MOTIVATION: Spatial transcriptomics holds great promise for revolutionizing biology and medicine by providing gene expression profiles with spatial information. Until recently, spatial resolution has been limited, but advances in high-throughput in situ imaging technologies now offer new opportunities by covering thousands of genes at a single-cell or even subcellular resolution, necessitating databases dedicated to comprehensive coverage and analysis with user-friendly intefaces. RESULTS: We introduce the HISSTA database, which facilitates the archival and analysis of in situ transcriptome data at single-cell resolution from various human tissues. We have collected and annotated spatial transcriptome data generated by MERFISH, CosMx SMI, and Xenium techniques, encompassing 112 samples and 28 million cells across 16 tissue types from 63 studies. To decipher spatial contexts, we have implemented advanced tools for cell type annotation, spatial colocalization, spatial cellular communication, and niche analyses. Notably, all datasets and annotations are interactively accessible through Vitessce, allowing users to focus on regions of interest and examine gene expression in detail. HISSTA is a unique database designed to manage the rapidly growing dataset of in situ transcriptomes at single-cell resolution. Given its comprehensive data content and advanced analysis tools with interactive visualizations, HISSTA is poised to significantly impact cancer diagnosis, precision medicine, and digital pathology. AVAILABILITY AND IMPLEMENTATION: HISSTA is freely accessible at https://kbds.re.kr/hissta/. The source code is available at https://doi.org/10.5281/zenodo.14904523.

Training large AI models on numerous GPUs consumes a massive amount of energy, making power delivery one of the largest limiting factors in building and operating datacenters for AI workloads. However, we observe that not all energy consumed during training directly contributes to end-to-end throughput; a significant portion can be removed without slowing down training. We call this portion energy bloat.

Oobleck enables resilient distributed training of large DNN models with guaranteed fault tolerance. It takes a planning-execution co-design approach, where it first generates a set of heterogeneous pipeline templates and instantiates at least f + 1 logically equivalent pipeline replicas to tolerate any f simultaneous failures. During execution, it relies on already-replicated model states across the replicas to provide fast recovery. Oobleck provably guarantees that some combination of the initially created pipeline templates can be used to cover all available resources after f or fewer simultaneous failures, thereby avoiding resource idling at all times. Evaluation on large DNN models with billions of parameters shows that Oobleck provides consistently high throughput, and it outperforms state-of-the-art fault tolerance solutions like Bamboo and Varuna by up to 13.9×.

In multi-tenant systems, the CPU overhead of distributed file systems (DFSes) is increasingly a burden to application performance. CPU and memory interference cause degraded and unstable application and storage performance, in particular for operation latency. Recent client-local DFSes for persistent memory (PM) accelerate this trend. DFS offload to SmartNICs is a promising solution to these problems, but it is challenging to fit the complex demands of a DFS onto simple SmartNIC processors located across PCIe.

Traditional CPUs and cloud systems based on them have embraced the hardware-based trusted execution environments to securely isolate computation from malicious OS or hardware attacks. However, GPUs and their cloud deployments have yet to include such support for hardware-based trusted computing. As large amounts of sensitive data are offloaded to GPU acceleration in cloud environments, ensuring the security of the data is a current and pressing need. As deployed today, the outsourced GPU model is vulnerable to attacks from compromised privileged software. To support isolated remote execution on GPUs even under vulnerable operating systems, this paper proposes a novel hardware and software architecture, called HIX (Heterogeneous Isolated eXecution). HIX does not require modifications to the GPU architecture to offer protections: Instead, it offers security by modifying the I/O interconnect between the CPU and GPU, and by refactoring the GPU device driver to work from within the CPU trusted environment. A result of the architectural choices behind HIX is that the concept can be applied to other offload accelerators besides GPUs. This work implements the proposed HIX architecture on an emulated machine with KVM and QEMU. Experimental results from the emulated security support with a real GPU show that the performance overhead for security is curtailed to 26% on average for the Rodinia benchmark, while providing secure isolated GPU computing.

SUMMARY: Predictive biomarkers for patient stratification play critical roles in realizing the paradigm of precision medicine. Molecular characteristics such as somatic mutations and expression signatures represent the primary source of putative biomarker genes for patient stratification. However, evaluation of such candidate biomarkers is still cumbersome and requires multistep procedures especially when using massive public omics data. Here, we present an interactive web application that divides patients from large cohorts (e.g. The Cancer Genome Atlas, TCGA) dynamically into two groups according to the mutation, copy number variation or gene expression of query genes. It further supports users to examine the prognostic value of resulting patient groups based on survival analysis and their association with the clinical features as well as the previously annotated molecular subtypes, facilitated with a rich and interactive visualization. Importantly, we also support custom omics data with clinical information. AVAILABILITY AND IMPLEMENTATION: CaPSSA (Cancer Patient Stratification and Survival Analysis) runs on a web-browser and is freely available without restrictions at http://www.kobic.re.kr/capssa/. The source code is available on https://github.com/yjjang/capssa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase. AVAILABILITY AND IMPLEMENTATION: miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr. CONTACT: [email protected].