The recent explosion of chemical and biological information calls for fundamentally novel ways of dealing with big data in the life sciences. This problem can potentially be addressed by the latest technological breakthroughs on both software and hardware frontiers. In particular, the latest advances in artificial intelligence (AI) enable cognitive data processing at very large-scale by means of deep learning (DL).

Computer systems – both hardware and software – currently represent an active barrier to the scientific investigation of genomic data. Answering even relatively simple questions requires assembling disparate software tools (for alignment, variant calling, and filtering) into an analytics pipeline, and then solving practical IT problems in order to get that pipeline to function stably and at scale. This project will employ a whole system approach for providing a framework for genomic analysis.

Many of the most successful approaches commonly used in data-science applications (e.g., machine learning) come with little or no guarantees. Notable examples include convolutional neural networks (CNNs) and data-fitting formulations based on non-convex loss functions. In both cases, the training procedures are based on optimizing over intractable problems.

Inhaled environmental and occupational exposures such as air pollution and allergens are known to have a profound effect on our respiratory and immunological health. This collaborative project seeks to better understand how the human body responds adversely to these perturbants by developing and applying new computational models for analyses of integrated molecular data sets, collectively known as 'omics profiling (e.g., genomics, proteomics, metabolomics, epigenomics, transcriptomics, and polymorphisms).

Fake news and misinformation have been a serious problem for a long time and the advent of social media has made it more acute, particularly in the context of the 2016 U.S. Presidential election. This illustrates how social networks and media have started playing a fundamental role in the lives of most people--they influence the way we receive, assimilate, and share information with others.

The Learning Factory Digital Twin project is integrating advanced materials research with emerging manufacturing technologies to make products lighter, stronger, smarter, more durable and energy efficient, while minimizing production costs.

Immune checkpoint inhibitors, or ICIs, are a powerful new treatment option for a variety of tumors, but efficacy varies between patients and mild to life-threatening side effects can occur. The bacteria that reside in a patient's gut have been shown to impact ICI efficacy and to predict the development of colitis side-effects, but it is not clear specifically which bacteria impact ICI response or toxicity.

Breast tumor genetics can change during disease progression, leading to distinct tumor cell populations that often contribute to therapeutic resistance. We propose to perform state-of-the-art, single-cell genomic sequencing on breast cancer biopsies and circulating tumor DNA (also known as liquid biopsies) to evaluate genetic changes during the course of a patient's therapy.

As type-specific treatments are being developed for patients with epithelial ovarian cancer, it has become important to accurately diagnose the distinct cancer types. Our vision is to establish an international network for AI-based, privacy-protected pathology quality assurance. As proof of concept, we propose to develop and deploy a machine learning-based ovarian cancer histopathology classifier.