Artificial intelligence (AI)-based multi-modal fusion algorithms are pivotal in emulating clinical practice by integrating data from diverse sources. However, most of the existing multi-modal models focus on designing new modal fusion methods, ignoring critical role of feature representation. Enhancing feature representativeness can address the noise caused by modal heterogeneity at the source, enabling high performance even with small datasets and simple architectures. Here, we introduce DeepOmix-FLEX (Fusion with Learning Enhanced feature representation for X-modal or FLEX in short), a multi-modal fusion model that integrates clinical data, proteomic data, metabolomic data, and pathology images across different scales and modalities, with a focus on advanced feature learning and representation. FLEX contains a Feature Encoding Trainer structure that can train feature encoding, thus achieving fusion of inter-feature and inter-modal. FLEX achieves a mean AUC of 0.887 for prediction of chronic kidney disease progression on an internal dataset, exceeding the mean AUC of 0.727 using conventional clinical variables. Following external validation and interpretability analyses, our model demonstrated favorable generalizability and validity, as well as the ability to exploit markers. In summary, FLEX highlights the potential of AI algorithms to integrate multi-modal data and optimize the allocation of healthcare resources through accurate prediction.

The determination of transcriptome profiles that mediate immune therapy in cancer remains a major clinical and biological challenge. Despite responses induced by immune-check points inhibitors (ICIs) in diverse tumor types and all the big breakthroughs in cancer immunotherapy, most patients with solid tumors do not respond to ICI therapies. It still remains a big challenge to predict the ICI treatment response. Here, we propose a framework with multiple prior knowledge networks guided for immune checkpoints inhibitors prediction-DeepOmix-ICI (or ICInet for short). ICInet can predict the immune therapy response by leveraging geometric deep learning and prior biological knowledge graphs of gene-gene interactions. Here, we demonstrate more than 600 ICI-treated patients with ICI response data and gene expression profile to apply on ICInet. ICInet was used for ICI therapy responses prediciton across different cancer types-melanoma, gastric cancer and bladder cancer, which includes 7 cohorts from different data sources. ICInet is able to robustly generalize into multiple cancer types. Moreover, the performance of ICInet in those cancer types can outperform other ICI biomarkers in the clinic. Our model [area under the curve (AUC = 0.85)] generally outperformed other measures, including tumor mutational burden (AUC = 0.62) and programmed cell death ligand-1 score (AUC = 0.74). Therefore, our study presents a prior-knowledge guided deep learning method to effectively select immunotherapy-response-associated biomarkers, thereby improving the prediction of immunotherapy response for precision oncology.

In common medical procedures, the time-consuming and expensive nature of obtaining test results plagues doctors and patients. Digital pathology research allows using computational technologies to manage data, presenting an opportunity to improve the efficiency of diagnosis and treatment. Artificial intelligence (AI) has a great advantage in the data analytics phase. Extensive research has shown that AI algorithms can produce more up-to-date and standardized conclusions for whole slide images. In conjunction with the development of high-throughput sequencing technologies, algorithms can integrate and analyze data from multiple modalities to explore the correspondence between morphological features and gene expression. This review investigates using the most popular image data, hematoxylin-eosin stained tissue slide images, to find a strategic solution for the imbalance of healthcare resources. The article focuses on the role that the development of deep learning technology has in assisting doctors' work and discusses the opportunities and challenges of AI.

RNA-seq technology offers the promise of rapid comprehensive discovery of long intervening noncoding RNAs (lincRNAs). Basic tools such as Tophat and Cufflinks have been widely used for RNA-seq assembly. However, advanced bioinformatics methodologies that allow in-depth analysis of lincRNAs are lacking. Here, we describe a computational protocol that is especially designed for the identification of novel lincRNAs and the prediction of the function. The protocol mainly includes two open-access tools, CNCI and ncFANs. CNCI allows users to distinguish noncoding from protein-coding transcripts and to retrieve novel lincRNAs. ncFANs integrates expression profiles of protein-coding and lincRNA genes to construct coexpression networks. Such networks are subsequently used to perform function predictions of unknown lincRNAs. This protocol will allow users to apply these procedures without the need of additional training. All the tools in current protocol are available http://www.bioinfo.org/np/.

NFS is considered to be the bottleneck in cluster computing environment because of its limited resources and centralized data management. With the development of hardware, NFS server has more than one I/O channel, more storage space and more powerful CPU. In this paper, we describe the design and the implementation of a new logical file system called United-FS. It can make storage devices connected to multiple I/O channels work concurrently and cooperatively. It can be exported by NFS server to provide a single file system image to clients by hiding a variety of native file systems built on different type of storage devices. This paper also compares the United-FS with the software RAID system both from theoretical analysis and experiments. The results show that United-FS is much more flexible and its performance is better than software RAID in most cases.

BACKGROUND: Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various levels. In recent years, large-scale NAT screens in several model organisms have produced much data, but there is no database to assemble all these data. AntiCODE intends to function as an integrated NAT database for this purpose. RESULTS: This release of antiCODE contains more than 30,000 non-redundant natural sense-antisense transcript pairs from 12 eukaryotic model organisms. In order to provide an integrated NAT research platform, efficient browser, search and Blast functions have been included to enable users to easily access information through parameters such as species, accession number, overlapping patterns, coding potential etc. In addition to the collected information, antiCODE also introduces a simple classification system to facilitate the study of natural antisense transcripts. CONCLUSION: Though a few similar databases also dealing with NATs have appeared lately, antiCODE is the most comprehensive among these, comprising almost all currently detected NAT pairs.