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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.
A qualitative study of Machine Learning practices and engineering challenges in Earth Observation
(2021)
Machine Learning (ML) is ubiquitously on the advance. Like many domains, Earth Observation (EO) also increasingly relies on ML applications, where ML methods are applied to process vast amounts of heterogeneous and continuous data streams to answer socially and environmentally relevant questions. However, developing such ML- based EO systems remains challenging: Development processes and employed workflows are often barely structured and poorly reported. The application of ML methods and techniques is considered to be opaque and the lack of transparency is contradictory to the responsible development of ML-based EO applications. To improve this situation a better understanding of the current practices and engineering-related challenges in developing ML-based EO applications is required. In this paper, we report observations from an exploratory study where five experts shared their view on ML engineering in semi-structured interviews. We analysed these interviews with coding techniques as often applied in the domain of empirical software engineering. The interviews provide informative insights into the practical development of ML applications and reveal several engineering challenges. In addition, interviewees participated in a novel workflow sketching task, which provided a tangible reflection of implicit processes. Overall, the results confirm a gap between theoretical conceptions and real practices in ML development even though workflows were sketched abstractly as textbook-like. The results pave the way for a large-scale investigation on requirements for ML engineering in EO.
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
(2022)
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.
Graph databases employ graph structures such as nodes, attributes and edges to model and store relationships among data. To access this data, graph query languages (GQL) such as Cypher are typically used, which might be difficult to master for end-users. In the context of relational databases, sequence to SQL models, which translate natural language questions to SQL queries, have been proposed. While these Neural Machine Translation (NMT) models increase the accessibility of relational databases, NMT models for graph databases are not yet available mainly due to the lack of suitable parallel training data. In this short paper we sketch an architecture which enables the generation of synthetic training data for the graph query language Cypher.
Focus on what matters: improved feature selection techniques for personal thermal comfort modelling
(2022)
Occupants' personal thermal comfort (PTC) is indispensable for their well-being, physical and mental health, and work efficiency. Predicting PTC preferences in a smart home can be a prerequisite to adjusting the indoor temperature for providing a comfortable environment. In this research, we focus on identifying relevant features for predicting PTC preferences. We propose a machine learning-based predictive framework by employing supervised feature selection techniques. We apply two feature selection techniques to select the optimal sets of features to improve the thermal preference prediction performance. The experimental results on a public PTC dataset demonstrated the efficiency of the feature selection techniques that we have applied. In turn, our PTC prediction framework with feature selection techniques achieved state-of-the-art performance in terms of accuracy, Cohen's kappa, and area under the curve (AUC), outperforming conventional methods.