A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Kernel testing compares cell states in single-cell data.
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
A new method for state estimation on complex networks.
The Linear Attention Recurrent Neural Network (LARNN) is a recurrent attention module derived from the Long Short-Term Memory (LSTM) cell and ideas from the consciousness Recurrent Neural Network (RNN). Yes, it LARNNs. The LARNN uses attention on its past cell state values for a limited window size . The formulas ar…
Single-cell RNA sequencing (scRNA-seq) has revolutionized biological discovery, providing an unbiased picture of cellular heterogeneity in tissues. While scRNA-seq has been used extensively to provide insight into both healthy systems and diseases, it has not been used for disease prediction or diagnostics. Graph Atten…
SnapMMD forecasts cell differentiation outcomes from snapshot data.
Forest Fire Clustering discovers cell types from single-cell data.
Develops a method to infer cell trajectories from RNA sequencing data.
Extends NAS to learn both intra-cell and inter-cell architectures for language modeling.
Two simple homotopy equivalent 2-complexes K2 and L2 are related by an algebraic criterion of their corresponding presentations as stated in [HoMeSier]. Frank Quinn set it into a topological context (see [Qu1]) and call these 2-complexes related by an s-move. Using elementary 3-expansions, K2 extends to 3-cells in K3 r…
Improved LSTM cell for high-frequency trading forecasts.
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by…
We introduce Independently Recurrent Long Short-term Memory cells: IndyLSTMs. These differ from regular LSTM cells in that the recurrent weights are not modeled as a full matrix, but as a diagonal matrix, i.e.\ the output and state of each LSTM cell depends on the inputs and its own output/state, as opposed to the inpu…
Cell-based NAS search spaces are redundant and lack novelty.
We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve this integer program, we propose a column generation formulation where the prici…
In this work we present a modification in the conventional flow of information through a LSTM network, which we consider well suited for RNNs in general. The modification leads to a iterative scheme where the computations performed by the LSTM cell are repeated over a constant input and cell state values, while updatin…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …
LSTMs and GRUs are the most common recurrent neural network architectures used to solve temporal sequence problems. The two architectures have differing data flows dealing with a common component called the cell state (also referred to as the memory). We attempt to enhance the memory by presenting a modification that w…
Cellina uses supervised disentanglement to predict cell behavior in tissues.
Deep learning identifies transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity.
CT improves neural network performance on cell complex data.
TIMELY improves consistency in labeling blood cell images.
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to …
In this paper, we consider the problem of reducing the bit error rate of flash-based solid state drives (SSDs) when cells are subject to inter-cell interference (ICI). By observing that the outputs of adjacent victim cells can be correlated due to common aggressors, we propose a novel channel model to accurately repres…
SimCD simultaneously clusters cells and identifies differential gene expression in scRNA-seq data.
CST-YOLO improves blood cell detection with YOLOv7 and CNN-Swin Transformer.
New features from early battery cycles predict lifetime with high accuracy.
We focus on the problem of unsupervised cell outlier detection and repair in mixed-type tabular data. Traditional methods are concerned only with detecting which rows in the dataset are outliers. However, identifying which cells are corrupted in a specific row is an important problem in practice, and the very first ste…
Selecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs an…
Short proofs for complex Tverberg theorems using prime powers.
A novel criterion selects optimal distance metrics for cell profile analysis.
Better neural arithmetic logic units improve cell counting model generalization.
New method learns cell trajectories and network interactions from single-cell data.
Feature selection predicts immune state changes in RA mouse model.
Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has …
sgdGMF efficiently estimates generalized matrix factorization models for single-cell RNA sequencing data.
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 technical effects that may erroneously set some observations of gene expression leve…
Recurrent Neural Networks (RNN), Long Short-Term Memory Networks (LSTM), and Memory Networks which contain memory are popularly used to learn patterns in sequential data. Sequential data has long sequences that hold relationships. RNN can handle long sequences but suffers from the vanishing and exploding gradient probl…
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 technical effects that may erroneously set some observations of gene expression leve…
It is shown how the coherent states permit to find different geometrical objects as the geodesics, the conjugate locus, the cut locus, the Calabi's diastasis and its domain of definition, the Euler-Poincaré characteristic, the number of Borel-Morse cells, the Kodaira embedding theorem.
There are time series that are amenable to recurrent neural network (RNN) solutions when treated as sequences, but some series, e.g. asynchronous time series, provide a richer variation of feature types than current RNN cells take into account. In order to address such situations, we introduce a unified RNN that handle…
The paper introduces a new -LSTM cell for volatility forecasting using stylized facts.
Accurate and robust cell nuclei classification is the cornerstone for a wider range of tasks in digital and Computational Pathology. However, most machine learning systems require extensive labeling from expert pathologists for each individual problem at hand, with no or limited abilities for knowledge transfer between…
LOT framework embeds high-dimensional cell data into interpretable Euclidean space.
Long Short-Term Memory (LSTM) infers the long term dependency through a cell state maintained by the input and the forget gate structures, which models a gate output as a value in [0,1] through a sigmoid function. However, due to the graduality of the sigmoid function, the sigmoid gate is not flexible in representing m…
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
Complex numbers have long been favoured for digital signal processing, yet complex representations rarely appear in deep learning architectures. RNNs, widely used to process time series and sequence information, could greatly benefit from complex representations. We present a novel complex gated recurrent cell, which i…
Novel framework predicts cell responses to perturbations using GRNs.