BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes

Machine learning is helping the interpretation of biological complexity by enabling the inference and classification of cellular, organismal and ecological phenotypes based on large datasets, e.g. from genomic, transcriptomic and metagenomic analyses. A number of available algorithms can help search these datasets to uncover patterns associated with specific traits, including disease-related attributes. While, in many instances, treating an algorithm as a black box is sufficient, it is interesting to pursue an enhanced understanding of how system variables end up contributing to a specific output, as an avenue towards new mechanistic insight. Here we address this challenge through a suite of algorithms, named BowSaw, which takes advantage of the structure of a trained random forest algorithm to identify combinations of variables (“rules”) frequently used for classification. We first apply BowSaw to a simulated dataset, and show that the algorithm can accurately recover the sets of variables used to generate the phenotypes through complex Boolean rules, even under challenging noise levels. We next apply our method to data from the integrative Human Microbiome Project and find previously unreported high-order combinations of microbial taxa putatively associated with Crohn’s disease. By leveraging the structure of trees within a random forest, BowSaw provides a new way of using decision trees to generate testable biological hypotheses.Accepted manuscrip

Interpretable classifiers using rules and Bayesian analysis: Building a better stroke prediction model

We aim to produce predictive models that are not only accurate, but are also interpretable to human experts. Our models are decision lists, which consist of a series of if … then. . . statements (e.g., if high blood pressure, then stroke) that discretize a high-dimensional, multivariate feature space into a series of simple, readily interpretable decision statements. We introduce a generative model called Bayesian Rule Lists that yields a posterior distribution over possible decision lists. It employs a novel prior structure to encourage sparsity. Our experiments show that Bayesian Rule Lists has predictive accuracy on par with the current top algorithms for prediction in machine learning. Our method is motivated by recent developments in personalized medicine, and can be used to produce highly accurate and interpretable medical scoring systems. We demonstrate this by producing an alternative to the CHADS₂ score, actively used in clinical practice for estimating the risk of stroke in patients that have atrial fibrillation. Our model is as interpretable as CHADS₂, but more accurate.National Science Foundation (U.S.) (Grant IIS-1053407

An Interpretable Stroke Prediction Model using Rules and Bayesian Analysis

We aim to produce predictive models that are not only accurate, but are also interpretable to human experts. Our models are decision lists, which consist of a series of if...then... statements (for example, if high blood pressure, then stroke) that discretize a high-dimensional, multivariate feature space into a series of simple, readily inter- pretable decision statements. We introduce a generative model called the Bayesian List Machine which yields a posterior distribution over possible decision lists. It employs a novel prior structure to encourage sparsity. Our experiments show that the Bayesian List Machine has predictive accuracy on par with the current top algorithms for prediction in machine learning. Our method is motivated by recent developments in personalized medicine, and can be used to produce highly accurate and interpretable medical scoring systems. We demonstrate this by producing an alternative to the CHADS2 score, actively used in clinical practice for estimating the risk of stroke in patients that have atrial brillation. Our model is as interpretable as CHADS2, but more accurate

Analyzing and Interpreting Neural Networks for NLP: A Report on the First BlackboxNLP Workshop

The EMNLP 2018 workshop BlackboxNLP was dedicated to resources and techniques specifically developed for analyzing and understanding the inner-workings and representations acquired by neural models of language. Approaches included: systematic manipulation of input to neural networks and investigating the impact on their performance, testing whether interpretable knowledge can be decoded from intermediate representations acquired by neural networks, proposing modifications to neural network architectures to make their knowledge state or generated output more explainable, and examining the performance of networks on simplified or formal languages. Here we review a number of representative studies in each category