Related papers: Artificial Intelligence and Deep Learning Algorith…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Congenital heart disease is among the most common fetal abnormalities and birth defects. Despite identifying numerous risk factors influencing its onset, a comprehensive understanding of its genesis and management across diverse populations…
Inherited retinal diseases (IRDs) are a diverse group of genetic disorders that lead to progressive vision loss and are a major cause of blindness in working-age adults. The complexity and heterogeneity of IRDs pose significant challenges…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
Evolutionary algorithms (EAs) are population-based metaheuristics, originally inspired by aspects of natural evolution. Modern varieties incorporate a broad mixture of search mechanisms, and tend to blend inspiration from nature with…
Recent advancements in artificial intelligence (AI) have revolutionized cardiovascular medicine, particularly through integration with computed tomography (CT), magnetic resonance imaging (MRI), electrocardiography (ECG) and ultrasound…
Life finds a way. For sessile organisms like plants, the need to adapt to changes in the environment is even more poignant. For humanity, the need to develop crops that can grow in diverse environments and feed our growing population is an…
Neural machine learning methods, such as deep neural networks (DNN), have achieved remarkable success in a number of complex data processing tasks. These methods have arguably had their strongest impact on tasks such as image and audio…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Artificial intelligence (AI) techniques have significant potential to enable effective, robust and automated image phenotyping including identification of subtle patterns. AI-based detection searches the image space to find the regions of…
Explainable Artificial Intelligence (AI) in the form of an interpretable and semiautomatic approach to stage grading ocular pathologies such as Diabetic retinopathy, Hypertensive retinopathy, and other retinopathies on the backdrop of major…
Motivation: Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patterns along the…
Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…
A deep generative model such as a GAN learns to model a rich set of semantic and physical rules about the target distribution, but up to now, it has been obscure how such rules are encoded in the network, or how a rule could be changed. In…
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular…
Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…