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Zachary Schlamowitz

Publications and source records attributed to Zachary Schlamowitz.

3 recordsLinked to original sources

Moment kernels: a simple and scalable approach for equivariance to rotations and reflections in deep convolutional networks

Translation equivariance is a central reason convolutional neural networks have been successful in computer vision. Other symmetries, such as rotations and reflections, are similarly important in fields such as biomedical image analysis, but equivariant methods for these symmetries remain less widely adopted, especially in 3D. Existing approaches often rely on group convolutions, harmonic bases, irreducible representations, or specialized libraries, which can obscure the explicit form of admissible kernels for practitioners. We introduce moment kernels, a simple Cartesian parameterization of convolution kernels equivariant to orthogonal transformations, $O(d)$, between tensor-valued feature fields. We prove that every such $O(d)$-equivariant kernel can be represented as a sum of radial functions of $|x|$ multiplied by products of coordinate components $x^i$ and Kronecker deltas. This gives a complete, dimension-agnostic kernel family complementary to harmonic-basis approaches and implementable using standard convolution modules. We implement a discrete version of moment-kernel networks and evaluate on biomedical tasks with different transformation laws: invariant 2D image classification and equivariant 3D affine-transform regression for brain MRI. Across these tasks, moment kernels improve worst-case orientation consistency and remain trainable in 3D, while avoiding the orientation-channel expansion required by group convolutions, which reaches 48 orientations for 90-degree rotations and reflections in 3D. The resulting models provide exact consistency under grid-preserving rotations and reflections, and remain practical for standard CNN workflows.

cs.CV

Examining the Link Between Peroxiredoxin Proteins and Mutually Exclusive Transcription Factor Activation With a Mathematical Model

Oxidative stress is a fundamental stimulus to which eukaryotic cells respond via many channels. Among these channels are both protein systems that process oxidative stress, such as the 2-Cys peroxiredoxin-thioredoxin system (PTRS), as well as changes in transcriptional activity that target outcomes such as growth, damage control and repair, or cell death. Recent work has revealed connections between the PTRS and temporal phases of transcriptional activity involving famous transcription factors like p53 and FOXO1. To examine potential mechanisms for these connections, we implement an existing dynamical systems mathematical model for the PTRS. We hypothesize that dose-dependent hyperoxidation events enact ultrasensitive switches by which the PTRS can categorize stress severity and activate appropriate transcriptional responses. Using numerical simulations of the PTRS in human cells, we provide a proof of principle for staggered, switchlike hyperoxidation of peroxiredoxins (Prx) as well as an underlying mechanism requiring simultaneous signaling by Prx I and II. Then, we use our model to make testable predictions about individual Prx knockouts as well as the affinity for hydrogen peroxide of Prx across oxidation states. This study provides direction for future experimental work and sheds light into the mechanisms underlying oxidative stress response in human cells.

q-bio.BM

The DOPE Distance is SIC: A Stable, Informative, and Computable Metric on Time Series And Ordered Merge Trees

Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains such as the interval and the circle. We present the ``dynamic ordered persistence editing'' (DOPE) distance, which we prove is stable and informative while satisfying metric properties. We then devise a simple $O(N^2)$ dynamic programming algorithm to compute it on the interval and an $O(N^3)$ algorithm to compute it on the circle. Surprisingly, we accomplish this by ignoring all of the hierarchical information of the merge tree and simply focusing on a sequence of ordered critical points, which can be interpreted as a time series. Thus our algorithm is more similar to string edit distance and dynamic time warping than it is to more conventional merge tree comparison algorithms. In the context of time series with the interval as a domain, we show empirically on the UCR time series classification dataset that DOPE performs better than bottleneck/Wasserstein distances between persistence diagrams.

cs.IR