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Deep learning has revolutionized many industries by enabling models to automatically learn complex patterns from raw data, reducing dependence on manual feature engineering. However, deep learning algorithms are sensitive to input data, and…

Diffusion probabilistic models (DPMs) and their extensions have emerged as competitive generative models yet confront challenges of efficient sampling. We propose a new bilateral denoising diffusion model (BDDM) that parameterizes both the…

Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is developed using cell death or apoptosis in heterogeneous cell…

We live within an increasingly technological, information-laden environment for the first time in human evolution.This subjects us, and will continue to subject us in an accelerating fashion, to an unremitting exposure to meaningful…

Inspired by recent findings that generative diffusion models learn semantically meaningful representations, we use them to discover the intrinsic hierarchical structure in biomedical 3D images using unsupervised segmentation. We show that…

Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…

Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…

We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…

Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…

Immune repertoires rely on diversity of T-cell and B-cell receptors to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out…

Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…

We extend the spatial $\Lambda$-Fleming-Viot process introduced in [Electron. J. Probab. 15 (2010) 162-216] to incorporate recombination. The process models allele frequencies in a population which is distributed over the two-dimensional…

Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…

The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…

We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…

Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…

Representations in the auditory cortex might be based on mechanisms similar to the visual ventral stream; modules for building invariance to transformations and multiple layers for compositionality and selectivity. In this paper we propose…

The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…

Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both…