  Can language models read biomedical texts and explain the biomedical
mechanisms discussed? In this work we introduce a biomedical mechanism
summarization task. Biomedical studies often investigate the mechanisms behind
how one entity (e.g., a protein or a chemical) affects another in a biological
context. The abstracts of these publications often include a focused set of
sentences that present relevant supporting statements regarding such
relationships, associated experimental evidence, and a concluding sentence that
summarizes the mechanism underlying the relationship. We leverage this
structure and create a summarization task, where the input is a collection of
sentences and the main entities in an abstract, and the output includes the
relationship and a sentence that summarizes the mechanism. Using a small amount
of manually labeled mechanism sentences, we train a mechanism sentence
classifier to filter a large biomedical abstract collection and create a
summarization dataset with 22k instances. We also introduce conclusion sentence
generation as a pretraining task with 611k instances. We benchmark the
performance of large bio-domain language models. We find that while the
pretraining task help improves performance, the best model produces acceptable
mechanism outputs in only 32% of the instances, which shows the task presents
significant challenges in biomedical language understanding and summarization.

Computation and Language;Artificial Intelligence;Information Retrieval;Machine Learning