Related papers: Quasi-universality in single-cell sequencing data

We propose experimentally feasible ways to probe universal features of absorbing phase transitions from two different approaches, both based on numerical validations. On one hand, we numerically study a probability distribution of…

Integrating heterogeneous datasets across different measurement platforms is a fundamental challenge in many scientific applications. A common example arises in deconvolution problems, such as cell type deconvolution, where one aims to…

Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…

Semi-supervised learning on real-world graphs is frequently challenged by heterophily, where the observed graph is unreliable or label-disassortative. Many existing graph neural networks either rely on a fixed adjacency structure or attempt…

Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…

We study spectral behavior of sparsely connected random networks under the random matrix framework. Sub-networks without any connection among them form a network having perfect community structure. As connections among the sub-networks are…

Sparse data is fundamental to scientific simulations in biology and physics, from single-cell gene expression to particle calorimetry, where exact zeros encode physical absence rather than weak signal. However, existing diffusion models…

We consider the problem of distributed inference where agents in a network observe a stream of private signals generated by an unknown state, and aim to uniquely identify this state from a finite set of hypotheses. We focus on scenarios…

Semi-supervised learning faces significant challenges in realistic scenarios where labeled data is scarce and unlabeled data follows unknown, arbitrary distributions. We formalize this critical yet under-explored paradigm as Universal…

Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are…

Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…

In many biological processes heterogeneity within cell populations is an important issue. In this work we consider populations where the behavior of every single cell can be described by a system of ordinary differential equations.…

Image-based sequencing of mRNA makes it possible to see where in a tissue sample a given gene is active, and thus discern large numbers of different cell types in parallel. This is crucial for gaining a better understanding of tissue…

The propagation of light through samples with random inhomogeneities can be described by way of transmission eigenchannels, which connect incoming and outgoing external propagating modes. Although the detailed structure of a disordered…

The propagation of waves through transmission eigenchannels in complex media is emerging as a new frontier of condensed matter and wave physics. A crucial step towards constructing a complete theory of eigenchannels is to demonstrate their…

Causal discovery, the task of inferring causal structure from data, has the potential to uncover mechanistic insights from biological experiments, especially those involving perturbations. However, causal discovery algorithms over larger…

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…

Transmission eigenchannels and associated eigenvalues, that give a full account of wave propagation in random media, have recently emerged as a major theme in theoretical and applied optics. Here we demonstrate, both analytically and…

In an era of unprecedented deluge of (mostly unstructured) data, graphs are proving more and more useful, across the sciences, as a flexible abstraction to capture complex relationships between complex objects. One of the main challenges…