The cell signaling structure function

Live cell microscopy captures 5-D $(x,y,z,channel,time)$ movies that display patterns of cellular motion and signaling dynamics. We present here an approach to finding spatiotemporal patterns of cell signaling dynamics in 5-D live cell microscopy movies unique in requiring no a priori knowledge of expected pattern dynamics, and no training data. The proposed cell signaling structure function (SSF) is a Kolmogorov structure function that optimally measures cell signaling state as nuclear intensity w.r.t. surrounding cytoplasm, a significant improvement compared to the current state-of-the-art cytonuclear ratio. SSF kymographs store at each spatiotemporal cell centroid the SSF value, or a functional output such as velocity. Patterns of similarity are identified via the metric normalized compression distance (NCD). The NCD is a reproducing kernel for a Hilbert space that represents the input SSF kymographs as points in a low dimensional embedding that optimally captures the pattern similarity identified by the NCD throughout the space. The only parameter is the expected cell radii ($\mu m$). A new formulation of the cluster structure function optimally estimates how meaningful an embedding from the RKHS representation. Results are presented quantifying the impact of ERK and AKT signaling between different oncogenic mutations, and by the relation between ERK signaling and cellular velocity patterns for movies of 2-D monolayers of human breast epithelial (MCF10A) cells, 3-D MCF10A spheroids under optogenetic manipulation of ERK, and human induced pluripotent stem cells

Data-Driven Representation Learning in Multimodal Feature Fusion

abstract: Modern machine learning systems leverage data and features from multiple modalities to gain more predictive power. In most scenarios, the modalities are vastly different and the acquired data are heterogeneous in nature. Consequently, building highly effective fusion algorithms is at the core to achieve improved model robustness and inferencing performance. This dissertation focuses on the representation learning approaches as the fusion strategy. Specifically, the objective is to learn the shared latent representation which jointly exploit the structural information encoded in all modalities, such that a straightforward learning model can be adopted to obtain the prediction. We first consider sensor fusion, a typical multimodal fusion problem critical to building a pervasive computing platform. A systematic fusion technique is described to support both multiple sensors and descriptors for activity recognition. Targeted to learn the optimal combination of kernels, Multiple Kernel Learning (MKL) algorithms have been successfully applied to numerous fusion problems in computer vision etc. Utilizing the MKL formulation, next we describe an auto-context algorithm for learning image context via the fusion with low-level descriptors. Furthermore, a principled fusion algorithm using deep learning to optimize kernel machines is developed. By bridging deep architectures with kernel optimization, this approach leverages the benefits of both paradigms and is applied to a wide variety of fusion problems. In many real-world applications, the modalities exhibit highly specific data structures, such as time sequences and graphs, and consequently, special design of the learning architecture is needed. In order to improve the temporal modeling for multivariate sequences, we developed two architectures centered around attention models. A novel clinical time series analysis model is proposed for several critical problems in healthcare. Another model coupled with triplet ranking loss as metric learning framework is described to better solve speaker diarization. Compared to state-of-the-art recurrent networks, these attention-based multivariate analysis tools achieve improved performance while having a lower computational complexity. Finally, in order to perform community detection on multilayer graphs, a fusion algorithm is described to derive node embedding from word embedding techniques and also exploit the complementary relational information contained in each layer of the graph.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201

Image processing system based on similarity/dissimilarity measures to classify binary images from contour-based features

Image Processing Systems (IPS) try to solve tasks like image classification or segmentation based on its content. Many authors proposed a variety of techniques to tackle the image classification task. Plenty of methods address the performance of the IPS [1], as long as the influence of many external circumstances, such as illumination, rotation, and noise [2]. However, there is an increasing interest in classifying shapes from binary images (BI). Shape Classification (SC) from BI considers a segmented image as a sample (backgroundsegmentation [3]) and aims to identify objects based in its shape..

Image processing system based on similarity/dissimilarity measures to classify binary images from contour-based features

Image Processing Systems (IPS) try to solve tasks like image classification or segmentation based on its content. Many authors proposed a variety of techniques to tackle the image classification task. Plenty of methods address the performance of the IPS [1], as long as the influence of many external circumstances, such as illumination, rotation, and noise [2]. However, there is an increasing interest in classifying shapes from binary images (BI). Shape Classification (SC) from BI considers a segmented image as a sample (backgroundsegmentation [3]) and aims to identify objects based in its shape..