arXiv subjects

Kejun Huang

Publications and source records attributed to Kejun Huang.

At least 19 recordsLinked to original sources

arXiv2026

DiSTILL: A Hybrid Cloud-HPC Workflow System for Reproducible Spatial Transcriptomics Analysis

Spatial transcriptomics workflows increasingly combine large annotated data objects, notebook-based analyses, and resource-intensive statistical models that must be executed on high-performance computing (HPC) systems. In practice, these workflows are often difficult to reproduce because configuration, validation, stage execution, and artifact handling are fragmented across $\textit{ad hoc}$ scripts and manually edited notebooks. We present $\textit{DiSTILL}$ (Disease Diagnosis from Spatial Transcriptomics via Interpretable Latent Learning), a hybrid cloud$-$HPC workflow system for reproducible spatial transcriptomics (ST) analysis. DiSTILL combines an application programming interface (API) backend built with $\texttt{FastAPI}$, a web frontend, a dataset and preset registry, and a Python pipeline generator that materializes run-specific execution bundles and $\texttt{SLURM}$ submission scripts. The system supports local, Secure Shell (SSH)-mediated, and pull-based poller execution modes, enabling HPC submission in environments where persistent API-initiated automation is restricted. We describe the system through the lens of an inflammatory bowel disease (IBD) ST workflow that operationalizes the analytical pipeline of Tan $\textit{et al.}$ into an auditable application layer. Accordingly, the contribution of this paper is a workflow systems contribution centered on reproducible execution, queue-based orchestration, configuration semantics, and deployment across a split cloud$-$HPC architecture. The broader application goal of DiSTILL is to support user-supplied datasets that satisfy the schema assumptions of the wrapped analytical pipeline.

q-bio.GN↗

arXiv2025

HOQRI: Higher-order QR Iteration for Low Multilinear Rank Approximation of Large and Sparse Tensors

We propose a new algorithm called higher-order QR iteration (HOQRI) for computing low multilinear rank approximation (LMLRA), also known as the Tucker decomposition, of large and sparse tensors. Compared to the celebrated higher-order orthogonal iterations (HOOI), HOQRI relies on a simple orthogonalization step in each iteration rather than a more sophisticated singular value decomposition step as in HOOI. More importantly, when dealing with extremely large and sparse data tensors, HOQRI completely eliminates the intermediate memory explosion by defining a new sparse tensor operation called TTMcTC (short for tensor times matrix chains times core). Furthermore, recognizing that the orthonormal constraints form a Cartesian product of Stiefel manifolds, we introduce the framework of manifold optimization and show that HOQRI guarantees convergence to the set of stationary points. Numerical experiments on synthetic and real data showcase the effectiveness of HOQRI.

math.NA↗

arXiv2022

Adaptive Learning for the Resource-Constrained Classification Problem

Resource-constrained classification tasks are common in real-world applications such as allocating tests for disease diagnosis, hiring decisions when filling a limited number of positions, and defect detection in manufacturing settings under a limited inspection budget. Typical classification algorithms treat the learning process and the resource constraints as two separate and sequential tasks. Here we design an adaptive learning approach that considers resource constraints and learning jointly by iteratively fine-tuning misclassification costs. Via a structured experimental study using a publicly available data set, we evaluate a decision tree classifier that utilizes the proposed approach. The adaptive learning approach performs significantly better than alternative approaches, especially for difficult classification problems in which the performance of common approaches may be unsatisfactory. We envision the adaptive learning approach as an important addition to the repertoire of techniques for handling resource-constrained classification problems.

cs.LG↗

arXiv2022

JULIA: Joint Multi-linear and Nonlinear Identification for Tensor Completion

Tensor completion aims at imputing missing entries from a partially observed tensor. Existing tensor completion methods often assume either multi-linear or nonlinear relationships between latent components. However, real-world tensors have much more complex patterns where both multi-linear and nonlinear relationships may coexist. In such cases, the existing methods are insufficient to describe the data structure. This paper proposes a Joint mUlti-linear and nonLinear IdentificAtion (JULIA) framework for large-scale tensor completion. JULIA unifies the multi-linear and nonlinear tensor completion models with several advantages over the existing methods: 1) Flexible model selection, i.e., it fits a tensor by assigning its values as a combination of multi-linear and nonlinear components; 2) Compatible with existing nonlinear tensor completion methods; 3) Efficient training based on a well-designed alternating optimization approach. Experiments on six real large-scale tensors demonstrate that JULIA outperforms many existing tensor completion algorithms. Furthermore, JULIA can improve the performance of a class of nonlinear tensor completion methods. The results show that in some large-scale tensor completion scenarios, baseline methods with JULIA are able to obtain up to 55% lower root mean-squared-error and save 67% computational complexity.

cs.LG↗

arXiv2020

Computing Large-Scale Matrix and Tensor Decomposition with Structured Factors: A Unified Nonconvex Optimization Perspective

The proposed article aims at offering a comprehensive tutorial for the computational aspects of structured matrix and tensor factorization. Unlike existing tutorials that mainly focus on {\it algorithmic procedures} for a small set of problems, e.g., nonnegativity or sparsity-constrained factorization, we take a {\it top-down} approach: we start with general optimization theory (e.g., inexact and accelerated block coordinate descent, stochastic optimization, and Gauss-Newton methods) that covers a wide range of factorization problems with diverse constraints and regularization terms of engineering interest. Then, we go `under the hood' to showcase specific algorithm design under these introduced principles. We pay a particular attention to recent algorithmic developments in structured tensor and matrix factorization (e.g., random sketching and adaptive step size based stochastic optimization and structure-exploiting second-order algorithms), which are the state of the art---yet much less touched upon in the literature compared to {\it block coordinate descent} (BCD)-based methods. We expect that the article to have an educational values in the field of structured factorization and hope to stimulate more research in this important and exciting direction.

eess.SP↗

arXiv2019

Hyperspectral Super-resolution: A Coupled Nonnegative Block-term Tensor Decomposition Approach

Hyperspectral super-resolution (HSR) aims at fusing a hyperspectral image (HSI) and a multispectral image (MSI) to produce a super-resolution image (SRI). Recently, a coupled tensor factorization approach was proposed to handle this challenging problem, which admits a series of advantages over the classic matrix factorization-based methods. In particular, modeling the HSI and MSI as low-rank tensors following the {\it canonical polyadic decomposition} (CPD) model, the approach is able to provably identify the SRI, under some mild conditions. However, the latent factors in the CPD model have no physical meaning, which makes utilizing prior information of spectral images as constraints or regularizations difficult---but using such information is often important in practice, especially when the data is noisy. In this work, we propose an alternative coupled tensor decomposition approach, where the HSI and MSI are assumed to follow the {\it block-term decomposition (BTD)} model. Notably, the new method also entails identifiability of the SRI under realistic conditions. More importantly, when modeling a spectral image as a BTD tensor, the latent factors have clear physical meaning, and thus prior knowledge about spectral images can be naturally incorporated. Simulations using real hyperspectral images are employed to showcase the effectiveness of the proposed approach with nonnegativity constraints.

eess.SP↗

arXiv2019

Crowdsourcing via Pairwise Co-occurrences: Identifiability and Algorithms

The data deluge comes with high demands for data labeling. Crowdsourcing (or, more generally, ensemble learning) techniques aim to produce accurate labels via integrating noisy, non-expert labeling from annotators. The classic Dawid-Skene estimator and its accompanying expectation maximization (EM) algorithm have been widely used, but the theoretical properties are not fully understood. Tensor methods were proposed to guarantee identification of the Dawid-Skene model, but the sample complexity is a hurdle for applying such approaches---since the tensor methods hinge on the availability of third-order statistics that are hard to reliably estimate given limited data. In this paper, we propose a framework using pairwise co-occurrences of the annotator responses, which naturally admits lower sample complexity. We show that the approach can identify the Dawid-Skene model under realistic conditions. We propose an algebraic algorithm reminiscent of convex geometry-based structured matrix factorization to solve the model identification problem efficiently, and an identifiability-enhanced algorithm for handling more challenging and critical scenarios. Experiments show that the proposed algorithms outperform the state-of-art algorithms under a variety of scenarios.

cs.LG↗

arXiv2019

SNAP: Finding Approximate Second-Order Stationary Solutions Efficiently for Non-convex Linearly Constrained Problems

This paper proposes low-complexity algorithms for finding approximate second-order stationary points (SOSPs) of problems with smooth non-convex objective and linear constraints. While finding (approximate) SOSPs is computationally intractable, we first show that generic instances of the problem can be solved efficiently. More specifically, for a generic problem instance, certain strict complementarity (SC) condition holds for all Karush-Kuhn-Tucker (KKT) solutions (with probability one). The SC condition is then used to establish an equivalence relationship between two different notions of SOSPs, one of which is computationally easy to verify. Based on this particular notion of SOSP, we design an algorithm named the Successive Negative-curvature grAdient Projection (SNAP), which successively performs either conventional gradient projection or some negative curvature based projection steps to find SOSPs. SNAP and its first-order extension SNAP$^+$, require $\mathcal{O}(1/\epsilon^{2.5})$ iterations to compute an $(\epsilon, \sqrt{\epsilon})$-SOSP, and their per-iteration computational complexities are polynomial in the number of constraints and problem dimension. To our knowledge, this is the first time that first-order algorithms with polynomial per-iteration complexity and global sublinear rate have been designed to find SOSPs of the important class of non-convex problems with linear constraints.

math.OC↗

arXiv2019

Block-Randomized Stochastic Proximal Gradient for Low-Rank Tensor Factorization

This work considers the problem of computing the canonical polyadic decomposition (CPD) of large tensors. Prior works mostly leverage data sparsity to handle this problem, which is not suitable for handling dense tensors that often arise in applications such as medical imaging, computer vision, and remote sensing. Stochastic optimization is known for its low memory cost and per-iteration complexity when handling dense data. However, exisiting stochastic CPD algorithms are not flexible enough to incorporate a variety of constraints/regularizations that are of interest in signal and data analytics. Convergence properties of many such algorithms are also unclear. In this work, we propose a stochastic optimization framework for large-scale CPD with constraints/regularizations. The framework works under a doubly randomized fashion, and can be regarded as a judicious combination of randomized block coordinate descent (BCD) and stochastic proximal gradient (SPG). The algorithm enjoys lightweight updates and small memory footprint. In addition, this framework entails considerable flexibility---many frequently used regularizers and constraints can be readily handled under the proposed scheme. The approach is also supported by convergence analysis. Numerical results on large-scale dense tensors are employed to showcase the effectiveness of the proposed approach.

eess.SP↗

arXiv2019

Learning Nonlinear Mixtures: Identifiability and Algorithm

Linear mixture models have proven very useful in a plethora of applications, e.g., topic modeling, clustering, and source separation. As a critical aspect of the linear mixture models, identifiability of the model parameters is well-studied, under frameworks such as independent component analysis and constrained matrix factorization. Nevertheless, when the linear mixtures are distorted by an unknown nonlinear functions -- which is well-motivated and more realistic in many cases -- the identifiability issues are much less studied. This work proposes an identification criterion for a nonlinear mixture model that is well grounded in many real-world applications, and offers identifiability guarantees. A practical implementation based on a judiciously designed neural network is proposed to realize the criterion, and an effective learning algorithm is proposed. Numerical results on synthetic and real-data corroborate effectiveness of the proposed method.

cs.LG↗

arXiv2018

Nonnegative Matrix Factorization for Signal and Data Analytics: Identifiability, Algorithms, and Applications

Nonnegative matrix factorization (NMF) has become a workhorse for signal and data analytics, triggered by its model parsimony and interpretability. Perhaps a bit surprisingly, the understanding to its model identifiability---the major reason behind the interpretability in many applications such as topic mining and hyperspectral imaging---had been rather limited until recent years. Beginning from the 2010s, the identifiability research of NMF has progressed considerably: Many interesting and important results have been discovered by the signal processing (SP) and machine learning (ML) communities. NMF identifiability has a great impact on many aspects in practice, such as ill-posed formulation avoidance and performance-guaranteed algorithm design. On the other hand, there is no tutorial paper that introduces NMF from an identifiability viewpoint. In this paper, we aim at filling this gap by offering a comprehensive and deep tutorial on model identifiability of NMF as well as the connections to algorithms and applications. This tutorial will help researchers and graduate students grasp the essence and insights of NMF, thereby avoiding typical `pitfalls' that are often times due to unidentifiable NMF formulations. This paper will also help practitioners pick/design suitable factorization tools for their own problems.

eess.SP↗

arXiv2018

Learning Hidden Markov Models from Pairwise Co-occurrences with Application to Topic Modeling

We present a new algorithm for identifying the transition and emission probabilities of a hidden Markov model (HMM) from the emitted data. Expectation-maximization becomes computationally prohibitive for long observation records, which are often required for identification. The new algorithm is particularly suitable for cases where the available sample size is large enough to accurately estimate second-order output probabilities, but not higher-order ones. We show that if one is only able to obtain a reliable estimate of the pairwise co-occurrence probabilities of the emissions, it is still possible to uniquely identify the HMM if the emission probability is \emph{sufficiently scattered}. We apply our method to hidden topic Markov modeling, and demonstrate that we can learn topics with higher quality if documents are modeled as observations of HMMs sharing the same emission (topic) probability, compared to the simple but widely used bag-of-words model.

cs.CL↗

arXiv2017

Kullback-Leibler Principal Component for Tensors is not NP-hard

We study the problem of nonnegative rank-one approximation of a nonnegative tensor, and show that the globally optimal solution that minimizes the generalized Kullback-Leibler divergence can be efficiently obtained, i.e., it is not NP-hard. This result works for arbitrary nonnegative tensors with an arbitrary number of modes (including two, i.e., matrices). We derive a closed-form expression for the KL principal component, which is easy to compute and has an intuitive probabilistic interpretation. For generalized KL approximation with higher ranks, the problem is for the first time shown to be equivalent to multinomial latent variable modeling, and an iterative algorithm is derived that resembles the expectation-maximization algorithm. On the Iris dataset, we showcase how the derived results help us learn the model in an \emph{unsupervised} manner, and obtain strikingly close performance to that from supervised methods.

eess.SP↗

arXiv2017

On Convergence of Epanechnikov Mean Shift

Epanechnikov Mean Shift is a simple yet empirically very effective algorithm for clustering. It localizes the centroids of data clusters via estimating modes of the probability distribution that generates the data points, using the `optimal' Epanechnikov kernel density estimator. However, since the procedure involves non-smooth kernel density functions, the convergence behavior of Epanechnikov mean shift lacks theoretical support as of this writing---most of the existing analyses are based on smooth functions and thus cannot be applied to Epanechnikov Mean Shift. In this work, we first show that the original Epanechnikov Mean Shift may indeed terminate at a non-critical point, due to the non-smoothness nature. Based on our analysis, we propose a simple remedy to fix it. The modified Epanechnikov Mean Shift is guaranteed to terminate at a local maximum of the estimated density, which corresponds to a cluster centroid, within a finite number of iterations. We also propose a way to avoid running the Mean Shift iterates from every data point, while maintaining good clustering accuracies under non-overlapping spherical Gaussian mixture models. This further pushes Epanechnikov Mean Shift to handle very large and high-dimensional data sets. Experiments show surprisingly good performance compared to the Lloyd's K-means algorithm and the EM algorithm.

stat.ML↗

arXiv2017

On Identifiability of Nonnegative Matrix Factorization

In this letter, we propose a new identification criterion that guarantees the recovery of the low-rank latent factors in the nonnegative matrix factorization (NMF) model, under mild conditions. Specifically, using the proposed criterion, it suffices to identify the latent factors if the rows of one factor are \emph{sufficiently scattered} over the nonnegative orthant, while no structural assumption is imposed on the other factor except being full-rank. This is by far the mildest condition under which the latent factors are provably identifiable from the NMF model.

cs.LG↗

arXiv2016

Anchor-Free Correlated Topic Modeling: Identifiability and Algorithm

In topic modeling, many algorithms that guarantee identifiability of the topics have been developed under the premise that there exist anchor words -- i.e., words that only appear (with positive probability) in one topic. Follow-up work has resorted to three or higher-order statistics of the data corpus to relax the anchor word assumption. Reliable estimates of higher-order statistics are hard to obtain, however, and the identification of topics under those models hinges on uncorrelatedness of the topics, which can be unrealistic. This paper revisits topic modeling based on second-order moments, and proposes an anchor-free topic mining framework. The proposed approach guarantees the identification of the topics under a much milder condition compared to the anchor-word assumption, thereby exhibiting much better robustness in practice. The associated algorithm only involves one eigen-decomposition and a few small linear programs. This makes it easy to implement and scale up to very large problem instances. Experiments using the TDT2 and Reuters-21578 corpus demonstrate that the proposed anchor-free approach exhibits very favorable performance (measured using coherence, similarity count, and clustering accuracy metrics) compared to the prior art.

stat.ML↗

arXiv2016

Robust Volume Minimization-Based Matrix Factorization for Remote Sensing and Document Clustering

This paper considers \emph{volume minimization} (VolMin)-based structured matrix factorization (SMF). VolMin is a factorization criterion that decomposes a given data matrix into a basis matrix times a structured coefficient matrix via finding the minimum-volume simplex that encloses all the columns of the data matrix. Recent work showed that VolMin guarantees the identifiability of the factor matrices under mild conditions that are realistic in a wide variety of applications. This paper focuses on both theoretical and practical aspects of VolMin. On the theory side, exact equivalence of two independently developed sufficient conditions for VolMin identifiability is proven here, thereby providing a more comprehensive understanding of this aspect of VolMin. On the algorithm side, computational complexity and sensitivity to outliers are two key challenges associated with real-world applications of VolMin. These are addressed here via a new VolMin algorithm that handles volume regularization in a computationally simple way, and automatically detects and {iteratively downweights} outliers, simultaneously. Simulations and real-data experiments using a remotely sensed hyperspectral image and the Reuters document corpus are employed to showcase the effectiveness of the proposed algorithm.

stat.ML↗

arXiv2016

Consensus-ADMM for General Quadratically Constrained Quadratic Programming

Non-convex quadratically constrained quadratic programming (QCQP) problems have numerous applications in signal processing, machine learning, and wireless communications, albeit the general QCQP is NP-hard, and several interesting special cases are NP-hard as well. This paper proposes a new algorithm for general QCQP. The problem is first reformulated in consensus optimization form, to which the alternating direction method of multipliers (ADMM) can be applied. The reformulation is done in such a way that each of the sub-problems is a QCQP with only one constraint (QCQP-1), which is efficiently solvable irrespective of (non-)convexity. The core components are carefully designed to make the overall algorithm more scalable, including efficient methods for solving QCQP-1, memory efficient implementation, parallel/distributed implementation, and smart initialization. The proposed algorithm is then tested in two applications: multicast beamforming and phase retrieval. The results indicate superior performance over prior state-of-the-art methods.

math.OC↗