Artificial intelligence for natural product drug discovery

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Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native env ...

Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social in ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

Machine learning (ML) enables artificial intelligent (AI) agents to learn autonomously from data obtained from their environment to perform tasks. Modern ML systems have proven to be extremely effective, reaching or even exceeding human intelligence. Altho ...

A range of behavioral and contextual factors, including eating and drinking behavior, mood, social context, and other daily activities, can significantly impact an individual's quality of life and overall well-being. Therefore, inferring everyday life aspe ...

In this thesis, we study two closely related directions: robustness and generalization in modern deep learning. Deep learning models based on empirical risk minimization are known to be often non-robust to small, worst-case perturbations known as adversari ...

The upcoming Square Kilometre Array Observatory will produce images of neutral hydrogen distribution during the epoch of reionization by observing the corresponding 21-cm signal. However, the 21-cm signal will be subject to instrumental limitations such as ...

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Epilepsy, a major neurological disease, requires careful diagnosis and treatment. However, the detection of epileptic seizures remains a significant challenge. Current clinical practice relies on expert analysis of EEG signals, a process that is time-consu ...

Deep learning models (DLM) are efficient replacements for computationally intensive optimization techniques. Musculoskeletal models (MSM) typically involve resource-intensive optimization processes for determining joint and muscle forces. Consequently, DLM ...

Mitigating the energy requirements of artificial intelligence requires novel physical substrates for computation. Phononic metamaterials have vanishingly low power dissipation and hence are a prime candidate for green, always-on computers. However, their u ...

Throughout history, the pace of knowledge and information sharing has evolved into an unthinkable speed and media. At the end of the XVII century, in Europe, the ideas that would shape the "Age of Enlightenment" were slowly being developed in coffeehouses, ...

Monitoring forests, in particular their response to climate and land use change, requires studying long time scales. While efficient deep learning methods have been developed to process short time series of satellite imagery, leveraging long time series of ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Earth scientists study a variety of problems with remote sensing data, but they most often consider them in isolation from each other, which limits information flows across disciplines. In this work, we present METEOR, a meta-learning methodology for Earth ...

Artificial intelligence for natural product drug discovery

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Design of Highly Functional Genome Editors by Modelling Crispr-cas Sequences

Machine learning-aided generative molecular design

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Predicting the long-term collective behaviour of fish pairs with deep learning

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Computational drug development for membrane protein targets

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

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Predicting protein interactions using geometric deep learning on protein surfaces

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Opportunities and challenges in design and optimization of protein function

Meta-learning to address diverse Earth observation problems across resolutions