Modern biomedical concept representations are mostly trained on synonymous concept names from a biomedical knowledge base, ignoring the inter-concept interactions and a concept’s local neighborhood in a knowledge base graph. In this paper, we introduce Biomedical Entity Representation with a Graph-Augmented Multi-Objective Transformer (BERGAMOT), which adopts the power of pre-trained language models (LMs) and graph neural networks to capture both inter-concept and intra-concept interactions from the multilingual UMLS graph. To obtain fine-grained graph representations, we introduce two additional graph-based objectives: (i) a node-level contrastive objective and (ii) the Deep Graph Infomax (DGI) loss, which maximizes the mutual information between a local subgraph and a high-level graph summary. We apply contrastive loss on textual and graph representations to make them less sensitive to surface forms and enable intermodal knowledge exchange. BERGAMOT achieves state-of-the-art results in zero-shot entity linking without task-specific supervision on 4 of 5 languages of the Mantra corpus and on 8 of 10 languages of the XL-BEL benchmark.

The recent integration of chemistry with natural language processing (NLP) has advanced drug discovery. Molecule representation in language models (LMs) is crucial in enhancing chemical understanding. We propose Augmented Molecular Retrieval (AMORE), a flexible zero-shot framework for assessment of Chemistry LMs of different natures: trained solely on molecules for chemical tasks and on a combined corpus of natural language texts and string-based structures. The framework relies on molecule augmentations that preserve an underlying chemical, such as kekulization and cycle replacements. We evaluate encoder-only and generative LMs by calculating a metric based on the similarity score between distributed representations of molecules and their augmentations. Our experiments on ChEBI-20 and QM9 benchmarks show that these models exhibit significantly lower scores than graph-based molecular models trained without language modeling objectives. Additionally, our results on the molecule captioning task for cross-domain models, MolT5 and Text+Chem T5, demonstrate that the lower the representation-based evaluation metrics, the lower the classical text generation metrics like ROUGE and METEOR.

Linking of biomedical entity mentions to various terminologies of chemicals, diseases, genes, adverse drug reactions is a challenging task, often requiring non-syntactic interpretation. A large number of biomedical corpora and state-of-the-art models have been introduced in the past five years. However, there are no general guidelines regarding the evaluation of models on these corpora in single- and cross-terminology settings. In this work, we perform a comparative evaluation of various benchmarks and study the efficiency of state-of-the-art neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) for linking of three entity types across three domains: research abstracts, drug labels, and user-generated texts on drug therapy in English. We have made the source code and results available at https://github.com/insilicomedicine/Fair-Evaluation-BERT.