Collecting multiple types of data on the same set of subjects is common in modern scientific applications including, genomics, metabolomics, and neuroimaging. Joint and Individual Variance Explained (JIVE) seeks a low-rank approximation of the joint variation between two or more sets of features captured on common subjects and isolates this variation from that unique to eachset of features. We develop an expectation-maximization (EM) algorithm to estimate a probabilistic model for the JIVE framework. The model extends probabilistic principal components analysis to multiple data sets. Our maximum likelihood approach simultaneously estimates joint and individual components, which can lead to greater accuracy compared to other methods. We apply ProJIVE to measures of brain morphometry and cognition in Alzheimer's disease. ProJIVE learns biologically meaningful courses of variation, and the joint morphometry and cognition subject scores are strongly related to more expensive existing biomarkers. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Code to reproduce the analysis is available on our GitHub page.

Clustering is one of the most common tasks in data science, and given the ubiquity of timeseries data, one is naturally inclined to cluster it. In order to perform Euclidean clustering (such as k-means clustering) on timeseries data, one must first map the data into Euclidean space. This is traditionally accomplished with a sliding window.

Despite the striking success of general protein folding models such as AlphaFold2(AF2, Jumper et al. (2021)), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise a previously overlooked issue that FAPE tends to face gradient vanishing problem on high-rotational-error targets. To address this fundamental limitation, we propose a novel geodesic loss called Frame Aligned Frame Error (FAFE, denoted as F2E to distinguish from FAPE), which enables the model to better optimize both the rotational and translational errors between two frames. We then prove that F2E can be reformulated as a group-aware geodesic loss, which translates the optimization of the residue-to-residue error to optimizing group-to-group geodesic frame distance. By fine-tuning AF2 with our proposed new loss function, we attain a correct rate of 52.3\% (DockQ $>$ 0.23) on an evaluation set and 43.8\% correct rate on a subset with low homology, with substantial improvement over AF2 by 182\% and 100\% respectively.

This paper presents a new, provably-convergent algorithm for computing the flag-mean and flag-median of a set of points on a flag manifold under the chordal metric. The flag manifold is a mathematical space consisting of flags, which are sequences of nested subspaces of a vector space that increase in dimension. The flag manifold is a superset of a wide range of known matrix spaces, including Stiefel and Grassmanians, making it a general object that is useful in a wide variety computer vision problems. To tackle the challenge of computing first order flag statistics, we first transform the problem into one that involves auxiliary variables constrained to the Stiefel manifold. The Stiefel manifold is a space of orthogonal frames, and leveraging the numerical stability and efficiency of Stiefel-manifold optimization enables us to compute the flag-mean effectively. Through a series of experiments, we show the competence of our method in Grassmann and rotation averaging, as well as principal component analysis. We release our source code under https://github.com/nmank/FlagAveraging.

This paper derives a perturbation bound on the optimal subspace estimator obtained from a subset of its canonical projections contaminated by noise. This fundamental result has important implications in matrix completion, subspace clustering, and related problems.

Finding prototypes (e.g., mean and median) for a dataset is central to a number of common machine learning algorithms. Subspaces have been shown to provide useful, robust representations for datasets of images, videos and more. Since subspaces correspond to points on a Grassmann manifold, one is led to consider the idea of a subspace prototype for a Grassmann-valued dataset. While a number of different subspace prototypes have been described, the calculation of some of these prototypes has proven to be computationally expensive while other prototypes are affected by outliers and produce highly imperfect clustering on noisy data. This work proposes a new subspace prototype, the flag median, and introduces the FlagIRLS algorithm for its calculation. We provide evidence that the flag median is robust to outliers and can be used effectively in algorithms like Linde-Buzo-Grey (LBG) to produce improved clusterings on Grassmannians. Numerical experiments include a synthetic dataset, the MNIST handwritten digits dataset, the Mind's Eye video dataset and the UCF YouTube action dataset. The flag median is compared the other leading algorithms for computing prototypes on the Grassmannian, namely, the $\ell_2$-median and to the flag mean. We find that using FlagIRLS to compute the flag median converges in $4$ iterations on a synthetic dataset. We also see that Grassmannian LBG with a codebook size of $20$ and using the flag median produces at least a $10\%$ improvement in cluster purity over Grassmannian LBG using the flag mean or $\ell_2$-median on the Mind's Eye dataset.

Such 2D representations have lower dimensionality than audio waveforms and they easily fit advanced deep learning architectures mainly developed for computer visi on applications. Mel frequency cepstral coefficient (MFCC), short-time Fourier transformation (STFT), discrete wavel et transformation (DWT) are among the most pervasive 2D signal representations which essentially visualize frequ ency-magnitude distribution of a given reconstructed signal ove r time. Thus far, the best sound classification accuracy has been achieved for deep learning algorithms trained on 2D signal representations [1, 2]. However, it has been shown th at despite achieving high performance, the approaches based on 2D representations are very vulnerable against adversar ial attacks [3]. Unfortunately, this poses a strict security is sue because crafted adversarial examples not only mislead the target model toward a wrong label, but also, they are transfe r-able to other models including conventional algorithms suc h as support vector machines (SVM) [3].