Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlook

Deep learning has become a powerful tool in computational biology, revolutionising the analysis and interpretation of biological data over time. In our article review, we delve into various aspects of deep learning in computational biology. Specifically, we examine its history, advantages, and challenges. Our focus is on two primary applications: DNA sequence classification and prediction, as well as protein structure prediction from sequence data. Additionally, we provide insights into the outlook for this field. To fully harness the potential of deep learning in computational biology, it is crucial to address the challenges that come with it. These challenges include the requirement for large, labelled datasets and the interpretability of deep learning models. The use of deep learning in the analysis of DNA sequences has brought about a significant transformation in the detection of genomic variants and the analysis of gene expression. This has greatly contributed to the advancement of personalised medicine and drug discovery. Convolutional neural networks (CNNs) have been shown to be highly accurate in predicting genetic variations and gene expression levels. Deep learning techniques are used for analysing epigenetic data, including DNA methylation and histone modifications. This provides valuable insights into metabolic conditions and gene regulation. The field of protein structure prediction has been significantly impacted by deep learning, which has enabled accurate determination of the three-dimensional shape of proteins and prediction of their interactions. The future of deep learning in computational biology looks promising. With the development of advanced deep learning models and interpretation techniques, there is potential to overcome current challenges and further our understanding of biological systems.

OLGA : An Ontology and LSTM-based approach for generating Arithmetic Word Problems (AWPs) of transfer type

Machine generation of Arithmetic Word Problems (AWPs) is challenging as they express quantities and mathematical relationships and need to be consistent. ML-solvers require a large annotated training set of consistent problems with language variations. Exploiting domain-knowledge is needed for consistency checking whereas LSTM-based approaches are good for producing text with language variations. Combining these we propose a system, OLGA, to generate consistent word problems of TC (Transfer-Case) type, involving object transfers among agents. Though we provide a dataset of consistent 2-agent TC-problems for training, only about 36% of the outputs of an LSTM-based generator are found consistent. We use an extension of TC-Ontology, proposed by us previously, to determine the consistency of problems. Among the remaining 64%, about 40% have minor errors which we repair using the same ontology. To check consistency and for the repair process, we construct an instance-specific representation (ABox) of an auto-generated problem. We use a sentence classifier and BERT models for this task. The training set for these LMs is problem-texts where sentence-parts are annotated with ontology class-names. As three-agent problems are longer, the percentage of consistent problems generated by an LSTM-based approach drops further. Hence, we propose an ontology-based method that extends consistent 2-agent problems into consistent 3-agent problems. Overall, our approach generates a large number of consistent TC-type AWPs involving 2 or 3 agents. As ABox has all the information of a problem, any annotations can also be generated. Adopting the proposed approach to generate other types of AWPs is interesting future work.