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Open Access Publications from the University of California

Domain-inspired machine learning for hypothesis extraction in biological data

  • Author(s): Kumbier, Karl
  • Advisor(s): Yu, Bin
  • et al.
Abstract

Rapidly moving technologies are transforming the rate at which researchers accumulate information. Large, rich datasets hold promises of new insights into complex natural phenomena that will help advance the frontier of science. Here we aim to develop new statistics/data science principles and scalable algorithms for extracting reliable and reproducible information from these data.

Chapter 1 provides an overview of the work contained in this thesis. It discusses the growing availability of genomic data and the statistical machine learning tools that are being used to provide a systems-level understanding of genomic phenomena.

Chapter 2 introduces the predictability, computability, and stability (PCS) framework. The PCS framework builds on key ideas in machine learning, using predictability as a reality check and evaluating computational considerations in data collection, data storage and algorithm design. It augments predictability and computability with an overarching stability principle, which expands statistical uncertainty considerations to assesses how results vary with respect to choices (or perturbations) made across the data science life cycle. In this chapter, we develop PCS inference through perturbation intervals and PCS hypothesis testing to investigate the reliability of data results. We compare PCS inference with existing methods in high-dimensional sparse linear model simulations to demonstrate that our approach compares favorably to others, in terms of ROC curves, over a wide range of simulation settings. Finally, we propose documentation based on R Markdown, iPython, or Jupyter Notebook, with publicly available, reproducible codes and narratives to justify human choices made throughout an analysis.

As an example of the PCS framework in practice, chapter 3 develops the iterative Random Forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with same order of computational cost as Random Forests (RF). We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the early Drosophila embryo and alternative splicing of primary transcripts in human derived cell lines. In Drosophila, 80% of the pairwise transcription factor interactions iRF identified as stable have been previously reported as physical interactions. Moreover, novel third-order interactions, e.g. between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated splicing regulation, and identified novel 5th and 6th order interactions, indicative of multi-valent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens new avenues of inquiry into the molecular mechanisms underlying genome biology.

Chapter 4 refines iRF to explicitly map responses as a function of interacting features. Our proposed method, signed iRF (siRF), describes "subsets" of rules that frequently occur on RF decision paths. We refer to these rule subsets as signed interactions. RF decision paths containing the same signed interaction share not only a set of interacting features but also exhibit similar thresholding behavior, and thus describe a consistent functional relationship between interacting features and responses. We formulate stable and predictive importance metrics (SPIMs) to rank signed interactions in terms of their stability, predictive accuracy, and strength of interaction. For each SPIM, we define null importance metrics that characterize its expected behavior under known structure. We evaluate siRF in biologically inspired simulations and two case studies: predicting enhancer activity and spatial gene expression patterns. In the case of spatial gene expression patterns, siRF recovered all 11 reported links in the gap gene network. In the case of enhancer activity, siRF discovered rules that identify enhancer elements in Drosophila embryos with high precision, suggesting candidate biological mechanisms for experimental studies. By refining the process of interaction discovery, siRF has the potential to guide mechanistic inquiry into systems whose scale and complexity is beyond human comprehension.

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