arXiv subjects

Mahdi Esmailoghli

Publications and source records attributed to Mahdi Esmailoghli.

4 recordsLinked to original sources

arXiv2026

Supporting Workflow Reproducibility by Linking Bioinformatics Tools across Papers and Executable Code

Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description in a paper would improve workflow comprehension, support reproducibility, and facilitate reuse. This task requires the linking of bioinformatics tools in workflow code with their mentions in a published workflow description. Results: We present CoPaLink, an automated approach that integrates three components: named entity recognition (NER) for identifying tool mentions in scientific text, NER for tool mentions in workflow code, and entity resolution based on word embedding similarity. We propose approaches for all three steps, achieving a high individual F1-measure (77 - 90) and a joint accuracy of 66 when evaluated on Nextflow workflows using Sentence-BERT. CoPaLink leverages corpora of scientific articles and workflow executable code with curated tool annotations to bridge the gap between narrative descriptions and workflow implementations. Availability: The code is available at https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments and https://gitlab.liris.cnrs.fr/sharefair/copalink. The corpora are also available: CPL-Article (https://doi.org/10.5281/zenodo.20746904), CPL-Code (https://doi.org/10.5281/zenodo.20746970) and CPL-Gold-Entity-Resolution (https://doi.org/10.5281/zenodo.20746994).

cs.CL↗

arXiv2025

The Past Still Matters: A Temporally-Valid Data Discovery System

Over the past decade, the proliferation of public and enterprise data lakes has fueled intensive research into data discovery, aiming to identify the most relevant data from vast and complex corpora to support diverse user tasks. Significant progress has been made through the development of innovative index structures, similarity measures, and querying infrastructures. Despite these advances, a critical aspect remains overlooked: relevance is time-varying. Existing discovery methods largely ignore this temporal dimension, especially when explicit date/time metadata is missing. To fill this gap, we outline a vision for a data discovery system that incorporates the temporal dimension of data. Specifically, we define the problem of temporally-valid data discovery and argue that addressing it requires techniques for version discovery, temporal lineage inference, change log synthesis, and time-aware data discovery. We then present a system architecture to deliver these techniques, before we summarize research challenges and opportunities. As such, we lay the foundation for a new class of data discovery systems, transforming how we interact with evolving data lakes.

cs.DB↗

arXiv2024

Blend: A Unified Data Discovery System

Most research on data discovery has so far focused on improving individual discovery operators such as join, correlation, or union discovery. However, in practice, a combination of these techniques and their corresponding indexes may be necessary to support arbitrary discovery tasks. We propose BLEND, a comprehensive data discovery system that supports existing operators and enables their flexible pipelining. BLEND is based on a set of lower-level operators that serve as fundamental building blocks for more complex and sophisticated user tasks. To reduce the execution runtime of discovery pipelines, we propose a unified index structure and a rule-based optimizer that rewrites SQL statements into low-level operators when possible. We show the superior flexibility and efficiency of our system compared to ad-hoc discovery pipelines and stand-alone solutions.

cs.DB↗

arXiv2022

MATE: Multi-Attribute Table Extraction

A core operation in data discovery is to find joinable tables for a given table. Real-world tables include both unary and n-ary join keys. However, existing table discovery systems are optimized for unary joins and are ineffective and slow in the existence of n-ary keys. In this paper, we introduce MATE, a table discovery system that leverages a novel hash-based index that enables n-ary join discovery through a space-efficient super key. We design a filtering layer that uses a novel hash, XASH. This hash function encodes the syntactic features of all column values and aggregates them into a super key, which allows the system to efficiently prune tables with non-joinable rows. Our join discovery system is able to prune up to 1000x more false positives and leads to over 60x faster table discovery in comparison to state-of-the-art.

cs.DB↗