Related papers: An extensible web interface for databases and its …
Background: Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module plays an essential…
While LLMs enable a range of AI applications, interacting with multiple models and customizing workflows can be challenging, and existing LLM interfaces offer limited support for collaborative extension or real-world evaluation. In this…
Recursive query processing has experienced a recent resurgence, as a result of its use in many modern application domains, including data integration, graph analytics, security, program analysis, networking and decision making. Due to the…
While the biomedical community has published several "open data" sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from…
The recent breakthroughs in large language models (LLMs) are positioned to transition many areas of software. Database technologies particularly have an important entanglement with LLMs as efficient and intuitive database interactions are…
Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the…
Interactive tools make data analysis both more efficient and more accessible to a broad population. Simple interfaces such as Google Finance as well as complex visual exploration interfaces such as Tableau are effective because they are…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
High quality epidemiological modelling is essential in order to combat the spread of infectious diseases. In this contribution, we present SimPLoID, an epidemiological modelling framework based on the probabilistic logic programming…
There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which…
The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension…
Even though the core of the Prolog programming language has been standardized by ISO since 1995, it remains difficult to write complex Prolog programs that can run unmodified on multiple Prolog implementations. Indeed, implementations…
The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures challenge users in computational biology for utilizing the structural information and protein surface property…
Current tabling systems suffer from an increase in space complexity, time complexity or both when dealing with sequences due to the use of data structures for tabled subgoals and answers and the need to copy terms into and from the table…
The connect-fill-run workflow paradigm, widely adopted in mature software engineering, accelerates collaborative development. However, computational chemistry, computational materials science, and computational biology face persistent…
Over the last few years natural language interfaces (NLI) for databases have gained significant traction both in academia and industry. These systems use very different approaches as described in recent survey papers. However, these systems…
A natural language interface (NLI) to databases is an interface that translates a natural language question to a structured query that is executable by database management systems (DBMS). However, an NLI that is trained in the general…
OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router…
This paper examines how a "Distributed Heterogeneous Relational Data Warehouse" can be integrated in a Grid environment that will provide physicists with efficient access to large and small object collections drawn from databases at…
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…