Computer vision approaches have made huge advances with deep learning research. These algorithms can be employed as a basis for phenotyping of biological traits from imaging modalities. This can be employed, for example, in the context of facial photographs of rare diseases as a means of aiding diagnostic pathways, or as means to large scale phenotyping in histological imaging. With any data set, inherent biases and problems in the data available for training can have a detrimental impact on your models. I will describe some examples of such data set problems and outline how to build models that are not confounded – despite biases in the training data. 

Atherosclerosis is a manifestation of cardiovascular disease consisting of the buildup of inflamed arterial plaques. Because most heart attacks are caused by the rupture of unstable "vulnerable" plaque, the characterization of plaques and their vulnerability remains an outstanding problem in medicine.

Morphoelasticity is a mathematical framework commonly employed to describe tissue growth.

Its central premise is the decomposition of the deformation gradient into the product of an elastic tensor and a growth tensor.

In this talk, I will present some recent efforts to simulate intimal thickening -- the precursor to atherosclerosis -- using morphoelasticity theory.

The arterial wall is composed of three layers: the intima, media and adventitia. 

The intima is allowed to grow isotropically while the area of the media and adventitia is approximately conserved. 

All three layers are modeled as anisotropic hyperelastic materials, reinforced by collagen fibers.

We explore idealized axisymmetric arteries as well as more general geometries that are solved using the finite element method.

Results are discussed in the context of balloon-injury experiments on animals and Glagovian remodeling in humans.

Transdifferentiation, the process of converting from one cell type to another without going through a pluripotent state, has great promise for regenerative medicine. The identification of key transcription factors for reprogramming is limited by the cost of exhaustive experimental testing of plausible sets of factors, an approach that is inefficient and unscalable. We developed a predictive system (Mogrify) that combines gene expression data with regulatory network information to predict the reprogramming factors necessary to induce cell conversion. We have applied Mogrify to 173 human cell types and 134 tissues, defining an atlas of cellular reprogramming. Mogrify correctly predicts the transcription factors used in known transdifferentiations. Furthermore, we validated several new transdifferentiations predicted by Mogrify, including both into and out of the same cell type (keratinocytes). We provide a practical and efficient mechanism for systematically implementing novel cell conversions, facilitating the generalization of reprogramming of human cells. Predictions are made available via http://mogrify.net to help rapidly further the field of cell conversion.

Conical symplectic resolutions are one of the main objects in the contemporary mix of algebraic geometry and representation theory, 

known as geometric representation theory. They cover many interesting families of objects such as quiver varieties and hypertoric

varieties, and some simpler such as Springer resolutions. The last findings [Braverman, Finkelberg, Nakajima] say that they arise

as Higgs/Coulomb moduli spaces, coming from physics. Most of the gadgets attached to conical symplectic resolutions are rather

algebraic, such as their quatizations and $\mathcal{O}$-categories. We are rather interested in the symplectic topology of them, in particular 

finding smooth exact Lagrangians that appear in the central fiber of the (defining) resolution, as they are objects of the Fukaya category.

I am going to report on some developments in regularity theory of nonlinear, degenerate equations, with special emphasis on estimates involving linear and nonlinear potentials. I will cover three main cases: degenerate nonlinear equations, systems, non-uniformly elliptic operators. 

We will study the l1-homology of the 2-class in one relator groups. We will see that there are many qualitative and quantitive similarities between the l1-norm of the top dimensional class and the stable commutator length of the defining relation. As an application we construct manifolds with small simplicial volume.

This work in progress is joint with Clara Loeh.