Recent advancements have integrated Language Models (LMs) into a drug discovery pipeline. However, existing models mostly work with SMILES and SELFIES chemical string representations, which lack spatial features vital for drug discovery. Additionally, attempts to translate chemical 3D structures into text format encounter issues such as excessive length and insufficient atom connectivity information. To address these issues, we introduce nach0-pc, a model combining domain-specific encoder and textual representation to handle spatial arrangement of atoms effectively. Our approach utilizes a molecular point cloud encoder for concise and order-invariant structure representation. We introduce a novel pre-training scheme for molecular point clouds to distillate the knowledge from spatial molecular structures datasets. After fine-tuning within both single-task and multi-task frameworks, nach0-pc demonstrates performance comparable with other diffusion models in terms of generated samples quality across several established spatial molecular generation tasks. Notably, our model is a multi-task approach, in contrast to diffusion models being limited to single tasks. Additionally, it is capable of processing point cloud-related data, which language models are not capable of handling due to memory limitations. These lead to our model having reduced training and inference time while maintaining on par performance.

Medical data annotation requires highly qualified expertise. Despite the efforts devoted to medical entity linking in different languages, available data is very sparse in terms of both data volume and languages. In this work, we establish benchmarks for cross-lingual medical entity linking using clinical reports, clinical guidelines, and medical research papers. We present a test set filtering procedure designed to analyze the “hard cases” of entity linking approaching zero-shot cross-lingual transfer learning, evaluate state-of-the-art models, and draw several interesting conclusions based on our evaluation results.

MOTIVATION: Clinical trials are the essential stage of every drug development program for the treatment to become available to patients. Despite the importance of well-structured clinical trial databases and their tremendous value for drug discovery and development such instances are very rare. Presently large-scale information on clinical trials is stored in clinical trial registers which are relatively structured, but the mappings to external databases of drugs and diseases are increasingly lacking. The precise production of such links would enable us to interrogate richer harmonized datasets for invaluable insights. RESULTS: We present a neural approach for medical concept normalization of diseases and drugs. Our two-stage approach is based on Bidirectional Encoder Representations from Transformers (BERT). In the training stage, we optimize the relative similarity of mentions and concept names from a terminology via triplet loss. In the inference stage, we obtain the closest concept name representation in a common embedding space to a given mention representation. We performed a set of experiments on a dataset of abstracts and a real-world dataset of trial records with interventions and conditions mapped to drug and disease terminologies. The latter includes mentions associated with one or more concepts (in-KB) or zero (out-of-KB, nil prediction). Experiments show that our approach significantly outperforms baseline and state-of-the-art architectures. Moreover, we demonstrate that our approach is effective in knowledge transfer from the scientific literature to clinical trial data. AVAILABILITY AND IMPLEMENTATION: We make code and data freely available at https://github.com/insilicomedicine/DILBERT.

MOTIVATION: Drugs and diseases play a central role in many areas of biomedical research and healthcare. Aggregating knowledge about these entities across a broader range of domains and languages is critical for information extraction (IE) applications. To facilitate text mining methods for analysis and comparison of patient's health conditions and adverse drug reactions reported on the Internet with traditional sources such as drug labels, we present a new corpus of Russian language health reviews. RESULTS: The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labeled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labeled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labeled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multilabel sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. AVAILABILITY AND IMPLEMENTATION: We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

OBJECTIVE: Research on pharmacovigilance from social media data has focused on mining adverse drug events (ADEs) using annotated datasets, with publications generally focusing on 1 of 3 tasks: ADE classification, named entity recognition for identifying the span of ADE mentions, and ADE mention normalization to standardized terminologies. While the common goal of such systems is to detect ADE signals that can be used to inform public policy, it has been impeded largely by limited end-to-end solutions for large-scale analysis of social media reports for different drugs. MATERIALS AND METHODS: We present a dataset for training and evaluation of ADE pipelines where the ADE distribution is closer to the average 'natural balance' with ADEs present in about 7% of the tweets. The deep learning architecture involves an ADE extraction pipeline with individual components for all 3 tasks. RESULTS: The system presented achieved state-of-the-art performance on comparable datasets and scored a classification performance of F1 = 0.63, span extraction performance of F1 = 0.44 and an end-to-end entity resolution performance of F1 = 0.34 on the presented dataset. DISCUSSION: The performance of the models continues to highlight multiple challenges when deploying pharmacovigilance systems that use social media data. We discuss the implications of such models in the downstream tasks of signal detection and suggest future enhancements. CONCLUSION: Mining ADEs from Twitter posts using a pipeline architecture requires the different components to be trained and tuned based on input data imbalance in order to ensure optimal performance on the end-to-end resolution task.

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.