CLAIMED -- the open source framework for building coarse-grained operators for accelerated discovery in science

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.Comment: Received IEEE OSS Award 2023 - https://conferences.computer.org/services/2023/symposia/oss.htm

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation

TensorBank:Tensor Lakehouse for Foundation Model Training

Storing and streaming high dimensional data for foundation model training became a critical requirement with the rise of foundation models beyond natural language. In this paper we introduce TensorBank, a petabyte scale tensor lakehouse capable of streaming tensors from Cloud Object Store (COS) to GPU memory at wire speed based on complex relational queries. We use Hierarchical Statistical Indices (HSI) for query acceleration. Our architecture allows to directly address tensors on block level using HTTP range reads. Once in GPU memory, data can be transformed using PyTorch transforms. We provide a generic PyTorch dataset type with a corresponding dataset factory translating relational queries and requested transformations as an instance. By making use of the HSI, irrelevant blocks can be skipped without reading them as those indices contain statistics on their content at different hierarchical resolution levels. This is an opinionated architecture powered by open standards and making heavy use of open-source technology. Although, hardened for production use using geospatial-temporal data, this architecture generalizes to other use case like computer vision, computational neuroscience, biological sequence analysis and more

Apache Spark 2: master complex big data processing, stream analytics, and machine learning with Apache Spark

Apache Spark is an in-memory, cluster-based data processing system that provides a wide range of functionalities such as big data processing, analytics, machine learning, and more