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This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…
The digitization of biological specimens has revolutionized the field of morphology, creating large collections of 3D data, and microCT in particular. This revolution was initially supported by the development of open-source software tools,…
In machine learning (ML), Python serves as a convenient abstraction for working with key libraries such as PyTorch, scikit-learn, and others. Unlike DBMS, however, Python applications may lose important data, such as trained models and…
Object storage solutions potentially address long-standing performance issues with POSIX file systems for certain I/O workloads, and new storage technologies offer promising performance characteristics for data-intensive use cases. In this…
Encrypted database systems provide a great method for protecting sensitive data in untrusted infrastructures. These systems are built using either special-purpose cryptographic algorithms that support operations over encrypted data, or by…
In recent years, Transformers have achieved remarkable progress in computer vision tasks. However, their global modeling often comes with substantial computational overhead, in stark contrast to the human eye's efficient information…
With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively…
The Globus Data Grid architecture provides a scalable infrastructure for the management of storage resources and data that are distributed across Grid environments. These services are designed to support a variety of scientific…
Reliable Docker-based environment construction is a dominant bottleneck for scaling execution-grounded training and evaluation of software engineering agents. We introduce DockSmith, a specialized agentic Docker builder designed to address…
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
Time Series Management Systems (TSMS) are Database Management Systems that have been configured with the primary objective of processing and storing time series data. With the IoT expanding at exponential rates and there becoming…
DBSCAN is a classical density-based clustering procedure with tremendous practical relevance. However, DBSCAN implicitly needs to compute the empirical density for each sample point, leading to a quadratic worst-case time complexity, which…
Real-time data processing applications with low latency requirements have led to the increasing popularity of stream processing systems. While such systems offer convenient APIs that can be used to achieve data parallelism automatically,…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
In this article we present a tool for the verification of programs built on top replicated databases. The tool evaluates a sequential specification and deduces which operations need to be synchronized for the program to function properly in…
Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and…
In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…
LiDAR-based 3D object detection is crucial for various applications but often experiences performance degradation in real-world deployments due to domain shifts. While most studies focus on cross-dataset shifts, such as changes in…
Transactional data structure libraries (TDSL) combine the ease-of-programming of transactions with the high performance and scalability of custom-tailored concurrent data structures. They can be very efficient thanks to their ability to…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…