Dataset Information

Matrix Profile-Based Interpretable Time Series Classifier.

ABSTRACT: Time series classification (TSC) is a pervasive and transversal problem in various fields ranging from disease diagnosis to anomaly detection in finance. Unfortunately, the most effective models used by Artificial Intelligence (AI) systems for TSC are not interpretable and hide the logic of the decision process, making them unusable in sensitive domains. Recent research is focusing on explanation methods to pair with the obscure classifier to recover this weakness. However, a TSC approach that is transparent by design and is simultaneously efficient and effective is even more preferable. To this aim, we propose an interpretable TSC method based on the patterns, which is possible to extract from the Matrix Profile (MP) of the time series in the training set. A smart design of the classification procedure allows obtaining an efficient and effective transparent classifier modeled as a decision tree that expresses the reasons for the classification as the presence of discriminative subsequences. Quantitative and qualitative experimentation shows that the proposed method overcomes the state-of-the-art interpretable approaches.

SUBMITTER: Guidotti R

PROVIDER: S-EPMC8564499 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Matrix Profile-Based Interpretable Time Series Classifier.

Guidotti Riccardo R D'Onofrio Matteo M

Frontiers in artificial intelligence 20211020

Time series classification (TSC) is a pervasive and transversal problem in various fields ranging from disease diagnosis to anomaly detection in finance. Unfortunately, the most effective models used by Artificial Intelligence (AI) systems for TSC are not interpretable and hide the logic of the decision process, making them unusable in sensitive domains. Recent research is focusing on explanation methods to pair with the obscure classifier to recover this weakness. However, a TSC approach that i ...[more]

PMID: 34746768

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Project description:BackgroundGene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far from the gene promoters are often responsible for mediating gene transcription. Knowing their properties, regulatory activity, and genomic targets is crucial to the functional understanding of cellular events, ranging from cellular homeostasis to differentiation. Recent genome-wide investigation of epigenomic marks has indicated that enhancer elements could be enriched for certain epigenomic marks, such as, combinatorial patterns of histone modifications.MethodsOur efforts in this paper are motivated by these recent advances in epigenomic profiling methods, which have uncovered enhancer-associated chromatin features in different cell types and organisms. Specifically, in this paper, we use recent state-of-the-art Deep Learning methods and develop a deep neural network (DNN)-based architecture, called EP-DNN, to predict the presence and types of enhancers in the human genome. It uses as features, the expression levels of the histone modifications at the peaks of the functional sites as well as in its adjacent regions. We apply EP-DNN to four different cell types: H1, IMR90, HepG2, and HeLa S3. We train EP-DNN using p300 binding sites as enhancers, and TSS and random non-DHS sites as non-enhancers. We perform EP-DNN predictions to quantify the validation rate for different levels of confidence in the predictions and also perform comparisons against two state-of-the-art computational models for enhancer predictions, DEEP-ENCODE and RFECS.ResultsWe find that EP-DNN has superior accuracy and takes less time to make predictions. Next, we develop methods to make EP-DNN interpretable by computing the importance of each input feature in the classification task. This analysis indicates that the important histone modifications were distinct for different cell types, with some overlaps, e.g., H3K27ac was important in cell type H1 but less so in HeLa S3, while H3K4me1 was relatively important in all four cell types. We finally use the feature importance analysis to reduce the number of input features needed to train the DNN, thus reducing training time, which is often the computational bottleneck in the use of a DNN.ConclusionsIn this paper, we developed EP-DNN, which has high accuracy of prediction, with validation rates above 90 % for the operational region of enhancer prediction for all four cell lines that we studied, outperforming DEEP-ENCODE and RFECS. Then, we developed a method to analyze a trained DNN and determine which histone modifications are important, and within that, which features proximal or distal to the enhancer site, are important.

Dataset Information

Matrix Profile-Based Interpretable Time Series Classifier.

Publications

Matrix Profile-Based Interpretable Time Series Classifier.

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