Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

This paper addresses the following question of neural network identifiability: Does the input-output map realized by a feed-forward neural network with respect to a given nonlinearity uniquely specify the network architecture, weights, and biases? Existing literature on the subject Sussman 1992, Albertini, Sontag et.al 1993, Fefferman 1994 suggests that the answer should be yes, up to certain symmetries induced by the nonlinearity, and provided the networks under consideration satisfy certain "genericity conditions". The results in Sussman 1992 and Albertini, Sontag et.al 1993 apply to networks with a single hidden layer and in Fefferman 1994 the networks need to be fully connected. In an effort to answer the identifiability question in greater generality, we derive necessary genericity conditions for the identifiability of neural networks of arbitrary depth and connectivity with an arbitrary nonlinearity. Moreover, we construct a family of nonlinearities for which these genericity conditions are minimal, i.e., both necessary and sufficient. This family is large enough to approximate many commonly encountered nonlinearities to arbitrary precision in the uniform norm.

Graph neural networks have become one of the most important techniques to solve machine learning problems on graph-structured data. Recent work on vertex classification proposed deep and distributed learning models to achieve high performance and scalability. However, we find that the feature vectors of benchmark datasets are already quite informative for the classification task, and the graph structure only provides a means to denoise the data. In this paper, we develop a theoretical framework based on graph signal processing for analyzing graph neural networks. Our results indicate that graph neural networks only perform low-pass filtering on feature vectors and do not have the non-linear manifold learning property. We further investigate their resilience to feature noise and propose some insights on GCN-based graph neural network design.

Abstract-- We applied predefined kernels also known as filters or masks developed for image processing to convolution neural network. Instead of letting neural networks find its own kernels, we used 41 different general-purpose kernels of blurring, edge detecting, sharpening, discrete cosine transformation, etc. for the first layer of the convolution neural networks. This architecture, thus named as general filter convolutional neural network (GFNN), can reduce training time by 30% with a better accuracy compared to the regular convolutional neural network (CNN). GFNN also can be trained to achieve 90% accuracy with only 500 samples. Furthermore, even though these kernels are not specialized for the MNIST dataset, we achieved 99.56% accuracy without ensemble nor any other special algorithms.