Experimental biologists study diseases mostly through their abnormal molecular or cellular features. For example, they investigate genetic abnormalities in cancer, hormonal imbalances in diabetes, or an aberrant immune system in vascular diseases. Moreover, many diseases also have a mechanical component which is critical to their deadliness. Most notably, cancer kills typically through metastasis, where the cancer cells acquire the capability to remodel their adhesions and to migrate. Solid tumours are also characterised by physical changes in the extracellular matrix – the material surrounding the cells. While such physical changes are long known, only relatively recent research revealed that cells can sense altered physical properties and transduce them into chemical information. An example is the YAP/TAZ signalling pathway that can activate in response to altered matrix mechanics and that can drive tumour phenotypes such as the rate of cell proliferation.
Systems-biology models aim to study diseases holistically. In this talk, I will argue that physical signatures are a critical part of many diseases and therefore, need to be incorporated into systems-biology. Crucially, physical disease signatures bi-directionally interact with molecular and cellular signatures, presenting a major challenge to developing such models. I will present several examples of recent and ongoing work aimed at uncovering the relations between mechanical and molecular/cellular signatures in health and disease. I will discuss how blood vessel cells interact mechano-chemically with each other to regulate the passage of cells and nutrients between blood and tissue and how cancer cells grow and die in response to mechanical and geometrical stimuli.

Effectiveness of COVID-19 vaccines was first demonstrated in randomised trials, but many questions of vital importance to vaccination policies could only be addressed in subsequent observational studies. The pandemic led to a step change in the availability of population-level linked electronic health record data, analysed in privacy-protecting Trusted Research Environments, across the UK. I will discuss methodological approaches to estimating causal effects of COVID-19 vaccines, and their application in estimating vaccine effectiveness and quantifying waning vaccine effectiveness. I will present results from recent analyses using detailed linked data on up to 24 million people in the OpenSAFELY Trusted Research Environment, which was developed by the University of Oxford's Bennett Institute for Applied Data Science.

Understanding the molecular mechanisms that control the biology of health and disease requires development of models that traverse multiple scales of organisation in order to encapsulate the relationships between genes and linking to observable phenotypes. Measuring, parameterising and simulating the entire system that determines these phenotypes in exhaustive detail is typically impossible due to the underlying biological complexity, our limited knowledge and the paucity of available data. For example, approximately one third of human genes are poorly characterised and most genes perform multiple functions, which manifest according to the surrounding biochemical context. Indeed, new functions continue to emerge even for deeply studied genes. Therefore, simplifying abstractions in concert with empirical analysis of matched genome-scale and descriptive data are valuable strategies to fill knowledge gaps relevant to a focused biomedical question or hypothesis.

Epithelial plasticity is a key driver of cancer progression and is associated with the most life-threatening phenotypes; specifically, metastasis and drug resistance. Computational methods developed in my group enable modelling the molecular control of important cancer phenotypes. We applied a machine learning approach for genome-wide context-specific biochemical interaction network inference (CoSNI) to map gene function for the Epithelial to Mesenchymal Transition cell programme (EMT_MAP), predicting new mechanisms in control of cancer invasion. Analysis of patient data with EMT_MAP and our NetNC algorithm [Cancers 2020;12:2823; https://github.com/overton-group/NetNC] enabled discovery of candidate renal cancer prognostic markers with clear advantages over standard statistical approaches. NetNC recovers the network-defined signal in noisy data, for example distinguishing functional EMT Transcription Factor targets from ‘neutral’ binding sites and defining biologically coherent modules in renal cancer drug response time course data. These and other approaches, including SynLeGG (Nucleic Acids Research 2021;49:W613-8, www.overton-lab.uk/synlegg) and an information-theoretic approach to causality (GABI) offer mechanistic insights and opportunity to predict candidate cancer Achilles’ heels for drug discovery. Computational results were validated in follow-up experiments, towards new clinical tools for precision oncology.

Dynamical systems models are a powerful tool for analyzing interactions in ecosystems and their intrinsic properties such as stability and resilience. The human intestinal microbiome is a complex ecosystem of hundreds of microbial species, critical to our health, and when in a disrupted state termed dysbiosis, is involved in a variety of diseases.  Although dysbiosis remains incompletely understood, it is not caused by single pathogens, but instead involves broader disruptions to the microbial ecosystem.  Dynamical systems models would thus seem a natural approach for analyzing dysbiosis, but have been hampered by the scale of the human gut microbiome, which constitutes hundreds of thousands of potential ecological interactions, and is profiled using sparse and noisy measurements. Here we introduce a combined experimental and statistical machine learning approach that overcomes these challenges to provide the first comprehensive and predictive model of microbial dynamics at ecosystem-scale. We show that dysbiosis is characterized by competitive cycles of interactions among microbial species, in contrast to the healthy microbiome, which is stabilized by chains of positive interactions initiated by resistant starch-degrading bacteria. To achieve these results, we created cohorts of “humanized” gnotobiotic mice via fecal transplantation from healthy and dysbiotic human donors, and subjected mice to dietary and antibiotic perturbations, in the densest temporal interventional study to date. We demonstrate that our probabilistic machine learning method achieves scalability while maintaining interpretability on these data, by inferring a small number of modules of bacterial taxa that share common interactions and responses to perturbations. Our findings provide new insights into the mechanisms of microbial dysbiosis, have potential implications for therapies to restore the microbiome to treat disease, and moreover offer a powerful framework for analyzing other complex ecosystems.

In embryonic development, formation of the retinal vasculature is  critically dependent on prior establishment of a mesh of astrocytes.  
Astrocytes emerge from the optic nerve head and then migrate over the retinal surface in a radially symmetric manner and mature through 
differentiation.  We develop a PDE model describing the migration and  differentiation of astrocytes, and numerical simulations are compared to 
experimental data to assist in elucidating the mechanisms responsible for the distribution of astrocytes via parameter analysis. This is joint 
work with Timothy Secomb.

We introduce meta-factorization, a theory that describes matrix decompositions as solutions of linear matrix equations: the projector and the reconstruction equation. Meta-factorization reconstructs known factorizations, reveals their internal structures, and allows for introducing modifications, as illustrated with SVD, QR, and UTV factorizations. The prospect of meta-factorization also provides insights into computational aspects of generalized matrix inverses and randomized linear algebra algorithms. The relations between the Moore-Penrose pseudoinverse, generalized Nyström method, and the CUR decomposition are revealed here as an illustration. Finally, meta-factorization offers hints on the structure of new factorizations and provides the potential of creating them. 

In commutative algebra localizing a ring and its modules is a fundamental technique. In the general case of a Grothendieck abelian category or even a triangulated category with small direct sums this is replaced by forming the quotient category by a localizing subcategory. Therefore the classification of these localizing subcategories becomes an important problem. I will begin by recalling the case of the (derived) module category of a commutative noetherian ring due to Gabriel and Hopkins/Neeman, respectively, in order to give an idea how such a classification can look like.

The case of interest in this talk is the derived category D(G) of smooth representation in characteristic p of a p-adic Lie group G. This is motivated by the emerging p-adic Langlands program. In joint work with C. Heyer we have some modest initial results if G is compact pro-p or abelian. which I will present.

1pm Jonathan Tam: Markov decision processes with observation costs

We present a framework for a controlled Markov chain where the state of the chain is only given at chosen observation times and of a cost. Optimal strategies therefore involve the choice of observation times as well as the subsequent control values. We show that the corresponding value function satisfies a dynamic programming principle, which leads to a system of quasi-variational inequalities (QVIs). Next, we give an extension where the model parameters are not known a priori but are inferred from the costly observations by Bayesian updates. We then prove a comparison principle for a larger class of QVIs, which implies uniqueness of solutions to our proposed problem. We utilise penalty methods to obtain arbitrarily accurate solutions. Finally, we perform numerical experiments on three applications which illustrate our framework.

Preprint at https://arxiv.org/abs/2201.07908

1.45pm Remy Messadene: signature asymptotics, empirical processes, and optimal transport

Rough path theory provides one with the notion of signature, a graded family of tensors which characterise, up to a negligible equivalence class, and ordered stream of vector-valued data. In the last few years, use of the signature has gained traction in time-series analysis, machine learning, deep learning and more recently in kernel methods. In this work, we lay down the theoretical foundations for a connection between signature asymptotics, the theory of empirical processes, and Wasserstein distances, opening up the landscape and toolkit of the second and third in the study of the first. Our main contribution is to show that the Hambly-Lyons limit can be reinterpreted as a statement about the asymptotic behaviour of Wasserstein distances between two independent empirical measures of samples from the same underlying distribution. In the setting studied here, these measures are derived from samples from a probability distribution which is determined by geometrical properties of the underlying path.

2.30-3.00 Tea & coffee in the mezzananie

3-4pm Julien Berestycki: Extremal point process of the branching Brownian motion