Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs.

Motivation: Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies.

Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition.

Unlabelled: Spatial transcripome (ST) profiling can reveal cells' structural organizations and functional roles in tissues. However, deciphering the spatial context of gene expressions in ST data is a challenge-the high-order structure hiding in whole transcriptome space over 2D/3D spatial coordinates requires modeling and detection of interpretable high-order elements and components for further functional analysis and interpretation. This paper presents a new method GraphTucker-graph-regularized Tucker tensor decomposition for learning high-order factorization in ST data.

GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations.

Spatially-resolved RNA profiling has now been widely used to understand cells' structural organizations and functional roles in tissues, yet it is challenging to reconstruct the whole spatial transcriptomes due to various inherent technical limitations in tissue section preparation and RNA capture and fixation in the application of the spatial RNA profiling technologies. Here, we introduce a graph-guided neural tensor decomposition (GNTD) model for reconstructing whole spatial transcriptomes in tissues. GNTD employs a hierarchical tensor structure and formulation to explicitly model the high-order spatial gene expression data with a hierarchical nonlinear decomposition in a three-layer neural network, enhanced by spatial relations among the capture spots and gene functional relations for accurate reconstruction from highly sparse spatial profiling data.

Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network.

Motivation: Clustering spatial-resolved gene expression is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression co-localizations in tissue for detecting spatial expression patterns or functional relationships among the genes for biological interpretation in the spatial context. In this article, we present a convolutional neural network (CNN) regularized by the graph of protein-protein interaction (PPI) network to cluster spatially resolved gene expression.

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion.

High-throughput spatial-transcriptomics RNA sequencing (sptRNA-seq) based on in-situ capturing technologies has recently been developed to spatially resolve transcriptome-wide mRNA expressions mapped to the captured locations in a tissue sample. Due to the low RNA capture efficiency by in-situ capturing and the complication of tissue section preparation, sptRNA-seq data often only provides an incomplete profiling of the gene expressions over the spatial regions of the tissue. In this paper, we introduce a graph-regularized tensor completion model for imputing the missing mRNA expressions in sptRNA-seq data, namely FIST, Fast Imputation of Spatially-resolved transcriptomes by graph-regularized Tensor completion.

Development and Evaluation of an Adaptive Multi-DOF Finger with Mechanical-Sensor Integrated for Prosthetic Hand.

To realize the adaptive grasping of objects with diverse shapes and to capture the joint angles of the finger, a multi degree of freedom (DOF) adaptive finger for prosthetic hand is proposed in this paper. The fingers are designed with three joints. The maximum rotation angle of the finger joints is 90°.

Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants.

The local environment of the geographical origin of plants shaped their genetic variations through environmental adaptation. While the characteristics of the local environment correlate with the genotypes and other genomic features of the plants, they can also be indicative of genotype-phenotype associations providing additional information relevant to environmental dependence. In this study, we investigate how the geoclimatic features from the geographical origin of the accessions can be integrated with genomic features for phenotype prediction and association analysis using advanced canonical correlation analysis (CCA).

Multimodal 3D DenseNet for IDH Genotype Prediction in Gliomas.

Non-invasive prediction of isocitrate dehydrogenase () genotype plays an important role in tumor glioma diagnosis and prognosis. Recently, research has shown that radiology images can be a potential tool for genotype prediction, and fusion of multi-modality data by deep learning methods can further provide complementary information to enhance prediction accuracy. However, it still does not have an effective deep learning architecture to predict genotype with three-dimensional (3D) multimodal medical images.

A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer.

The aberrant alterations of biological functions are well known in tumorigenesis and cancer development. Hence, with advances in high-throughput sequencing technologies, capturing and quantifying the functional alterations in cancers based on expression profiles to explore cancer malignant process is highlighted as one of the important topics among cancer researches. In this article, we propose an algorithm for quantifying biological processes by using gene expression profiles over a sample population, which involves the idea of constructing principal curves to condense information of each biological process by a novel scoring scheme on an individualized manner.

Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection.

Cancer is a complex disease residing in various tissues of human body, accompanied with many abnormalities and mutations in genomes, transcriptome, and epigenome. Early detection plays a crucial role in extending survival time of all major cancer types. Recent advances in microarray and sequencing techniques have given more support to identifying effective biomarkers for early detection of cancer.

A feature selection method based on multiple kernel learning with expression profiles of different types.

Background: With the development of high-throughput technology, the researchers can acquire large number of expression data with different types from several public databases. Because most of these data have small number of samples and hundreds or thousands features, how to extract informative features from expression data effectively and robustly using feature selection technique is challenging and crucial. So far, a mass of many feature selection approaches have been proposed and applied to analyse expression data of different types.

The method for breast cancer grade prediction and pathway analysis based on improved multiple kernel learning.

Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer grade can markedly elevate the detection of early breast cancer and efficiently guide its treatment. With the advent of high-throughput profiling technology, a large number of data of different types are rapidly generated, and each data provides its unique biological insight.