Understanding the impact of societal and economic change on the labour market is important for many causes, such as automation or the post-carbon transition. Occupational mobility plays a role in how these changes impact the labour market because of indirect effects, brought on by the different levels of direct impact felt by individual occupations. We develop an agent-based model which uses a network representation of the labour market to understand these impacts. This network connects occupations that workers have transitioned between in the past, and captures the complex structure of relationships between occupations within the labour market. We develop these networks in both space and time using rich survey data to compare occupational mobility across the United States and through economic upturns and downturns to start understanding the factors that influence differences in occupational mobility.

For almost calibrated Lagrangian mean curvature flow it is known that all singularities are of Type II. To understand the finer structure of the singularities forming, it is thus necessary to understand the structure of general ancient solutions arising as potential limit flows at such singularities. We will discuss recent progress showing that ancient solutions with a blow-down a pair of static planes meeting along a 1-dimensional line are translators. This is joint work with J. Lotay and G. Szekelyhidi.

Let $N$ be a compact Riemannian manifold of dimension 3 or higher, and $g$ a Lipschitz non-negative (or non-positive) function on $N$. In joint works with Neshan Wickramasekera we prove that there exists a closed hypersurface $M$ whose mean curvature attains the values prescribed by $g$. Except possibly for a small singular set (of codimension 7 or higher), the hypersurface $M$ is $C^2$ immersed and two-sided (it admits a global unit normal); the scalar mean curvature at $x$ is $g(x)$ with respect to a global choice of unit normal. More precisely, the immersion is a quasi-embedding, namely the only non-embedded points are caused by tangential self-intersections: around such a non-embedded point, the local structure is given by two disks, lying on one side of each other, and intersecting tangentially (as in the case of two spherical caps touching at a point). A special case of PMC (prescribed-mean-curvature) hypersurfaces is obtained when $g$ is a constant, in which the above result gives a CMC (constant-mean-curvature) hypersurface for any prescribed value of the mean curvature.

Recent advances in Deep Learning have enabled us to explore new application domains in molecular biology and drug discovery - including those driven by complex processes that defy analytical modelling.  However, despite the combined forces of increased data, improving compute resources and continuous algorithmic innovation all bringing previously intractable problems into the realm of possibility, many advances are yet to make a tangible impact for life science discovery.  In this talk, Dr Marcin J. Skwark will discuss the challenge of bringing machine learning innovation to tangible real-world impact.  Following a general introduction of the topic, as well as newly available methods and data, he will focus on the modelling of COVID-19 variants and, in particular, the DeepChain Early Warning System (EWS) developed by InstaDeep in collaboration with BioNTech.  With thousands of new, possibly dangerous, SARS-CoV-2 variants emerging each month worldwide, it is beyond humanities combined capacity to experimentally determine the immune evasion and transmissibility characteristics of every one.  EWS builds on an experimentally tested AI-first computational biology platform to evaluate new variants in minutes, and is capable of risk monitoring variant lineages in near real-time.  This is done by combining an AI-driven protein structure prediction framework with large, spike protein sequence-oriented Transformer models to allow for rapid simulation-free assessment of the immune escape risk and expected fitness of new variants, conditioned on the current state of the world.  The system has been extensively validated in cooperation with BioNTech, both in terms of host cell infection propensity (including experimental assays of receptor binding affinity), and immune escape (pVNT assays with monoclonal antibodies and real-life donor sera). In these assessments, purely unsupervised, data-first methods of EWS have shown remarkable accuracy. EWS flags and ranks all but one of the SARS-CoV-2 Variants of Concern (Alpha, Beta, Gamma, Delta… Omicron), discriminates between subvariants (e.g. BA.1/BA.2/BA.4 etc. distinction) and for most of the adverse events allows for proactive response on the day of the observation. This allows for appropriate response on average six weeks before it is possible for domain experts using domain knowledge and epidemiological data. The performance of the system, according to internal benchmarks, improves with time, allowing for example for supporting the decisions on the emerging Omicron subvariants on the first days of their occurrence. EWS impact has been notable in general media [2, 3] for the system's applicability to a novel problem, ability to derive generalizable conclusions from unevenly distributed, sparse and noisy data, to deliver insights which otherwise necessitate long and costly experimental assays.

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.