相关论文: A Fast Multiple Attractor Cellular Automata with M…

Automated slice classification is clinically relevant since it can be incorporated into medical image segmentation workflows as a preprocessing step that would flag slices with a higher probability of containing tumors, thereby directing…

Machine learning classification problems are widespread in bioinformatics, but the technical knowledge required to perform model training, optimization, and inference can prevent researchers from utilizing this technology. This article…

Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…

Cellular automata and other discrete dynamical systems have long been studied as models of emergent complexity. Recently, neural cellular automata have been proposed as models to investigate the emerge of a more general artificial…

Challenges of assessing complexity and clonality in populations of mixed species arise in diverse areas of modern biology, including estimating diversity and clonality in microbiome populations, measuring patterns of T and B cell clonality,…

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…

We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained…

Detection and localization of image manipulations like splices are gaining in importance with the easy accessibility of image editing softwares. While detection generates a verdict for an image it provides no insight into the manipulation.…

Automated slicing aims to identify subsets of evaluation data where a trained model performs anomalously. This is an important problem for machine learning pipelines in production since it plays a key role in model debugging and comparison,…

We present a method for automatic cell classification in tissue samples using an automated training set from multiplexed immunofluorescence images. The method utilizes multiple markers stained in situ on a single tissue section on a robust…

In recent years, Deep Learning (DL) has shown promising results in conducting AI tasks such as computer vision and image segmentation. Specifically, Convolutional Neural Network (CNN) models in DL have been applied to prevention,detection,…

We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…

Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the…

Thanks to rapidly evolving sequencing techniques, the amount of genomic data at our disposal is growing increasingly large. Determining the gene structure is a fundamental requirement to effectively interpret gene function and regulation.…

Counting cells in fluorescent microscopy is a tedious, time-consuming task that researchers have to accomplish to assess the effects of different experimental conditions on biological structures of interest. Although such objects are…

Current research in clone detection suffers from poor ecosystems for evaluating precision of clone detection tools. Corpora of labeled clones are scarce and incomplete, making evaluation labor intensive and idiosyncratic, and limiting inter…

Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides that are found in DNA molecules. But, the regions of these genes that code for proteins may occupy only a small region of the…

Sequence classification is the task of predicting a class label given a sequence of observations. In many applications such as healthcare monitoring or intrusion detection, early classification is crucial to prompt intervention. In this…

We show that cellular automata can classify data by inducing a form of dynamical phase coexistence. We use Monte Carlo methods to search for general two-dimensional deterministic automata that classify images on the basis of activity, the…