Biomolecular Event Extraction using Natural Language Processing

Biomedical research and discoveries are communicated through scholarly publications and this literature is voluminous, rich in scientific text and growing exponentially by the day. Biomedical journals publish nearly three thousand research articles daily, making literature search a challenging proposition for researchers. Biomolecular events involve genes, proteins, metabolites, and enzymes that provide invaluable insights into biological processes and explain the physiological functional mechanisms. Text mining (TM) or extraction of such events automatically from big data is the only quick and viable solution to gather any useful information. Such events extracted from biological literature have a broad range of applications like database curation, ontology construction, semantic web search and interactive systems. However, automatic extraction has its challenges on account of ambiguity and the diverse nature of natural language and associated linguistic occurrences like speculations, negations etc., which commonly exist in biomedical texts and lead to erroneous elucidation. In the last decade, many strategies have been proposed in this field, using different paradigms like Biomedical natural language processing (BioNLP), machine learning and deep learning. Also, new parallel computing architectures like graphical processing units (GPU) have emerged as possible candidates to accelerate the event extraction pipeline. This paper reviews and provides a summarization of the key approaches in complex biomolecular big data event extraction tasks and recommends a balanced architecture in terms of accuracy, speed, computational cost, and memory usage towards developing a robust GPU-accelerated BioNLP system

Semantically linking molecular entities in literature through entity relationships

Background Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attribute to this goal by formally identifying the relations between genes, promoters, complexes and various other molecular entities found in text. More importantly, these studies help to enhance integration of text mining results with database facts. Results We describe, compare and evaluate two frameworks developed for the prediction of non-causal or 'entity' relations (REL) between gene symbols and domain terms. For the corresponding REL challenge of the BioNLP Shared Task of 2011, these systems ranked first (57.7% F-score) and second (41.6% F-score). In this paper, we investigate the performance discrepancy of 16 percentage points by benchmarking on a related and more extensive dataset, analysing the contribution of both the term detection and relation extraction modules. We further construct a hybrid system combining the two frameworks and experiment with intersection and union combinations, achieving respectively high-precision and high-recall results. Finally, we highlight extremely high-performance results (F-score > 90%) obtained for the specific subclass of embedded entity relations that are essential for integrating text mining predictions with database facts. Conclusions The results from this study will enable us in the near future to annotate semantic relations between molecular entities in the entire scientific literature available through PubMed. The recent release of the EVEX dataset, containing biomolecular event predictions for millions of PubMed articles, is an interesting and exciting opportunity to overlay these entity relations with event predictions on a literature-wide scale

High-precision bio-molecular event extraction from text using parallel binary classifiers

We have developed a machine learning framework to accurately extract complex genetic interactions from text. Employing type-specific classifiers, this framework processes research articles to extract various biological events. Subsequently, the algorithm identifies regulation events that take other events as arguments, allowing a nested structure of predictions. All predictions are merged into an integrated network, useful for visualization and for deduction of new biological knowledge. In this paper, we discuss several design choices for an event-based extraction framework. These detailed studies help improving on existing systems, which is illustrated by the relative performance gain of 10% of our system compared to the official results in the recent BioNLP'09 Shared Task. Our framework now achieves state-of-the-art performance with 37.43 recall, 54.81 precision and 44.48 F-score. We further present the first study of feature selection for bio-molecular event extraction from text. While producing more cost-effective models, feature selection can also lead to a better insight into the complexity of the challenge. Finally, this paper tries to bridge the gap between theoretical relation extraction from text and experimental work on bio-molecular interactions by discussing interesting opportunities to employ event-based text mining tools for real-life tasks such as hypothesis generation, database curation and knowledge discovery