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Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables Large Language Models to be applied to securely shared cohorts…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
Extracting meaningful insights from large and complex datasets poses significant challenges, particularly in ensuring the accuracy and relevance of retrieved information. Traditional data retrieval methods such as sequential search and…
Over the years, genetic programming (GP) has evolved, with many proposed variations, especially in how they represent a solution. Being essentially a program synthesis algorithm, it is capable of tackling multiple problem domains. Current…
We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster,…
Recent advances in Text-to-SQL have largely focused on the SQLite dialect, neglecting the diverse landscape of SQL dialects like BigQuery and PostgreSQL. This limitation is due to the diversity in SQL syntaxes and functions, along with the…
We present the data model, design choices, and performance of ProvSQL, a general and easy-to-deploy provenance tracking and probabilistic database system implemented as a PostgreSQL extension. ProvSQL's data and query models closely reflect…
Large-scale distributed graph-parallel computing is challenging. On one hand, due to the irregular computation pattern and lack of locality, it is hard to express parallelism efficiently. On the other hand, due to the scale-free nature,…
We introduce Raqlet, a source-to-source compilation framework that addresses the fragmentation of recursive querying engines spanning relational (recursive SQL), graph (Cypher, GQL), and deductive (Datalog) systems. Recent standards such as…
Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by integrating external knowledge, leading to improved accuracy and relevance. However, scaling RAG pipelines remains computationally expensive as retrieval sizes…
This article highlights some of the key operating principles of Grover algorithm. These principles were used to develop a new oracle function, that illustrates the possibility of using Grover algorithm for solving more realistic and…
While the publication of datasets in scientific repositories has become broadly recognised, the repositories tend to have increasing semantic-related problems. For instance, they present various data reuse obstacles for machine-actionable…
To process data more efficiently, big data frameworks provide data abstractions to developers. However, due to the abstraction, there may be many challenges for developers to understand and debug the data processing code. To uncover the…
Natural language processing is used for solving a wide variety of problems. Some scholars and interest groups working with language resources are not well versed in programming, so there is a need for a good graphical framework that allows…
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be…
Conversational search (CS) requires a complex software engineering pipeline that integrates query reformulation, ranking, and response generation. CS researchers currently face two barriers: the lack of a unified framework for efficiently…
Temporally indexed data are essential in a wide range of fields and of interest to machine learning researchers. Time series data, however, are often scarce or highly sensitive, which precludes the sharing of data between researchers and…
Graph structures offer a versatile framework for representing diverse patterns in nature and complex systems, applicable across domains like molecular chemistry, social networks, and transportation systems. While diffusion models have…
A private data federation is a set of autonomous databases that share a unified query interface offering in-situ evaluation of SQL queries over the union of the sensitive data of its members. Owing to privacy concerns, these systems do not…
Even for a conservative estimate, 80% of enterprise data reside in unstructured files, stored in data lakes that accommodate heterogeneous formats. Classical search engines can no longer meet information seeking needs, especially when the…