Robust Tensor Completion via Capped Frobenius Norm.

Tensor completion (TC) refers to restoring the missing entries in a given tensor by making use of the low-rank structure. Most existing algorithms have excellent performance in Gaussian noise or impulsive noise scenarios. Generally speaking, the Frobenius-norm-based methods achieve excellent performance in additive Gaussian noise, while their recovery severely degrades in impulsive noise. Although the algorithms using the lp -norm ( ) or its variants can attain high restoration accuracy in the presence of gross errors, they are inferior to the Frobenius-norm-based methods when the noise is Gaussian-distributed. Therefore, an approach that is able to perform well in both Gaussian noise and impulsive noise is desired. In this work, we use a capped Frobenius norm to restrain outliers, which corresponds to a form of the truncated least-squares loss function. The upper bound of our capped Frobenius norm is automatically updated using normalized median absolute deviation during iterations. Therefore, it achieves better performance than the lp -norm with outlier-contaminated observations and attains comparable accuracy to the Frobenius norm without tuning parameter in Gaussian noise. We then adopt the half-quadratic theory to convert the nonconvex problem into a tractable multivariable problem, that is, convex optimization with respect to (w.r.t.) each individual variable. To address the resultant task, we exploit the proximal block coordinate descent (PBCD) method and then establish the convergence of the suggested algorithm. Specifically, the objective function value is guaranteed to be convergent while the variable sequence has a subsequence converging to a critical point. Experimental results based on real-world images and videos exhibit the superiority of the devised approach over several state-of-the-art algorithms in terms of recovery performance. MATLAB code is available at https://github.com/Li-X-P/Code-of-Robust-Tensor-Completion.

Multisubject Task-Related fMRI Data Processing via a Two-Stage Generalized Canonical Correlation Analysis.

Functional magnetic resonance imaging (fMRI) is one of the most popular methods for studying the human brain. Task-related fMRI data processing aims to determine which brain areas are activated when a specific task is performed and is usually based on the Blood Oxygen Level Dependent (BOLD) signal. The background BOLD signal also reflects systematic fluctuations in regional brain activity which are attributed to the existence of resting-state brain networks. We propose a new fMRI data generating model which takes into consideration the existence of common task-related and resting-state components. We first estimate the common task-related temporal component, via two successive stages of generalized canonical correlation analysis and, then, we estimate the common task-related spatial component, leading to a task-related activation map. The experimental tests of our method with synthetic data reveal that we are able to obtain very accurate temporal and spatial estimates even at very low Signal to Noise Ratio (SNR), which is usually the case in fMRI data processing. The tests with real-world fMRI data show significant advantages over standard procedures based on General Linear Models (GLMs).

Multi-subject Task-related fMRI Data Analysis via Generalized Canonical Correlation Analysis.

Functional magnetic resonance imaging (fMRI) is one of the most popular methods for studying the human brain. It measures brain activity, by detecting local changes of Blood Oxygen Level Dependent (BOLD) signal in the brain, over time, and can be used in both task-related and resting-state studies. In task-related studies, our aim is to determine which brain areas are activated when a specific task is performed. Various unsupervised multivariate statistical methods are being increasingly employed in fMRI data analysis. Their main goal is to extract information from a dataset, often with no prior knowledge of the experimental conditions. Generalized canonical correlation analysis (gCCA) is a well known statistical method that can be considered as a way to estimate a linear subspace, which is "common" to multiple random linear subspaces. We propose a new fMRI data generating model which takes into consideration the existence of common task-related and resting-state components. We estimate the common spatial task-related component via a two-stage gCCA. We test our theoretical results using real-world fMRI data. Our experimental findings corroborate our theoretical results, rendering our approach a very good candidate for multi-subject task-related fMRI processing.Clinical Relevance-This work provides a set of methods for amplifying and recovering commonalities across subjects that appear in data from multi-subject task-related fMRI experiments.

A recursive framework for predicting the time-course of drug sensitivity.

The biological processes involved in a drug's mechanisms of action are oftentimes dynamic, complex and difficult to discern. Time-course gene expression data is a rich source of information that can be used to unravel these complex processes, identify biomarkers of drug sensitivity and predict the response to a drug. However, the majority of previous work has not fully utilized this temporal dimension. In these studies, the gene expression data is either considered at one time-point (before the administration of the drug) or two time-points (before and after the administration of the drug). This is clearly inadequate in modeling dynamic gene-drug interactions, especially for applications such as long-term drug therapy. In this work, we present a novel REcursive Prediction (REP) framework for drug response prediction by taking advantage of time-course gene expression data. Our goal is to predict drug response values at every stage of a long-term treatment, given the expression levels of genes collected in the previous time-points. To this end, REP employs a built-in recursive structure that exploits the intrinsic time-course nature of the data and integrates past values of drug responses for subsequent predictions. It also incorporates tensor completion that can not only alleviate the impact of noise and missing data, but also predict unseen gene expression levels (GEXs). These advantages enable REP to estimate drug response at any stage of a given treatment from some GEXs measured in the beginning of the treatment. Extensive experiments on two datasets corresponding to multiple sclerosis patients treated with interferon are included to showcase the effectiveness of REP.

STELAR: Spatio-temporal Tensor Factorization with Latent Epidemiological Regularization.

Accurate prediction of the transmission of epidemic diseases such as COVID-19 is crucial for implementing effective mitigation measures. In this work, we develop a tensor method to predict the evolution of epidemic trends for many regions simultaneously. We construct a 3-way spatio-temporal tensor (location, attribute, time) of case counts and propose a nonnegative tensor factorization with latent epidemiological model regularization named STELAR. Unlike standard tensor factorization methods which cannot predict slabs ahead, STELAR enables long-term prediction by incorporating latent temporal regularization through a system of discrete-time difference equations of a widely adopted epidemiological model. We use latent instead of location/attribute-level epidemiological dynamics to capture common epidemic profile sub-types and improve collaborative learning and prediction. We conduct experiments using both county- and state-level COVID-19 data and show that our model can identify interesting latent patterns of the epidemic. Finally, we evaluate the predictive ability of our method and show superior performance compared to the baselines, achieving up to 21% lower root mean square error and 25% lower mean absolute error for county-level prediction.

Low-Rank Tensor Models for Improved Multi-Dimensional MRI: Application to Dynamic Cardiac T 1 Mapping.

Multi-dimensional, multi-contrast magnetic resonance imaging (MRI) has become increasingly available for comprehensive and time-efficient evaluation of various pathologies, providing large amounts of data and offering new opportunities for improved image reconstructions. Recently, a cardiac phase-resolved myocardial T 1 mapping method has been introduced to provide dynamic information on tissue viability. Improved spatio-temporal resolution in clinically acceptable scan times is highly desirable but requires high acceleration factors. Tensors are well-suited to describe inter-dimensional hidden structures in such multi-dimensional datasets. In this study, we sought to utilize and compare different tensor decomposition methods, without the use of auxiliary navigator data. We explored multiple processing approaches in order to enable high-resolution cardiac phase-resolved myocardial T 1 mapping. Eight different low-rank tensor approximation and processing approaches were evaluated using quantitative analysis of accuracy and precision in T 1 maps acquired in six healthy volunteers. All methods provided comparable T 1 values. However, the precision was significantly improved using local processing, as well as a direct tensor rank approximation. Low-rank tensor approximation approaches are well-suited to enable dynamic T 1 mapping at high spatio-temporal resolutions.

Anchor-Free Correlated Topic Modeling.

In topic modeling, identifiability of the topics is an essential issue. Many topic modeling approaches have been developed under the premise that each topic has a characteristic anchor word that only appears in that topic. The anchor-word assumption is fragile in practice, because words and terms have multiple uses; yet it is commonly adopted because it enables identifiability guarantees. Remedies in the literature include using three- or higher-order word co-occurence statistics to come up with tensor factorization models, but such statistics need many more samples to obtain reliable estimates, and identifiability still hinges on additional assumptions, such as consecutive words being persistently drawn from the same topic. In this work, we propose a new topic identification criterion using second order statistics of the words. The criterion is theoretically guaranteed to identify the underlying topics even when the anchor-word assumption is grossly violated. An algorithm based on alternating optimization, and an efficient primal-dual algorithm are proposed to handle the resulting identification problem. The former exhibits high performance and is completely parameter-free; the latter affords up to 200 times speedup relative to the former, but requires step-size tuning and a slight sacrifice in accuracy. A variety of real text copora are employed to showcase the effectiveness of the approach, where the proposed anchor-free method demonstrates substantial improvements compared to a number of anchor-word based approaches under various evaluation metrics.

Locally Low-Rank Tensor Regularization for High-Resolution Quantitative Dynamic MRI.

Quantitative dynamic MRI acquisitions have the potential to diagnose diffuse diseases in conjunction with functional abnormalities. However, their resolutions are limited due to the long acquisition time. Such datasets are multi-dimensional, exhibiting interactions between ≥ 4 dimensions, which cannot be easily identified using sparsity or low-rank matrix methods. Hence, low-rank tensors are a natural fit to model such data. But in the presence of multitude of different tissue types in the field-of-view, it is difficult to find an appropriate value of tensor rank, which avoids under- or over-regularization. In this work, we propose a locally low-rank tensor regularization approach to enable high-resolution quantitative dynamic MRI. We show this approach successfully enables dynamic T 1 mapping at high spatio-temporal resolutions.

Turbo-SMT: Parallel Coupled Sparse Matrix-Tensor Factorizations and Applications.

How can we correlate the neural activity in the human brain as it responds to typed words, with properties of these terms (like 'edible', 'fits in hand')? In short, we want to find latent variables, that jointly explain both the brain activity, as well as the behavioral responses. This is one of many settings of the Coupled Matrix-Tensor Factorization (CMTF) problem. Can we enhance any CMTF solver, so that it can operate on potentially very large datasets that may not fit in main memory? We introduce Turbo-SMT, a meta-method capable of doing exactly that: it boosts the performance of any CMTF algorithm, produces sparse and interpretable solutions, and parallelizes any CMTF algorithm, producing sparse and interpretable solutions (up to 65 fold). Additionally, we improve upon ALS, the work-horse algorithm for CMTF, with respect to efficiency and robustness to missing values. We apply Turbo-SMT to BrainQ, a dataset consisting of a (nouns, brain voxels, human subjects) tensor and a (nouns, properties) matrix, with coupling along the nouns dimension. Turbo-SMT is able to find meaningful latent variables, as well as to predict brain activity with competitive accuracy. Finally, we demonstrate the generality of Turbo-SMT, by applying it on a Facebook dataset (users, 'friends', wall-postings); there, Turbo-SMT spots spammer-like anomalies.

Good-Enough Brain Model: Challenges, Algorithms, and Discoveries in Multisubject Experiments.

Given a simple noun such as apple, and a question such as "Is it edible?," what processes take place in the human brain? More specifically, given the stimulus, what are the interactions between (groups of) neurons (also known as functional connectivity) and how can we automatically infer those interactions, given measurements of the brain activity? Furthermore, how does this connectivity differ across different human subjects? In this work, we show that this problem, even though originating from the field of neuroscience, can benefit from big data techniques; we present a simple, novel good-enough brain model, or GeBM in short, and a novel algorithm Sparse-SysId, which are able to effectively model the dynamics of the neuron interactions and infer the functional connectivity. Moreover, GeBM is able to simulate basic psychological phenomena such as habituation and priming (whose definition we provide in the main text). We evaluate GeBM by using real brain data. GeBM produces brain activity patterns that are strikingly similar to the real ones, where the inferred functional connectivity is able to provide neuroscientific insights toward a better understanding of the way that neurons interact with each other, as well as detect regularities and outliers in multisubject brain activity measurements.

Turbo-SMT: Accelerating Coupled Sparse Matrix-Tensor Factorizations by 200×.

How can we correlate the neural activity in the human brain as it responds to typed words, with properties of these terms (like 'edible', 'fits in hand')? In short, we want to find latent variables, that jointly explain both the brain activity, as well as the behavioral responses. This is one of many settings of the Coupled Matrix-Tensor Factorization (CMTF) problem. Can we accelerate any CMTF solver, so that it runs within a few minutes instead of tens of hours to a day, while maintaining good accuracy? We introduce TURBO-SMT, a meta-method capable of doing exactly that: it boosts the performance of any CMTF algorithm, by up to 200×, along with an up to 65 fold increase in sparsity, with comparable accuracy to the baseline. We apply TURBO-SMT to BRAINQ, a dataset consisting of a (nouns, brain voxels, human subjects) tensor and a (nouns, properties) matrix, with coupling along the nouns dimension. TURBO-SMT is able to find meaningful latent variables, as well as to predict brain activity with competitive accuracy.