The use of heuristics to assess the convergence and compress the output of Markov chain Monte Carlo can be sub-optimal in terms of the empirical approximations that are produced. Here we consider the problem of retrospectively selecting a subset of states, of fixed cardinality, from the sample path such that the approximation provided by their empirical distribution is close to optimal. A novel method is proposed, based on greedy minimisation of a kernel Stein discrepancy, that is suitable for problems where heavy compression is required. Theoretical results guarantee consistency of the method and its effectiveness is demonstrated in the challenging context of parameter inference for ordinary differential equations. Software is available in the Stein Thinning package in Python, R and MATLAB.

Motivated by the desire to automate classification of neuron morphologies, we designed a topological signature, the Topological Morphology Descriptor (TMD),  that assigns a so-called “barcode" to any geometric tree (i.e, any finite binary tree embedded in R^3). We showed that the TMD effectively determines  reliable clusterings of random and neuronal trees. Moreover, using the TMD we performed an objective, stable classification of pyramidal cells in the rat neocortex, based only on the shape of their dendrites.

We have also reverse-engineered the TMD, in order to digitally synthesize dendrites, to compensate for the relatively small number of available biological reconstructions. The algorithm we developed, called Topological Neuron Synthesis (TNS), stochastically generates a geometric tree from a barcode, in a biologically grounded manner. The synthesized neurons are statistically indistinguishable from real neurons of the same type, in terms of morpho-electrical properties and  connectivity. We synthesized networks of structurally altered neurons, revealing principles linking branching properties to the structure of large-scale networks.  We have also successfully applied these classification and synthesis techniques to microglia and astrocytes, two other types of cells that populate the brain.

In this talk I will provide an overview of the TMD and the TNS and then describe the results of our theoretical and computational analysis of their behavior and properties.

This talk is based on work in collaborations led by Lida Kanari at the Blue Brain Project.

This is a preparatory study for our ultimate goal of understanding the various instabilities associated with an electrodes-coated dielectric membrane that is subject to mechanical stretching and electric loading. Leaving out electric loading for the moment, we consider bifurcations from the homogeneous solution of a circular or square hyperelastic sheet that is subjected to equibiaxial stretching under either force- or displacement-controlled edge conditions. We derive the condition for axisymmetric necking and show, for the class of strain-energy functions considered, that the critical stretch for necking is greater than the critical stretch for the Treloar-Kearsley (TK) instability and less than the critical stretch for the limiting-point instability. Abaqus simulations are conducted to verify the bifurcation conditions and the expectation that the TK instability should occur first under force control, but when the edge displacement is controlled the TK instability is suppressed, and it is the necking instability that will be observed. It is also demonstrated that axisymmetric necking follows a growth/propagation process typical of all such localization problems.

The placenta is the essential organ of maternal-fetal interactions, where nutrient, oxygen, and waste exchange occur. In recent studies, differences in the morphology of the placental chorionic surface vascular network (PCSVN) have been associated with developmental disorders such as autism. This suggests that the PCSVN could potentially serve as a biomarker for the early diagnosis and treatment of autism. Studying PCSVN features in large cohorts requires a reliable and automated mechanism to extract the vascular networks. In this talk, we present a method for PCSVN extraction. Our algorithm builds upon a directional multiscale mathematical framework based on a combination of shearlets and Laplacian eigenmaps and can isolate vessels with high success in high-contrast images such as those produced in CT scans. 

Connectivity and percolation are two well studied phenomena in random graphs. 

In this talk we will discuss higher-dimensional analogues of connectivity and percolation that occur in random simplicial complexes.

Simplicial complexes are a natural generalization of graphs that consist of vertices, edges, triangles, tetrahedra, and higher dimensional simplexes.

We will mainly focus on random geometric complexes. These complexes are generated by taking the vertices to be a random point process, and adding simplexes according to their geometric configuration.

Our generalized notions of connectivity and percolation use the language of homology - an algebraic-topological structure representing cycles of different dimensions.

In this talk we will discuss recent results analyzing phase transitions related to these topological phenomena. 

The experimental evidence of the existence of a feedback between growth and stress in tumors poses challenging questions. First, the rheological properties (the constitutive equations) of aggregates of malignant cells are to identified. Secondly, the feedback law (the "growth law") that relates stress and mitotic and apoptotic rate should be understood. We address these questions on the basis of a theoretical analysis of in vitro experiments that involve the growth of tumor spheroids. We show that solid tumors exhibit several mechanical features of a poroelastic material, where the cellular component behaves like an elastic solid. When the solid component of the spheroid is loaded at the boundary, the cellular aggregate grows up to an asymptotic volume that depends on the exerted compression.
Residual stress shows up when solid tumors are radially cut, highlighting a peculiar tensional pattern.
The features of the mechanobiological system can be explained in terms of a feedback of mechanics on the cell proliferation rate as modulated by the availability of nutrient, that is radially damped by the balance between diffusion and consumption. The volumetric growth profiles and the pattern of residual stress can be theoretically reproduced assuming a dependence of the target stress on the concentration of nutrient which is specific of the malignant tissue.