arXiv subjects

Sheeba Samuel

Publications and source records attributed to Sheeba Samuel.

16 recordsLinked to original sources

arXiv2026

ReproScore: Separating Readiness from Outcome in Research Software Reproducibility Assessment

Digital libraries curate millions of research software artefacts yet lack scalable infrastructure for assessing whether those artefacts remain executable. Existing automated assessment tools treat static repository completeness -- what a repository contains -- as a proxy for execution success -- whether it runs. We term this the readiness-outcome conflation and present ReproScore, a two-tier framework that explicitly separates reproducibility readiness (RRS) from reproducibility outcome (ROS), combining them into a coverage-adaptive Composite Score (RCS). RRS comprises 26 sub-metrics across five categories; ROS provides execution-based probes when sandbox infrastructure is available; a community rubric externalises weighting priorities as versioned YAML profiles. Evaluated on 423 GitHub repositories from a large-scale ground-truth corpus spanning five failure modes, two complementary findings emerge: the environment category strongly discriminates failure mode, confirming static signals capture meaningful structural differences; yet RRS exhibits near-zero binary success correlation, empirically quantifying the readiness-outcome gap at repository scale. Together, these findings validate the architectural separation as both necessary and non-trivial, positioning ReproScore as scalable infrastructure for reproducibility-aware curation in digital library workflows.

cs.SE↗

arXiv2026

Containing the Reproducibility Gap: Automated Repository-Level Containerization for Scholarly Jupyter Notebooks

Computational reproducibility is fundamental to trustworthy science, yet remains difficult to achieve in practice across various research workflows, including Jupyter notebooks published alongside scholarly articles. Environment drift, undocumented dependencies and implicit execution assumptions frequently prevent independent re-execution of published research. Despite existing reproducibility guidelines, scalable and systematic infrastructure for automated assessment remains limited. We present an automated, web-oriented reproducibility engineering pipeline that reconstructs and evaluates repository-level execution environments for scholarly notebooks. The system performs dependency inference, automated container generation, and isolated execution to approximate the notebook's original computational context. We evaluate the approach on 443 notebooks from 116 GitHub repositories referenced by publications in PubMed Central. Execution outcomes are classified into four categories: resolved environment failures, persistent logic or data errors, reproducibility drift, and container-induced regressions. Our results show that containerization resolves 66.7% of prior dependency-related failures and substantially improves execution robustness. However, a significant reproducibility gap remains: 53.7% of notebooks exhibit low output fidelity, largely due to persistent runtime failures and stochastic non-determinism. These findings indicate that standardized containerization is essential for computational stability but insufficient for full bit-wise reproducibility. The framework offers a scalable solution for researchers, editors, and archivists seeking systematic, automated assessment of computational artifacts.

cs.SE↗

arXiv2026

Learning to be Reproducible: Custom Loss Design for Robust Neural Networks

To enhance the reproducibility and reliability of deep learning models, we address a critical gap in current training methodologies: the lack of mechanisms that ensure consistent and robust performance across runs. Our empirical analysis reveals that even under controlled initialization and training conditions, the accuracy of the model can exhibit significant variability. To address this issue, we propose a Custom Loss Function (CLF) that reduces the sensitivity of training outcomes to stochastic factors such as weight initialization and data shuffling. By fine-tuning its parameters, CLF explicitly balances predictive accuracy with training stability, leading to more consistent and reliable model performance. Extensive experiments across diverse architectures for both image classification and time series forecasting demonstrate that our approach significantly improves training robustness without sacrificing predictive performance. These results establish CLF as an effective and efficient strategy for developing more stable, reliable and trustworthy neural networks.

cs.LG↗

arXiv2024

Explainability of Deep Learning-Based Plant Disease Classifiers Through Automated Concept Identification

While deep learning has significantly advanced automatic plant disease detection through image-based classification, improving model explainability remains crucial for reliable disease detection. In this study, we apply the Automated Concept-based Explanation (ACE) method to plant disease classification using the widely adopted InceptionV3 model and the PlantVillage dataset. ACE automatically identifies the visual concepts found in the image data and provides insights about the critical features influencing the model predictions. This approach reveals both effective disease-related patterns and incidental biases, such as those from background or lighting that can compromise model robustness. Through systematic experiments, ACE helped us to identify relevant features and pinpoint areas for targeted model improvement. Our findings demonstrate the potential of ACE to improve the explainability of plant disease classification based on deep learning, which is essential for producing transparent tools for plant disease management in agriculture.

cs.CV↗

arXiv2024

Harnessing multiple LLMs for Information Retrieval: A case study on Deep Learning methodologies in Biodiversity publications

Deep Learning (DL) techniques are increasingly applied in scientific studies across various domains to address complex research questions. However, the methodological details of these DL models are often hidden in the unstructured text. As a result, critical information about how these models are designed, trained, and evaluated is challenging to access and comprehend. To address this issue, in this work, we use five different open-source Large Language Models (LLMs): Llama-3 70B, Llama-3.1 70B, Mixtral-8x22B-Instruct-v0.1, Mixtral 8x7B, and Gemma 2 9B in combination with Retrieval-Augmented Generation (RAG) approach to extract and process DL methodological details from scientific publications automatically. We built a voting classifier from the outputs of five LLMs to accurately report DL methodological information. We tested our approach using biodiversity publications, building upon our previous research. To validate our pipeline, we employed two datasets of DL-related biodiversity publications: a curated set of 100 publications from our prior work and a set of 364 publications from the Ecological Informatics journal. Our results demonstrate that the multi-LLM, RAG-assisted pipeline enhances the retrieval of DL methodological information, achieving an accuracy of 69.5% (417 out of 600 comparisons) based solely on textual content from publications. This performance was assessed against human annotators who had access to code, figures, tables, and other supplementary information. Although demonstrated in biodiversity, our methodology is not limited to this field; it can be applied across other scientific domains where detailed methodological reporting is essential for advancing knowledge and ensuring reproducibility. This study presents a scalable and reliable approach for automating information extraction, facilitating better reproducibility and knowledge transfer across studies.

cs.IR↗

arXiv2024

Enhancing Explainability in Multimodal Large Language Models Using Ontological Context

Recently, there has been a growing interest in Multimodal Large Language Models (MLLMs) due to their remarkable potential in various tasks integrating different modalities, such as image and text, as well as applications such as image captioning and visual question answering. However, such models still face challenges in accurately captioning and interpreting specific visual concepts and classes, particularly in domain-specific applications. We argue that integrating domain knowledge in the form of an ontology can significantly address these issues. In this work, as a proof of concept, we propose a new framework that combines ontology with MLLMs to classify images of plant diseases. Our method uses concepts about plant diseases from an existing disease ontology to query MLLMs and extract relevant visual concepts from images. Then, we use the reasoning capabilities of the ontology to classify the disease according to the identified concepts. Ensuring that the model accurately uses the concepts describing the disease is crucial in domain-specific applications. By employing an ontology, we can assist in verifying this alignment. Additionally, using the ontology's inference capabilities increases transparency, explainability, and trust in the decision-making process while serving as a judge by checking if the annotations of the concepts by MLLMs are aligned with those in the ontology and displaying the rationales behind their errors. Our framework offers a new direction for synergizing ontologies and MLLMs, supported by an empirical study using different well-known MLLMs.

cs.CV↗

arXiv2024

Evaluating the method reproducibility of deep learning models in the biodiversity domain

Artificial Intelligence (AI) is revolutionizing biodiversity research by enabling advanced data analysis, species identification, and habitats monitoring, thereby enhancing conservation efforts. Ensuring reproducibility in AI-driven biodiversity research is crucial for fostering transparency, verifying results, and promoting the credibility of ecological findings.This study investigates the reproducibility of deep learning (DL) methods within the biodiversity domain. We design a methodology for evaluating the reproducibility of biodiversity-related publications that employ DL techniques across three stages. We define ten variables essential for method reproducibility, divided into four categories: resource requirements, methodological information, uncontrolled randomness, and statistical considerations. These categories subsequently serve as the basis for defining different levels of reproducibility. We manually extract the availability of these variables from a curated dataset comprising 61 publications identified using the keywords provided by biodiversity experts. Our study shows that the dataset is shared in 47% of the publications; however, a significant number of the publications lack comprehensive information on deep learning methods, including details regarding randomness.

cs.IR↗

arXiv2024

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

cs.CE↗

arXiv2024

From human experts to machines: An LLM supported approach to ontology and knowledge graph construction

The conventional process of building Ontologies and Knowledge Graphs (KGs) heavily relies on human domain experts to define entities and relationship types, establish hierarchies, maintain relevance to the domain, fill the ABox (or populate with instances), and ensure data quality (including amongst others accuracy and completeness). On the other hand, Large Language Models (LLMs) have recently gained popularity for their ability to understand and generate human-like natural language, offering promising ways to automate aspects of this process. This work explores the (semi-)automatic construction of KGs facilitated by open-source LLMs. Our pipeline involves formulating competency questions (CQs), developing an ontology (TBox) based on these CQs, constructing KGs using the developed ontology, and evaluating the resultant KG with minimal to no involvement of human experts. We showcase the feasibility of our semi-automated pipeline by creating a KG on deep learning methodologies by exploiting scholarly publications. To evaluate the answers generated via Retrieval-Augmented-Generation (RAG) as well as the KG concepts automatically extracted using LLMs, we design a judge LLM, which rates the generated content based on ground truth. Our findings suggest that employing LLMs could potentially reduce the human effort involved in the construction of KGs, although a human-in-the-loop approach is recommended to evaluate automatically generated KGs.

cs.CL↗

arXiv2023

Reproducible Domain-Specific Knowledge Graphs in the Life Sciences: a Systematic Literature Review

Knowledge graphs (KGs) are widely used for representing and organizing structured knowledge in diverse domains. However, the creation and upkeep of KGs pose substantial challenges. Developing a KG demands extensive expertise in data modeling, ontology design, and data curation. Furthermore, KGs are dynamic, requiring continuous updates and quality control to ensure accuracy and relevance. These intricacies contribute to the considerable effort required for their development and maintenance. One critical dimension of KGs that warrants attention is reproducibility. The ability to replicate and validate KGs is fundamental for ensuring the trustworthiness and sustainability of the knowledge they represent. Reproducible KGs not only support open science by allowing others to build upon existing knowledge but also enhance transparency and reliability in disseminating information. Despite the growing number of domain-specific KGs, a comprehensive analysis concerning their reproducibility has been lacking. This paper addresses this gap by offering a general overview of domain-specific KGs and comparing them based on various reproducibility criteria. Our study over 19 different domains shows only eight out of 250 domain-specific KGs (3.2%) provide publicly available source code. Among these, only one system could successfully pass our reproducibility assessment (14.3%). These findings highlight the challenges and gaps in achieving reproducibility across domain-specific KGs. Our finding that only 0.4% of published domain-specific KGs are reproducible shows a clear need for further research and a shift in cultural practices.

cs.IR↗

arXiv2023

Concept explainability for plant diseases classification

Plant diseases remain a considerable threat to food security and agricultural sustainability. Rapid and early identification of these diseases has become a significant concern motivating several studies to rely on the increasing global digitalization and the recent advances in computer vision based on deep learning. In fact, plant disease classification based on deep convolutional neural networks has shown impressive performance. However, these methods have yet to be adopted globally due to concerns regarding their robustness, transparency, and the lack of explainability compared with their human experts counterparts. Methods such as saliency-based approaches associating the network output to perturbations of the input pixels have been proposed to give insights into these algorithms. Still, they are not easily comprehensible and not intuitive for human users and are threatened by bias. In this work, we deploy a method called Testing with Concept Activation Vectors (TCAV) that shifts the focus from pixels to user-defined concepts. To the best of our knowledge, our paper is the first to employ this method in the field of plant disease classification. Important concepts such as color, texture and disease related concepts were analyzed. The results suggest that concept-based explanation methods can significantly benefit automated plant disease identification.

cs.CV↗

arXiv2023

Computational reproducibility of Jupyter notebooks from biomedical publications

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

cs.DL↗

arXiv2022

Computational reproducibility of Jupyter notebooks from biomedical publications

Jupyter notebooks allow to bundle executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. Here, we analyze the computational reproducibility of 9625 Jupyter notebooks from 1117 GitHub repositories associated with 1419 publications indexed in the biomedical literature repository PubMed Central. 8160 of these were written in Python, including 4169 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 2684 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 396 notebooks ran through without any errors, including 245 that produced results identical to those reported in the original. Running the other notebooks resulted in exceptions. We zoom in on common problems and practices, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

cs.CE↗

arXiv2022

Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities

The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on the exploration of large datasets. Current scientific research is often interdisciplinary, making data integration a critical technique for combining data from different scientific domains. Research data management is a critical part of this paradigm, through the proposition and development of methods, techniques, and practices for managing scientific data through their life cycle. Research on microbial communities follows the same pattern of production of large amounts of data obtained, for instance, from sequencing organisms present in environmental samples. Data on microbial communities can come from a multitude of sources and can be stored in different formats. For example, data from metagenomics, metatranscriptomics, metabolomics, and biological imaging are often combined in studies. In this article, we describe the design and current state of implementation of an integrative research data management framework for the Cluster of Excellence Balance of the Microverse aiming to allow for data on microbial communities to be more easily discovered, accessed, combined, and reused. This framework is based on research data repositories and best practices for managing workflows used in the analysis of microbial communities, which includes recording provenance information for tracking data derivation.

cs.DB↗

arXiv2020

ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks

Computational notebooks have gained widespread adoption among researchers from academia and industry as they support reproducible science. These notebooks allow users to combine code, text, and visualizations for easy sharing of experiments and results. They are widely shared in GitHub, which currently has more than 100 million repositories making it the largest host of source code in the world. Recent reproducibility studies have indicated that there exist good and bad practices in writing these notebooks which can affect their overall reproducibility. We present ReproduceMeGit, a visualization tool for analyzing the reproducibility of Jupyter Notebooks. This will help repository users and owners to reproduce and directly analyze and assess the reproducibility of any GitHub repository containing Jupyter Notebooks. The tool provides information on the number of notebooks that were successfully reproducible, those that resulted in exceptions, those with different results from the original notebooks, etc. Each notebook in the repository along with the provenance information of its execution can also be exported in RDF with the integration of the ProvBook tool.

cs.CY↗

arXiv2020

Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles

Machine learning (ML) is an increasingly important scientific tool supporting decision making and knowledge generation in numerous fields. With this, it also becomes more and more important that the results of ML experiments are reproducible. Unfortunately, that often is not the case. Rather, ML, similar to many other disciplines, faces a reproducibility crisis. In this paper, we describe our goals and initial steps in supporting the end-to-end reproducibility of ML pipelines. We investigate which factors beyond the availability of source code and datasets influence reproducibility of ML experiments. We propose ways to apply FAIR data practices to ML workflows. We present our preliminary results on the role of our tool, ProvBook, in capturing and comparing provenance of ML experiments and their reproducibility using Jupyter Notebooks.

cs.LG↗