Related papers: Towards the Latent Transcriptome

Latent space models are widely used for analyzing high-dimensional discrete data matrices, such as patient-feature matrices in electronic health records (EHRs), by capturing complex dependence structures through low-dimensional embeddings.…

In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…

The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the…

An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…

We study the behavior of a Time-Aware Long Short-Term Memory Autoencoder, a state-of-the-art method, in the context of learning latent representations from irregularly sampled patient data. We identify a key issue in the way such recurrent…

RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accurate measurement of relative transcript abundances from the…

Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been…

We present SMILES-embeddings derived from the internal encoder state of a Transformer [1] model trained to canonize SMILES as a Seq2Seq problem. Using a CharNN [2] architecture upon the embeddings results in higher quality interpretable…

Offline handwriting recognition systems require cropped text line images for both training and recognition. On the one hand, the annotation of position and transcript at line level is costly to obtain. On the other hand, automatic line…

Machine learning (ML) tools such as encoder-decoder convolutional neural networks (CNN) can represent incredibly complex nonlinear functions which map between combinations of images and scalars. For example, CNNs can be used to map…

Ultra high-throughput sequencing of transcriptomes (RNA-Seq) is a widely used method for quantifying gene expression levels due to its low cost, high accuracy and wide dynamic range for detection. However, the nature of RNA-Seq makes it…

Clinical medical data, especially in the intensive care unit (ICU), consist of multivariate time series of observations. For each patient visit (or episode), sensor data and lab test results are recorded in the patient's Electronic Health…

Powerful deep learning tools, such as convolutional neural networks (CNN), are able to learn the input-output relationships of large complicated systems directly from data. Encoder-decoder deep CNNs are able to extract features directly…

Vector embeddings derived from large language models (LLMs) show promise in capturing latent information from the literature. Interestingly, these can be integrated into material embeddings, potentially useful for data-driven predictions of…

Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate…

In contrast to RNNs, which compress their history into a single hidden state, Transformers can attend to all past tokens directly. However, standard Transformers rely solely on the hidden state from the previous layer to represent the…

Accurate synthesis of a full 3D MR image containing tumours from available MRI (e.g. to replace an image that is currently unavailable or corrupted) would provide a clinician as well as downstream inference methods with important…

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…

Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…

This paper develops a model that addresses sentence embedding, a hot topic in current natural language processing research, using recurrent neural networks with Long Short-Term Memory (LSTM) cells. Due to its ability to capture long term…