Characterizing the Survival-Associated Interactions Between Tumor-Infiltrating Lymphocytes and Tumors From Pathological Images and Multi-Omics Data.

The tumor-infiltrating lymphocytes (TILs) and its correlation with tumors have shown significant values in the development of cancers. Many observations indicated that the combination of the whole-slide pathological images (WSIs) and genomic data can better characterize the immunological mechanisms of TILs. However, the existing image-genomic studies evaluated the TILs by the combination of pathological image and single-type of omics data (e.g., mRNA), which is difficulty in assessing the underlying molecular processes of TILs holistically. Additionally, it is still very challenging to characterize the intersections between TILs and tumor regions in WSIs and the high dimensional genomic data also brings difficulty for the integrative analysis with WSIs. Based on the above considerations, we proposed an end-to-end deep learning framework i.e., IMO-TILs that can integrate pathological image with multi-omics data (i.e., mRNA and miRNA) to analyze TILs and explore the survival-associated interactions between TILs and tumors. Specifically, we firstly apply the graph attention network to describe the spatial interactions between TILs and tumor regions in WSIs. As to genomic data, the Concrete AutoEncoder (i.e., CAE) is adopted to select survival-associated Eigengenes from the high-dimensional multi-omics data. Finally, the deep generalized canonical correlation analysis (DGCCA) accompanied with the attention layer is implemented to fuse the image and multi-omics data for prognosis prediction of human cancers. The experimental results on three cancer cohorts derived from the Cancer Genome Atlas (TCGA) indicated that our method can both achieve higher prognosis results and identify consistent imaging and multi-omics bio-markers correlated strongly with the prognosis of human cancers.

S2Snet: deep learning for low molecular weight RNA identification with nanopore.

Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacterium smegmatis porin A nanopore trap. Although it can achieve desirable classification results, compared with deep learning (DL) methods, this classic machine learning requires domain knowledge to manually extract features, which is sophisticated, labor-intensive and time-consuming. Meanwhile, the generated original RNA structural events are not strictly equal in length, which is incompatible with the input requirements of DL models. To alleviate this issue, we propose a sequence-to-sequence (S2S) module that transforms the unequal length sequence (UELS) to the equal length sequence. Furthermore, to automatically extract features from the RNA structural events, we propose a sequence-to-sequence neural network based on DL. In addition, we add an attention mechanism to capture vital information for classification, such as dwell time and blockage amplitude. Through quantitative and qualitative analysis, the experimental results have achieved about a 2% performance increase (accuracy) compared to the previous method. The proposed method can also be applied to other nanopore platforms, such as the famous Oxford nanopore. It is worth noting that the proposed method is not only aimed at pursuing state-of-the-art performance but also provides an overall idea to process nanopore data with UELS.

Brain Functional Interaction of Acupuncture Effects in Diarrhea-Dominant Irritable Bowel Syndrome.

Acupuncture is a traditional Chinese medicine treatment that has widely been used to modulate gastrointestinal dysfunction caused by irritable bowel syndrome (IBS) and to alleviate the resulting pain. Recent studies have shown that gastrointestinal dysfunction caused by IBS is associated with dysregulation of the brain's central and peripheral nervous system, while functional magnetic resonance imaging (fMRI) helps explore functional abnormality of the brain. However, previous studies rarely used fMRI to study the correlations between brain functional connection, interaction, or segregation (e.g., network degree and clustering coefficient) and acupuncture stimulation in IBS. To bridge this knowledge gap, we study the changed brain functional connection, interaction, and segregation before and after acupuncture stimulation for diarrhea-dominant IBS (IBS-D) with the help of complex network methods based on fMRI. Our results indicate that the abnormal functional connections (FCs) in the right hippocampus, right superior occipital gyrus, left lingual gyrus, left middle occipital gyrus, and the cerebellum, and abnormal network degree in right middle occipital gyrus, where normal controls are significantly different from IBS-D patients, are improved after acupuncture stimulation. These changed FCs and the network degree before and after acupuncture stimulation have significant correlations with the changed clinical information including IBS symptom severity score (r = -0.54, p = 0.0065) and IBS quality of life (r = 0.426, p = 0.038). We conclude that the changes of the brain functional connection, interaction, and segregation in the hippocampus, middle and superior occipital gyrus, cerebellum, and the lingual gyrus may be related to acupuncture stimulation. The abnormal functional connection, interaction, and segregation in IBS-D may be improved after acupuncture stimulation.