive abnormal changes in these indicators could potentially be an early sign of respiratory infections such as COVID-19. Thus, wearables and smartphones should play a significant role in combating COVID-19 through the early detection supported by other contextual data and artificial intelligence (AI) techniques. In this paper, we investigate the role of the heart measurements (i.e., HRV and BPM) collected from wearables and smartphones in demonstrating early onsets of the inflammatory response to the COVID-19. The AI framework consists of two blocks: an interpretable prediction model to classify the HRV measurements status (as normal or affected by inflammation) and a recurrent neural network (RNN) to analyze users’ daily status (i.e., textual logs in a mobile application). Both classification decisions are integrated to generate the final decision as either “potentially COVID-19 infected” or “no evident signs of infection”. We used a publicly available dataset, which comprises 186 patients with more than 3200 HRV readings and numerous user textual logs. The first evaluation of the approach showed an accuracy of 83.34 ± 1.68% with 0.91, 0.88, 0.89 precision, recall, and F1-Score, respectively, in predicting the infection two days before the onset of the symptoms supported by a model interpretation using the local interpretable model-agnostic explanations (LIME).

Interpretable Modeling for Short- and Medium-Term Electricity Demand Forecasting

We consider the problem of short- and medium-term electricity demand forecasting by using past demand and daily weather forecast information. Conventionally, many researchers have directly applied regression analysis. However, interpreting the effect of weather on the demand is difficult with the existing methods. In this study, we build a statistical model that resolves this interpretation issue. A varying coefficient model with basis expansion is used to capture the nonlinear structure of the weather effect. This approach results in an interpretable model when the regression coefficients are nonnegative. To estimate the nonnegative regression coefficients, we employ nonnegative least squares. Three real data analyses show the practicality of our proposed statistical modeling. Two of them demonstrate good forecast accuracy and interpretability of our proposed method. In the third example, we investigate the effect of COVID-19 on electricity demand. The interpretation would help make strategies for energy-saving interventions and demand response.

Explainable health prediction from facial features with transfer learning

In the recent years, Artificial Intelligence (AI) has been widely deployed in the healthcare industry. The new AI technology enables efficient and personalized healthcare systems for the public. In this paper, transfer learning with pre-trained VGGFace model is applied to identify sick symptoms based on the facial features of a person. As the deep learning model’s operation is unknown for making a decision, this paper investigates the use of Explainable AI (XAI) techniques for soliciting explanations for the predictions made by the model. Various XAI techniques including Integrated Gradient, Explainable region-based AI (XRAI) and Local Interpretable Model-Agnostic Explanations (LIME) are studied. XAI is crucial to increase the model’s transparency and reliability for practical deployment. Experimental results demonstrate that the attribution method can give proper explanations for the decisions made by highlighting important attributes in the images. The facial features that account for positive and negative classes predictions are highlighted appropriately for effective visualization. XAI can help to increase accountability and trustworthiness of the healthcare system as it provides insights for understanding how a conclusion is derived from the AI model.

New explainability method for BERT-based model in fake news detection

The ubiquity of social media and their deep integration in the contemporary society has granted new ways to interact, exchange information, form groups, or earn money—all on a scale never seen before. Those possibilities paired with the widespread popularity contribute to the level of impact that social media display. Unfortunately, the benefits brought by them come at a cost. Social Media can be employed by various entities to spread disinformation—so called ‘Fake News’, either to make a profit or influence the behaviour of the society. To reduce the impact and spread of Fake News, a diverse array of countermeasures were devised. These include linguistic-based approaches, which often utilise Natural Language Processing (NLP) and Deep Learning (DL). However, as the latest advancements in the Artificial Intelligence (AI) domain show, the model’s high performance is no longer enough. The explainability of the system’s decision is equally crucial in real-life scenarios. Therefore, the objective of this paper is to present a novel explainability approach in BERT-based fake news detectors. This approach does not require extensive changes to the system and can be attached as an extension for operating detectors. For this purposes, two Explainable Artificial Intelligence (xAI) techniques, Local Interpretable Model-Agnostic Explanations (LIME) and Anchors, will be used and evaluated on fake news data, i.e., short pieces of text forming tweets or headlines. This focus of this paper is on the explainability approach for fake news detectors, as the detectors themselves were part of previous works of the authors.

An interpretable machine learning model based on a quick pre-screening system enables accurate deterioration risk prediction for COVID-19

A high-performing interpretable model is proposed to predict the risk of deterioration in coronavirus disease 2019 (COVID-19) patients. The model was developed using a cohort of 3028 patients diagnosed with COVID-19 and exhibiting common clinical symptoms that were internally verified (AUC 0.8517, 95% CI 0.8433, 0.8601). A total of 15 high risk factors for deterioration and their approximate warning ranges were identified. This included prothrombin time (PT), prothrombin activity, lactate dehydrogenase, international normalized ratio, heart rate, body-mass index (BMI), D-dimer, creatine kinase, hematocrit, urine specific gravity, magnesium, globulin, activated partial thromboplastin time, lymphocyte count (L%), and platelet count. Four of these indicators (PT, heart rate, BMI, HCT) and comorbidities were selected for a streamlined combination of indicators to produce faster results. The resulting model showed good predictive performance (AUC 0.7941 95% CI 0.7926, 0.8151). A website for quick pre-screening online was also developed as part of the study.

iEnhancer-CLA: Self-attention-based interpretable model for enhancers and their strength prediction

Enhancer is a class of non-coding DNA cis-acting elements that plays a crucial role in the development of eukaryotes for their transcription. Computational methods for predicting enhancers have been developed and achieve satisfactory performance. However, existing computational methods suffer from experience-based feature engineering and lack of interpretability, which not only limit the representation ability of the models to some extent, but also make it difficult to provide interpretable analysis of the model prediction findings.In this paper, we propose a novel deep-learning-based model, iEnhancer-CLA, for identifying enhancers and their strengths. Specifically, iEnhancer-CLA automatically learns sequence 1D features through multiscale convolutional neural networks (CNN), and employs a self-attention mechanism to represent global features formed by multiple elements (multibody effects). In particular, the model can provide an interpretable analysis of the enhancer motifs and key base signals by decoupling CNN modules and generating self-attention weights. To avoid the bias of setting hyperparameters manually, we construct Bayesian optimization methods to obtain model global optimization hyperparameters. The results demonstrate that our method outperforms existing predictors in terms of accuracy for identifying enhancers and their strengths. Importantly, our analyses found that the distribution of bases in enhancers is uneven and the base G contents are more enriched, while the distribution of bases in non-enhancers is relatively even. This result contributes to the improvement of prediction performance and thus facilitates revealing an in-depth understanding of the potential functional mechanisms of enhancers.