The use of AI in knowledge dense domains, e.g., chemistry, medicine, biology, etc. - is extremely promising, but often suffers from slow deployment and adaptation to different tasks. We propose a methodology to quickly capture the intent and expertise of a domain expert in order to train personalized AI models for specific tasks. Specifically we focus on the domain of polymer materials design and discovery: it often takes 10 years or more to design, synthesize, test, and introduce a new polymer material into the market. One way to accelerate up the design of polymer materials is through the use of computational methods to design the material, such as combinatorial screening, generative models, inverse design, etc. The drawback of these methods is that they generate a large number of candidates for new molecules, which then need to be manually reviewed by subject matter experts who select only a dozen for further investigation. Our solution is a human-in-the-loop methodology where we rank the candidates according to a utility function that is learned via the continued interaction with the subject matter experts, but which is also constrained by specific chemical knowledge. We prove the viability of our proposed methodology in a polymer production lab and we (i) evaluate against datasets of polymers previously produced in the lab as well as (ii) producing several novel materials that are undergoing experimental development, and (iii) quantitatively show that standard synthetic accessibility scores do not inform about patterns of SME decisions.

Data analysis tasks often require grouping of information to identify trends and associations. However, as the number of elements rises to the hundreds and thousands the cost of having a person perform the groupings unassisted quickly becomes prohibitive. Previous approaches have combined traditional clustering techniques with manual interaction steps, yielding human-in-the-loop clustering algorithms that incorporate user feedback by reweighting features or adjusting a similarity function. But in the real world, many grouping tasks lack both a feature set and a well-defined (dis)similarity metric, having only a subject matter expert with an implicit understanding of the correct relationships between elements based on the domain and the task at hand. We present a refine-and-lock clustering interaction model and demonstrate its effectiveness for cognitive-assisted human clustering over other interaction models such as split/merge and must-link/can't-link. Our approach offers effective automatic clustering assistance even in the absence of clear features or a definitive similarity metric; ensures that every cluster has final user approval; and exhibits at least a 3.94× improvement over other interactive clustering approaches in time to completion.

We present KnIT, the Knowledge Integration Toolkit, a system for accelerating scientific discovery and predicting previously unknown protein-protein interactions. Such predictions enrich biological research and are pertinent to drug discovery and the understanding of disease. Unlike a prior study, KnIT is now fully automated and demonstrably scalable. It extracts information from the scientific literature, automatically identifying direct and indirect references to protein interactions, which is knowledge that can be represented in network form. It then reasons over this network with techniques such as matrix factorization and graph diffusion to predict new, previously unknown interactions. The accuracy and scope of KnIT's knowledge extractions are validated using comparisons to structured, manually curated data sources as well as by performing retrospective studies that predict subsequent literature discoveries using literature available prior to a given date. The KnIT methodology is a step towards automated hypothesis generation from text, with potential application to other scientific domains.

Keeping up with the ever-expanding flow of data and publications is untenable and poses a fundamental bottleneck to scientific progress. Current search technologies typically find many relevant documents, but they do not extract and organize the information content of these documents or suggest new scientific hypotheses based on this organized content. We present an initial case study on KnIT, a prototype system that mines the information contained in the scientific literature, represents it explicitly in a queriable network, and then further reasons upon these data to generate novel and experimentally testable hypotheses. KnIT combines entity detection with neighbor-text feature analysis and with graph-based diffusion of information to identify potential new properties of entities that are strongly implied by existing relationships. We discuss a successful application of our approach that mines the published literature to identify new protein kinases that phosphorylate the protein tumor suppressor p53. Retrospective analysis demonstrates the accuracy of this approach and ongoing laboratory experiments suggest that kinases identified by our system may indeed phosphorylate p53. These results establish proof of principle for automated hypothesis generation and discovery based on text mining of the scientific literature.