Helena Balabin

The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models. However, representations based on a single modality are inherently limited.To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs (KGs). This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations in a shared embedding space. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against three baseline models trained on either one of the modalities (i.e. text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.084 (i.e. from 0.881 to 0.965). Finally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications.We make the source code and the Python package of STonKGs available at GitHub (https://github.com/stonkgs/stonkgs) and PyPI (https://pypi.org/project/stonkgs/). The pre-trained STonKGs models and the task-specific classification models are respectively available at https://huggingface.co/stonkgs/stonkgs-150k and https://zenodo.org/communities/stonkgs.Supplementary data are available at Bioinformatics online.

In recent years, representations from brain activity patterns and pre-trained language models have been linked to each other based on neural fits to validate hypotheses about language processing. Nonetheless, open questions remain about what intrinsic properties of language processing these neural fits reflect and whether they differ across neural fit approaches, brain networks, and models. In this study, we use parallel sentence and functional magnetic resonance imaging data to perform a comprehensive analysis of four paradigms (masked language modeling, pragmatic coherence, semantic comparison, and contrastive learning) representing linguistic hypotheses about sentence processing. We include three sentence embedding models for each paradigm, resulting in a total of 12 models, and examine differences in their neural fit to four different brain networks using regression-based neural encoding and Representational Similarity Analysis (RSA). Among the different models tested, GPT-2, SkipThoughts, and S-RoBERTa yielded the strongest correlations with language network patterns, whereas contrastive learning-based models resulted in overall low neural fits. Our findings demonstrate that neural fits vary across brain networks and models representing the same linguistic hypothesis (e.g., GPT-2 and GPT-3). More importantly, we show the need for both neural encoding and RSA as complementary methods to provide full understanding of neural fits. All code used in the analysis is publicly available: https://github.com/lcn-kul/sentencefmricomparison.