Medically-oriented design for explainable AI for stress prediction from physiological measurements.

BACKGROUND: In the last decade, a lot of attention has been given to develop artificial intelligence (AI) solutions for mental health using machine learning. To build trust in AI applications, it is crucial for AI systems to provide for practitioners and patients the reasons behind the AI decisions. This is referred to as Explainable AI. While there has been significant progress in developing stress prediction models, little work has been done to develop explainable AI for mental health. METHODS: In this work, we address this gap by designing an explanatory AI report for stress prediction from wearable sensors. Because medical practitioners and patients are likely to be familiar with blood test reports, we modeled the look and feel of the explanatory AI on those of a standard blood test report. The report includes stress prediction and the physiological signals related to stressful episodes. In addition to the new design for explaining AI in mental health, the work includes the following contributions: Methods to automatically generate different components of the report, an approach for evaluating and validating the accuracies of the explanations, and a collection of ground truth of relationships between physiological measurements and stress prediction. RESULTS: Test results showed that the explanations were consistent with ground truth. The reference intervals for stress versus non-stress were quite distinctive with little variation. In addition to the quantitative evaluations, a qualitative survey, conducted by three expert psychiatrists confirmed the usefulness of the explanation report in understanding the different aspects of the AI system. CONCLUSION: In this work, we have provided a new design for explainable AI used in stress prediction based on physiological measurements. Based on the report, users and medical practitioners can determine what biological features have the most impact on the prediction of stress in addition to any health-related abnormalities. The effectiveness of the explainable AI report was evaluated using a quantitative and a qualitative assessment. The stress prediction accuracy was shown to be comparable to state-of-the-art. The contributions of each physiological signal to the stress prediction was shown to correlate with ground truth. In addition to these quantitative evaluations, a qualitative survey with psychiatrists confirmed the confidence and effectiveness of the explanation report in the stress made by the AI system. Future work includes the addition of more explanatory features related to other emotional states of the patient, such as sadness, relaxation, anxiousness, or happiness.

Strike: a protein-protein interaction classification approach.

Protein-protein interaction has proven to be a valuable biological knowledge and an initial point for understanding how the cell internally works. In this chapter, we introduce a novel approach termed STRIKE which uses String Kernel to predict protein-protein interaction. STRIKE classifies protein pairs into "interacting" and "non-interacting" sets based solely on amino acid sequence information. The classification is performed by applying the string kernel approach, which has been shown to achieve good performance on text categorization and protein sequence classification. Two proteins are classified as "interacting" if they contain similar substrings of amino acids. Strings' similarity would allow one to infer homology which could lead to a very similar structural relationship. To evaluate the performance of STRIKE, we apply it to classify into "interacting" and "non-interacting" protein pairs. The dataset of the protein pairs are generated from the yeast protein interaction literature. The dataset is supported by different lines of experimental evidence. STRIKE was able to achieve reasonable improvement over the existing protein-protein interaction prediction methods.

Protein-protein interaction based on pairwise similarity.

BACKGROUND: Protein-protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS) method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. RESULTS: To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. CONCLUSION: Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.