1600-1645 - Philip Maini
1645-1705 - Edward Morrissey
1705-1725 - Heather Harrington
1725-1800 - Drinks and networking

The talks will be followed by a drinks reception.

Tickets can be obtained from https://www.eventbrite.co.uk/e/qbiox-colloquium-trinity-term-2018-ticke….
(As ever, tickets are not necessary, but they do help in judging catering requirements.)

PHILIP MAINI

Does mathematics have anything to do with biology? In this talk, I will review a number of interdisciplinary collaborations in which I have been involved over the years that have coupled mathematical modelling with experimental studies to try to advance our understanding of processes in biology and medicine. Examples will include somatic evolution in tumours, collective cell movement in epithelial sheets, cell invasion in neural crest, and pattern formation in slime mold. These are examples where verbal reasoning models are misleading and insufficient, while mathematical models can enhance our intuition.

EDWARD MORRISEY

Fixation and spread of somatic mutations in adult human colonic epithelium Cancer causing mutations must become permanently fixed within tissues. I will describe how, by visualizing somatic clones, we investigated the means and timing with which this occurs in the human colonic epithelium. Modelling the effects of gene mutation, stem cell dynamics and subsequent lateral expansion revealed that fixation required two sequential steps. First, one of around seven active stem cells residing within each colonic gland has to be mutated. Second, the mutated stem cell has to replace neighbours to populate the entire gland. This process takes many years because stem cell replacement is infrequent (around once every 9 months). Subsequent clonal expansion due to gland fission is also rare for neutral mutations. Pro-oncogenic mutations can subvert both stem cell replacement to accelerate fixation and clonal expansion by gland fission to achieve high mutant allele frequencies with age. The benchmarking and quantification of these behaviours allows the advantage associated with different gene specific mutations to be compared and ranked irrespective of the cellular mechanisms by which they are conferred. The age related mutational burden of advantaged mutations can be predicted on a gene-by-gene basis to identify windows of opportunity to affect fixation and limit spread.

HEATHER HARRINGTON

Comparing models with data using computational algebra In this talk I will discuss how computational algebraic geometry and topology can be useful for studying questions arising in systems biology. In particular I will focus on the problem of comparing models and data through the lens of computational algebraic geometry and statistics. I will provide concrete examples of biological signalling systems that are better understood with the developed methods.

We present a state-sum construction of TFTs on r-spin surfaces which
uses a combinatorial model of r-spin structures. We give an example of
such a TFT which computes the Arf invariant for r even. We use the
combinatorial model and this TFT to calculate diffeomorphism classes of
r-spin surfaces with parametrized boundary.

Elements of a finitely generated group have a natural notion of length: namely the length of a shortest word over the generators that represents the element. This allows us to study the growth of such groups by considering the size of spheres with increasing radii. One current area of interest is the rationality or otherwise of the formal power series whose coefficients are the sphere sizes. I will describe a combinatorial way to study this series for the class of virtually abelian groups, introduced by Benson in the 1980s, and then outline its applications to other types of growth series.

Semidefinite convex optimization problems often have low-rank solutions that can be represented with O(p)-storage. However, semidefinite programming methods require us to store the matrix decision variable with size O(p^2), which prevents the application of virtually all convex methods at large scale.

Indeed, storage, not arithmetic computation, is now the obstacle that prevents us from solving large- scale optimization problems. A grand challenge in contemporary optimization is therefore to design storage-optimal algorithms that provably and reliably solve large-scale optimization problems in key scientific and engineering applications. An algorithm is called storage optimal if its working storage is within a constant factor of the memory required to specify a generic problem instance and its solution.

So far, convex methods have completely failed to satisfy storage optimality. As a result, the literature has largely focused on storage optimal non-convex methods to obtain numerical solutions. Unfortunately, these algorithms have been shown to be provably correct only under unverifiable and unrealistic statistical assumptions on the problem template. They can also sacrifice the key benefits of convexity, as they do not use key convex geometric properties in their cost functions.

To this end, my talk introduces a new convex optimization algebra to obtain numerical solutions to semidefinite programs with a low-rank matrix streaming model. This streaming model provides us an opportunity to integrate sketching as a new tool for developing storage optimal convex optimization methods that go beyond semidefinite programming to more general convex templates. The resulting algorithms are expected to achieve unparalleled results for scalable matrix optimization problems in signal processing, machine learning, and computer science.

Thompson's group F is a group of homeomorphisms of the unit interval which exhibits a strange mix of properties; on the one hand it has some self-similarity type properties one might expect of a really big group, but on the other hand it is finitely presented. I will give a proof of finite generation by expressing elements as pairs of binary trees.

Every topological space is metrisable once the symmetry axiom is abandoned and the codomain of the metric is allowed to take values in a suitable structure tailored to fit the topology (and every completely regular space is similarly metrisable while retaining symmetry). This result was popularised in 1988 by Kopperman, who used value semigroups as the codomain for the metric, and restated in 1997 by Flagg, using value quantales. In categorical terms, each of these constructions extends to an equivalence of categories between the category Top and a category of all L-valued metric spaces (where L ranges over either value semigroups or value quantales) and the classical \epsilon-\delta notion of continuous mappings. Thus, there are (at least) two metric formalisms for topology, raising the questions: 1) is any of the two actually useful for doing topology? and 2) are the two formalisms equally powerful for the purposes of topology? After reviewing Flagg's machinery I will attempt to answer the former affirmatively and the latter negatively. In more detail, the two approaches are equipotent when it comes to point-to-point topological consideration, but only Flagg's formalism captures 'higher order' topological aspects correctly, however at a price; there is no notion of product of value quantales. En route to establishing Flagg's formalism as convenient, it will be shown that both fine and coarse variants of homology and homotopy arise as left and right Kan extensions of genuinely metrically constructed functors, and a topologically relevant notion of tensor product of value quantales, a surrogate for the non-existent products, will be described. 


 

Nash-Williams showed that the collection of locally finite trees under the topological minor relation results in a BQO. Naturally, two interesting questions arise:

1.      What is the number \lambda of topological types of locally finite trees?

2.       What are the possible sizes of an equivalence class of locally finite trees?

 For (1), clearly, \omega_0 \leq \lambda \leq c and Matthiesen refined it to \omega_1 \leq \lambda \leq c. Thus, this question becomes non-trivial in the absence of the Continuum Hypothesis. In this paper we address both questions by showing - entirely within ZFC - that for a large collection of locally finite trees that includes those with countably many rays:

- \lambda = \omega_1, and

- the size of an equivalence class can only be either 1 or c.