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1. Interpretable online network dictionary learning for inferring long-range chromatin interactions

   https://doi.org/10.1371/journal.pcbi.1012095  

   Rana, Vishal; Peng, Jianhao; Pan, Chao; Lyu, Hanbaek; Cheng, Albert; Kim, Minji; Milenkovic, Olgica (May 2024, PLOS Computational Biology)

   Schlick, Tamar (Ed.)

   Dictionary learning (DL), implemented via matrix factorization (MF), is commonly used in computational biology to tackle ubiquitous clustering problems. The method is favored due to its conceptual simplicity and relatively low computational complexity. However, DL algorithms produce results that lack interpretability in terms of real biological data. Additionally, they are not optimized for graph-structured data and hence often fail to handle them in a scalable manner. In order to address these limitations, we propose a novel DL algorithm calledonline convex network dictionary learning(online cvxNDL). Unlike classical DL algorithms, online cvxNDL is implemented via MF and designed to handle extremely large datasets by virtue of its online nature. Importantly, it enables the interpretation of dictionary elements, which serve as cluster representatives, through convex combinations of real measurements. Moreover, the algorithm can be applied to data with a network structure by incorporating specialized subnetwork sampling techniques. To demonstrate the utility of our approach, we apply cvxNDL on 3D-genome RNAPII ChIA-Drop data with the goal of identifying important long-range interaction patterns (long-range dictionary elements). ChIA-Drop probes higher-order interactions, and produces data in the form of hypergraphs whose nodes represent genomic fragments. The hyperedges represent observed physical contacts. Our hypergraph model analysis has the objective of creating an interpretable dictionary of long-range interaction patterns that accurately represent global chromatin physical contact maps. Through the use of dictionary information, one can also associate the contact maps with RNA transcripts and infer cellular functions. To accomplish the task at hand, we focus on RNAPII-enriched ChIA-Drop data fromDrosophila MelanogasterS2 cell lines. Our results offer two key insights. First, we demonstrate that online cvxNDL retains the accuracy of classical DL (MF) methods while simultaneously ensuring unique interpretability and scalability. Second, we identify distinct collections of proximal and distal interaction patterns involving chromatin elements shared by related processes across different chromosomes, as well as patterns unique to specific chromosomes. To associate the dictionary elements with biological properties of the corresponding chromatin regions, we employ Gene Ontology (GO) enrichment analysis and perform multiple RNA coexpression studies. 

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2. Beyond Black-box Dictionary Learning for Waves

   Tetali, Harsha Vardhan; Alguri, K. Supreet; Harley, Joel B. (December 2019, Machine Learning and the Physical Sciences Workshop at the Conference on Neural Information Processing Systems (NeurIPS))

   This work discusses an optimization framework to embed dictionary learning frameworks with the wave equation as a strategy for incorporating prior scientific knowledge into a machine learning algorithm. We modify dictionary learning to study ultrasonic guided wave-based defect detection for non-destructive structural health monitoring systems. Specifically, this work involves altering the popular-SVD algorithm for dictionary learning by enforcing prior knowledge about the ultrasonic guided wave problem through a physics-based regularization derived from the wave equation. We confer it the name “wave-informed K-SVD.” Training dictionary on data simulated from a fixed string added with noise using both K-SVD and wave-informed K-SVD, we show an improved physical consistency of columns of dictionary matrix with the known modal behavior of different one-dimensional wave simulations is observed. 

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3. Physics-Constrained Dictionary Learning for Selective Laser Melting Process Monitoring

   Lu, Yanglong; Wang, Yan (May 2021, Proceedings of 2021 IISE Annual Conference & Expo)

   null (Ed.)

   Compressed sensing (CS) as a new data acquisition technique has been applied to monitor manufacturing processes. With a few measurements, sparse coefficient vectors can be recovered by solving an inverse problem and original signals can be reconstructed. Dictionary learning methods have been developed and applied in combination with CS to improve the sparsity level of the recovered coefficient vectors. In this work, a physics-constrained dictionary learning approach is proposed to solve both of reconstruction and classification problems by optimizing measurement, basis, and classification matrices simultaneously with the considerations of the application-specific restrictions. It is applied in image acquisitions in selective laser melting (SLM). The proposed approach includes the optimization in two steps. In the first stage, with the basis matrix fixed, the measurement matrix is optimized by determining the pixel locations for sampling in each image. The optimized measurement matrix only includes one non-zero entry in each row. The optimization of pixel locations is solved based on a constrained FrameSense algorithm. In the second stage, with the measurement matrix fixed, the basis and classification matrices are optimized based on the K-SVD algorithm. With the optimized basis matrix, the coefficient vector can be recovered with CS. The original signal can be reconstructed by the linear combination of the basis matrix and the recovered coefficient vector. The original signal can also be classified to identify different machine states by the linear combination of the classification matrix and the coefficient vector. 

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4. Decentralized Dictionary Learning Over Time-Varying Digraphs

   Daneshmand, A.; Sun, Y.; Scutari, G.; Facchinei, F.; Sadler, B. (September 2019, Journal of machine learning research)

   This paper studies Dictionary Learning problems wherein the learning task is distributed over a multi-agent network, modeled as a time-varying directed graph. This formulation is relevant, for instance, in Big Data scenarios where massive amounts of data are collected/stored in different locations (e.g., sensors, clouds) and aggregating and/or processing all data in a fusion center might be inefficient or unfeasible, due to resource limitations, communication overheads or privacy issues. We develop a unified decentralized algorithmic framework for this class of nonconvex problems, which is proved to converge to stationary solutions at a sublinear rate. The new method hinges on Successive Convex Approximation techniques, coupled with a decentralized tracking mechanism aiming at locally estimating the gradient of the smooth part of the sum-utility. To the best of our knowledge, this is the first provably convergent decentralized algorithm for Dictionary Learning and, more generally, bi-convex problems over (time-varying) (di)graphs 

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5. Integrating Neural Networks and Dictionary Learning for Multidimensional Clinical Characterizations from Functional Connectomics Data

   Niharika Shimona D’Souza, Mary Beth (October 2019, Medical Image Computing and Computer Assisted Intervention)

   We propose a unified optimization framework that combines neural networks with dictionary learning to model complex interactions between resting state functional MRI and behavioral data. The dictionary learning objective decomposes patient correlation matrices into a collection of shared basis networks and subject-specific loadings. These subject-specific features are simultaneously input into a neural network that predicts multidimensional clinical information. Our novel optimization framework combines the gradient information from the neural network with that of a conventional matrix factorization objective. This procedure collectively estimates the basis networks, subject loadings, and neural network weights most informative of clinical severity. We evaluate our combined model on a multi-score prediction task using 52 patients diagnosed with Autism Spectrum Disorder (ASD). Our integrated framework outperforms state-of-the-art methods in a ten-fold cross validated setting to predict three different measures of clinical severity. 

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