Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sentences (documents); (iii) We further modify and expand a graph kernel learning framework to enable concurrent exploitation of automatically induced AMR (semantic) and dependency structure (syntactic) representations. Our experiments show that our approach yields interaction extraction systems that are more robust in environments where there is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16

Regularized Data Programming with Automated Bayesian Prior Selection

The cost of manual data labeling can be a significant obstacle in supervised learning. Data programming (DP) offers a weakly supervised solution for training dataset creation, wherein the outputs of user-defined programmatic labeling functions (LFs) are reconciled through unsupervised learning. However, DP can fail to outperform an unweighted majority vote in some scenarios, including low-data contexts. This work introduces a Bayesian extension of classical DP that mitigates failures of unsupervised learning by augmenting the DP objective with regularization terms. Regularized learning is achieved through maximum a posteriori estimation with informative priors. Majority vote is proposed as a proxy signal for automated prior parameter selection. Results suggest that regularized DP improves performance relative to maximum likelihood and majority voting, confers greater interpretability, and bolsters performance in low-data regimes

Data Programming: Creating Large Training Sets, Quickly

Abstract Large labeled training sets are the critical building blocks of supervised learning methods and are key enablers of deep learning techniques. For some applications, creating labeled training sets is the most time-consuming and expensive part of applying machine learning. We therefore propose a paradigm for the programmatic creation of training sets called data programming in which users express weak supervision strategies or domain heuristics as labeling functions, which are programs that label subsets of the data, but that are noisy and may conflict. We show that by explicitly representing this training set labeling process as a generative model, we can "denoise" the generated training set, and establish theoretically that we can recover the parameters of these generative models in a handful of settings. We then show how to modify a discriminative loss function to make it noise-aware, and demonstrate our method over a range of discriminative models including logistic regression and LSTMs. Experimentally, on the 2014 TAC-KBP Slot Filling challenge, we show that data programming would have led to a new winning score, and also show that applying data programming to an LSTM model leads to a TAC-KBP score almost 6 F1 points over a state-of-the-art LSTM baseline (and into second place in the competition). Additionally, in initial user studies we observed that data programming may be an easier way for non-experts to create machine learning models when training data is limited or unavailable

Accelerating Science: A Computing Research Agenda

The emergence of "big data" offers unprecedented opportunities for not only accelerating scientific advances but also enabling new modes of discovery. Scientific progress in many disciplines is increasingly enabled by our ability to examine natural phenomena through the computational lens, i.e., using algorithmic or information processing abstractions of the underlying processes; and our ability to acquire, share, integrate and analyze disparate types of data. However, there is a huge gap between our ability to acquire, store, and process data and our ability to make effective use of the data to advance discovery. Despite successful automation of routine aspects of data management and analytics, most elements of the scientific process currently require considerable human expertise and effort. Accelerating science to keep pace with the rate of data acquisition and data processing calls for the development of algorithmic or information processing abstractions, coupled with formal methods and tools for modeling and simulation of natural processes as well as major innovations in cognitive tools for scientists, i.e., computational tools that leverage and extend the reach of human intellect, and partner with humans on a broad range of tasks in scientific discovery (e.g., identifying, prioritizing formulating questions, designing, prioritizing and executing experiments designed to answer a chosen question, drawing inferences and evaluating the results, and formulating new questions, in a closed-loop fashion). This calls for concerted research agenda aimed at: Development, analysis, integration, sharing, and simulation of algorithmic or information processing abstractions of natural processes, coupled with formal methods and tools for their analyses and simulation; Innovations in cognitive tools that augment and extend human intellect and partner with humans in all aspects of science.Comment: Computing Community Consortium (CCC) white paper, 17 page

Literature Based Discovery (LBD): Towards Hypothesis Generation and Knowledge Discovery in Biomedical Text Mining

Biomedical knowledge is growing in an astounding pace with a majority of this knowledge is represented as scientific publications. Text mining tools and methods represents automatic approaches for extracting hidden patterns and trends from this semi structured and unstructured data. In Biomedical Text mining, Literature Based Discovery (LBD) is the process of automatically discovering novel associations between medical terms otherwise mentioned in disjoint literature sets. LBD approaches proven to be successfully reducing the discovery time of potential associations that are hidden in the vast amount of scientific literature. The process focuses on creating concept profiles for medical terms such as a disease or symptom and connecting it with a drug and treatment based on the statistical significance of the shared profiles. This knowledge discovery approach introduced in 1989 still remains as a core task in text mining. Currently the ABC principle based two approaches namely open discovery and closed discovery are mostly explored in LBD process. This review starts with general introduction about text mining followed by biomedical text mining and introduces various literature resources such as MEDLINE, UMLS, MESH, and SemMedDB. This is followed by brief introduction of the core ABC principle and its associated two approaches open discovery and closed discovery in LBD process. This review also discusses the deep learning applications in LBD by reviewing the role of transformer models and neural networks based LBD models and its future aspects. Finally, reviews the key biomedical discoveries generated through LBD approaches in biomedicine and conclude with the current limitations and future directions of LBD.Comment: 43 Pages, 5 Figures, 4 Table