Multimodal Transformers for Biomedical Text and Knowledge Graph Data

Recent advances in Natural Language Processing have substantially improved contextualized representations of language. However, the inclusion of factual knowledge, particularly in the biomedical domain, remains challenging. Hence, many Language Models (LMs) are extended by Knowledge Graphs (KGs), but most approaches require entity linking (i.e., explicit alignment between text and KG entities). Inspired by single-stream multimodal Transformers operating on text, image and video data, this thesis proposes the Sophisticated Transformer trained on biomedical text and Knowledge Graphs (STonKGs). STonKGs incorporates a novel multimodal architecture based on a cross encoder that uses the attention mechanism on a concatenation of input sequences derived from text and KG triples, respectively. Over 13 million so-called text-triple pairs, coming from PubMed and assembled using the Integrated Network and Dynamical Reasoning Assembler (INDRA), were used in an unsupervised pre-training procedure to learn representations of biomedical knowledge in STonKGs. By comparing STonKGs to an NLP- and a KG-baseline (operating on either text or KG data) on a benchmark consisting of eight fine-tuning tasks, the proposed knowledge integration method applied in STonKGs was empirically validated. Specifically, on tasks with a comparatively small dataset size and a larger number of classes, STonKGs resulted in considerable performance gains, beating the F1-score of the best baseline by up to 0.083. Both the source code as well as the code used to implement STonKGs are made publicly available so that the proposed method of this thesis can be extended to many other biomedical applications

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs

While most approaches individually exploit unstructured data from the biomedical literature or structured data from biomedical knowledge graphs, their union can better exploit the advantages of such approaches, ultimately improving representations of biology. Using multimodal transformers for such purposes can improve performance on context dependent classication tasks, as demonstrated by our previous model, the Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs (STonKGs). In this work, we introduce ProtSTonKGs, a transformer aimed at learning all-encompassing representations of protein-protein interactions. ProtSTonKGs presents an extension to our previous work by adding textual protein descriptions and amino acid sequences (i.e., structural information) to the text- and knowledge graph-based input sequence used in STonKGs. We benchmark ProtSTonKGs against STonKGs, resulting in improved F1 scores by up to 0.066 (i.e., from 0.204 to 0.270) in several tasks such as predicting protein interactions in several contexts. Our work demonstrates how multimodal transformers can be used to integrate heterogeneous sources of information, paving the foundation for future approaches that use multiple modalities for biomedical applications

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

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 (KGEMs). 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. This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against two 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 0.083. Additionally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications. Finally, the source code and pre-trained STonKGs models are available at https://github.com/stonkgs/stonkgs and https://huggingface.co/stonkgs/stonkgs-150k