Jamie Haddock

Jamie Haddock, Deanna Needell

Iterative linear solvers have gained recent popularity due to their computational efficiency and low memory footprint for large-scale linear systems. The relaxation method, or Motzkin's method, can be viewed as an iterative method that projects the current estimation onto the solution hyperplane corresponding to the most violated constraint. Although this leads to an optimal selection strategy for consistent systems, for inconsistent least square problems, the strategy presents a tradeoff between convergence rate and solution accuracy. We provide a theoretical analysis that shows Motzkin's method offers an initially accelerated convergence rate and this acceleration depends on the dynamic range of the residual. We quantify this acceleration for Gaussian systems as a concrete example. Lastly, we include experimental evidence on real and synthetic systems that support the analysis.

Tyler Will, Runyu Zhang, Eli Sadovnik et al.

We introduce a new method based on nonnegative matrix factorization, Neural NMF, for detecting latent hierarchical structure in data. Datasets with hierarchical structure arise in a wide variety of fields, such as document classification, image processing, and bioinformatics. Neural NMF recursively applies NMF in layers to discover overarching topics encompassing the lower-level features. We derive a backpropagation optimization scheme that allows us to frame hierarchical NMF as a neural network. We test Neural NMF on a synthetic hierarchical dataset, the 20 Newsgroups dataset, and the MyLymeData symptoms dataset. Numerical results demonstrate that Neural NMF outperforms other hierarchical NMF methods on these data sets and offers better learned hierarchical structure and interpretability of topics.

Elena Sizikova, Joshua Vendrow, Xu Cao et al.

Automatic infectious disease classification from images can facilitate needed medical diagnoses. Such an approach can identify diseases, like tuberculosis, which remain under-diagnosed due to resource constraints and also novel and emerging diseases, like monkeypox, which clinicians have little experience or acumen in diagnosing. Avoiding missed or delayed diagnoses would prevent further transmission and improve clinical outcomes. In order to understand and trust neural network predictions, analysis of learned representations is necessary. In this work, we argue that automatic discovery of concepts, i.e., human interpretable attributes, allows for a deep understanding of learned information in medical image analysis tasks, generalizing beyond the training labels or protocols. We provide an overview of existing concept discovery approaches in medical image and computer vision communities, and evaluate representative methods on tuberculosis (TB) prediction and monkeypox prediction tasks. Finally, we propose NMFx, a general NMF formulation of interpretability by concept discovery that works in a unified way in unsupervised, weakly supervised, and supervised scenarios.

Hannah Friedman, Amani R. Maina-Kilaas, Julianna Schalkwyk et al. · mit

In this paper, we propose a new method for determining shared features of and measuring the distance between data sets or point clouds. Our approach uses the joint factorization of two data matrices $X_1,X_2$ into non-negative matrices $X_1 = AS_1, X_2 = AS_2$ to derive a similarity measure that determines how well the shared basis $A$ approximates $X_1, X_2$. We also propose a point cloud distance measure built upon this method and the learned factorization. Our method reveals structural differences in both image and text data. Potential applications include classification, detecting plagiarism or other manipulation, data denoising, and transfer learning.

Philip Chodrow, Nicole Eikmeier, Jamie Haddock

Spectral methods offer a tractable, global framework for clustering in graphs via eigenvector computations on graph matrices. Hypergraph data, in which entities interact on edges of arbitrary size, poses challenges for matrix representations and therefore for spectral clustering. We study spectral clustering for nonuniform hypergraphs based on the hypergraph nonbacktracking operator. After reviewing the definition of this operator and its basic properties, we prove a theorem of Ihara-Bass type which allows eigenpair computations to take place on a smaller matrix, often enabling faster computation. We then propose an alternating algorithm for inference in a hypergraph stochastic blockmodel via linearized belief-propagation which involves a spectral clustering step again using nonbacktracking operators. We provide proofs related to this algorithm that both formalize and extend several previous results. We pose several conjectures about the limits of spectral methods and detectability in hypergraph stochastic blockmodels in general, supporting these with in-expectation analysis of the eigeinpairs of our studied operators. We perform experiments in real and synthetic data that demonstrate the benefits of hypergraph methods over graph-based ones when interactions of different sizes carry different information about cluster structure.

Alejandra Castillo, Jamie Haddock, Iryna Hartsock et al.

The reconstruction of tensor-valued signals from corrupted measurements, known as tensor regression, has become essential in many multi-modal applications such as hyperspectral image reconstruction and medical imaging. In this work, we address the tensor linear system problem $\mathcal{A} \mathcal{X}=\mathcal{B}$, where $\mathcal{A}$ is a measurement operator, $\mathcal{X}$ is the unknown tensor-valued signal, and $\mathcal{B}$ contains the measurements, possibly corrupted by arbitrary errors. Such corruption is common in large-scale tensor data, where transmission, sensory, or storage errors are rare per instance but likely over the entire dataset and may be arbitrarily large in magnitude. We extend the Kaczmarz method, a popular iterative algorithm for solving large linear systems, to develop a Quantile Tensor Randomized Kaczmarz (QTRK) method robust to large, sparse corruptions in the observations $\mathcal{B}$. This approach combines the tensor Kaczmarz framework with quantile-based statistics, allowing it to mitigate adversarial corruptions and improve convergence reliability. We also propose and discuss the Masked Quantile Randomized Kaczmarz (mQTRK) variant, which selectively applies partial updates to handle corruptions further. We present convergence guarantees, discuss the advantages and disadvantages of our approaches, and demonstrate the effectiveness of our methods through experiments, including an application for video deblurring.

Jamie Haddock, Lara Kassab, Sixian Li et al.

We propose new semi-supervised nonnegative matrix factorization (SSNMF) models for document classification and provide motivation for these models as maximum likelihood estimators. The proposed SSNMF models simultaneously provide both a topic model and a model for classification, thereby offering highly interpretable classification results. We derive training methods using multiplicative updates for each new model, and demonstrate the application of these models to single-label and multi-label document classification, although the models are flexible to other supervised learning tasks such as regression. We illustrate the promise of these models and training methods on document classification datasets (e.g., 20 Newsgroups, Reuters).

Joshua Vendrow, Jamie Haddock, Deanna Needell

Nonnegative matrix factorization (NMF) has found many applications including topic modeling and document analysis. Hierarchical NMF (HNMF) variants are able to learn topics at various levels of granularity and illustrate their hierarchical relationship. Recently, nonnegative tensor factorization (NTF) methods have been applied in a similar fashion in order to handle data sets with complex, multi-modal structure. Hierarchical NTF (HNTF) methods have been proposed, however these methods do not naturally generalize their matrix-based counterparts. Here, we propose a new HNTF model which directly generalizes a HNMF model special case, and provide a supervised extension. We also provide a multiplicative updates training method for this model. Our experimental results show that this model more naturally illuminates the topic hierarchy than previous HNMF and HNTF methods.

Joshua Vendrow, Jamie Haddock, Elizaveta Rebrova et al.

Fully unsupervised topic models have found fantastic success in document clustering and classification. However, these models often suffer from the tendency to learn less-than-meaningful or even redundant topics when the data is biased towards a set of features. For this reason, we propose an approach based upon the nonnegative matrix factorization (NMF) model, deemed \textit{Guided NMF}, that incorporates user-designed seed word supervision. Our experimental results demonstrate the promise of this model and illustrate that it is competitive with other methods of this ilk with only very little supervision information.

Edwin Chau, Jamie Haddock

Matrix factorization techniques compute low-rank product approximations of high dimensional data matrices and as a result, are often employed in recommender systems and collaborative filtering applications. However, many algorithms for this task utilize an exact least-squares solver whose computation is time consuming and memory-expensive. In this paper we discuss and test a block Kaczmarz solver that replaces the least-squares subroutine in the common alternating scheme for matrix factorization. This variant trades a small increase in factorization error for significantly faster algorithmic performance. In doing so we find block sizes that produce a solution comparable to that of the least-squares solver for only a fraction of the runtime and working memory requirement.

Jamie Haddock, Lara Kassab, Sixian Li et al.

We propose several new models for semi-supervised nonnegative matrix factorization (SSNMF) and provide motivation for SSNMF models as maximum likelihood estimators given specific distributions of uncertainty. We present multiplicative updates training methods for each new model, and demonstrate the application of these models to classification, although they are flexible to other supervised learning tasks. We illustrate the promise of these models and training methods on both synthetic and real data, and achieve high classification accuracy on the 20 Newsgroups dataset.

Joshua Vendrow, Jamie Haddock, Deanna Needell et al.

Lyme disease is a rapidly growing illness that remains poorly understood within the medical community. Critical questions about when and why patients respond to treatment or stay ill, what kinds of treatments are effective, and even how to properly diagnose the disease remain largely unanswered. We investigate these questions by applying machine learning techniques to a large scale Lyme disease patient registry, MyLymeData, developed by the nonprofit LymeDisease.org. We apply various machine learning methods in order to measure the effect of individual features in predicting participants' answers to the Global Rating of Change (GROC) survey questions that assess the self-reported degree to which their condition improved, worsened, or remained unchanged following antibiotic treatment. We use basic linear regression, support vector machines, neural networks, entropy-based decision tree models, and $k$-nearest neighbors approaches. We first analyze the general performance of the model and then identify the most important features for predicting participant answers to GROC. After we identify the "key" features, we separate them from the dataset and demonstrate the effectiveness of these features at identifying GROC. In doing so, we highlight possible directions for future study both mathematically and clinically.

Miju Ahn, Nicole Eikmeier, Jamie Haddock et al.

There is currently an unprecedented demand for large-scale temporal data analysis due to the explosive growth of data. Dynamic topic modeling has been widely used in social and data sciences with the goal of learning latent topics that emerge, evolve, and fade over time. Previous work on dynamic topic modeling primarily employ the method of nonnegative matrix factorization (NMF), where slices of the data tensor are each factorized into the product of lower-dimensional nonnegative matrices. With this approach, however, information contained in the temporal dimension of the data is often neglected or underutilized. To overcome this issue, we propose instead adopting the method of nonnegative CANDECOMP/PARAPAC (CP) tensor decomposition (NNCPD), where the data tensor is directly decomposed into a minimal sum of outer products of nonnegative vectors, thereby preserving the temporal information. The viability of NNCPD is demonstrated through application to both synthetic and real data, where significantly improved results are obtained compared to those of typical NMF-based methods. The advantages of NNCPD over such approaches are studied and discussed. To the best of our knowledge, this is the first time that NNCPD has been utilized for the purpose of dynamic topic modeling, and our findings will be transformative for both applications and further developments.

Jesus A. De Loera, Jamie Haddock, Anna Ma et al.

Machine learning algorithms typically rely on optimization subroutines and are well-known to provide very effective outcomes for many types of problems. Here, we flip the reliance and ask the reverse question: can machine learning algorithms lead to more effective outcomes for optimization problems? Our goal is to train machine learning methods to automatically improve the performance of optimization and signal processing algorithms. As a proof of concept, we use our approach to improve two popular data processing subroutines in data science: stochastic gradient descent and greedy methods in compressed sensing. We provide experimental results that demonstrate the answer is ``yes'', machine learning algorithms do lead to more effective outcomes for optimization problems, and show the future potential for this research direction.