Resource library

Accurate transcription of audio recordings in psychotherapy would improve therapy effectiveness, clinician training, and safety monitoring. Although automatic speech recognition software is commercially available, its accuracy in mental health settings has not been well described. It is unclear which metrics and thresholds are appropriate for different clinical use cases, which may range from population descriptions to individual safety monitoring. Here…

A popular way to estimate the causal effect of a variable x on y from observational data is to use an instrumental variable (IV): a third variable z that affects y only through x. The more strongly z is associated with x, the more reliable the estimate is, but such strong IVs are difficult to find. Instead, practitioners combine more…

A third of adults in America use the Internet to diagnose medical concerns, and online symptom checkers are increasingly part of this process. These tools are powered by diagnosis models similar to clinical decision support systems, with the primary difference being the coverage of symptoms and diagnoses. To be useful to patients and physicians, these models must have high accuracy…

Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of the biomedical literature. Conventional text mining pipelines provide tools to automatically extract entities and relationships from the scientific literature, and partially replace expert curation, but such machine learning frameworks often…

The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient’s disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information…

Throughout our lives, we as humans acquire an intuitive understanding of our physical environments, a capacity that supports our imagination and planning abilities. Driven by our own curiosity, we learn about object motion and properties via self-curated targeted experiments, that teach us what we do not know. Recently, neural network models have been proposed that learn forward object dynamics from…

We propose a framework for training sequence tagging models with weak supervision consisting of multiple heuristic rules of unknown accuracy. In addition to supporting rules that vote on tags in the output sequence, we introduce a new type of weak supervision, called linking rules, that vote on how sequence elements should be grouped into spans with the same tag. These…

This work formalizes a deep learning baseline for aortic valve classification and outlines a general strategy for using weak supervision to train machine learning models using unlabeled medical images at scale.

This paper explores the applicability of weak supervision, or relying on higher level, noisier forms of supervision to label training data, specifically using data programming.