Michel Dumontier

Visara Urovi, Remzi Celebi, Chang Sun et al.

Data science is an interdisciplinary research area where scientists are typically working with data coming from different fields. When using and analyzing data, the scientists implicitly agree to follow standards, procedures, and rules set in these fields. However, guidance on the responsibilities of the data scientists and the other involved actors in a data science project is typically missing. While literature shows that novel frameworks and tools are being proposed in support of open-science, data reuse, and research data management, there are currently no frameworks that can fully express responsibilities of a data science project. In this paper, we describe the Transparency, Accountability, Privacy, and Societal Responsibility Matrix (TAPS-RM) as framework to explore social, legal, and ethical aspects of data science projects. TAPS-RM acts as a tool to provide users with a holistic view of their project beyond key outcomes and clarifies the responsibilities of actors. We map the developed model of TAPS-RM with well-known initiatives for open data (such as FACT, FAIR and Datasheets for datasets). We conclude that TAPS-RM is a tool to reflect on responsibilities at a data science project level and can be used to advance responsible data science by design.

Chang Sun, Johan van Soest, Michel Dumontier

Despite the remarkable success of Generative Adversarial Networks (GANs) on text, images, and videos, generating high-quality tabular data is still under development owing to some unique challenges such as capturing dependencies in imbalanced data, optimizing the quality of synthetic patient data while preserving privacy. In this paper, we propose DP-CGANS, a differentially private conditional GAN framework consisting of data transformation, sampling, conditioning, and networks training to generate realistic and privacy-preserving tabular data. DP-CGANS distinguishes categorical and continuous variables and transforms them to latent space separately. Then, we structure a conditional vector as an additional input to not only presents the minority class in the imbalanced data, but also capture the dependency between variables. We inject statistical noise to the gradients in the networking training process of DP-CGANS to provide a differential privacy guarantee. We extensively evaluate our model with state-of-the-art generative models on three public datasets and two real-world personal health datasets in terms of statistical similarity, machine learning performance, and privacy measurement. We demonstrate that our model outperforms other comparable models, especially in capturing dependency between variables. Finally, we present the balance between data utility and privacy in synthetic data generation considering the different data structure and characteristics of real-world datasets such as imbalance variables, abnormal distributions, and sparsity of data.

Mahmoud Ibrahim, Bart Elen, Chang Sun et al.

Generative models are increasingly used to augment medical imaging datasets for fairer AI. Yet a key assumption often goes unexamined: that generators themselves produce equally high-quality images across demographic groups. Models trained on imbalanced data can inherit these imbalances, yielding degraded synthesis quality for rare subgroups and struggling with demographic intersections absent from training. We refer to this as the imbalanced generator problem. Existing remedies such as loss reweighting operate at the optimization level and provide limited benefit when training signal is scarce or absent for certain combinations. We propose CompDiff, a hierarchical compositional diffusion framework that addresses this problem at the representation level. A dedicated Hierarchical Conditioner Network (HCN) decomposes demographic conditioning, producing a demographic token concatenated with CLIP embeddings as cross-attention context. This structured factorization encourages parameter sharing across subgroups and supports compositional generalization to rare or unseen demographic intersections. Experiments on chest X-rays (MIMIC-CXR) and fundus images (FairGenMed) show that CompDiff compares favorably against both standard fine-tuning and FairDiffusion across image quality (FID: 64.3 vs. 75.1), subgroup equity (ES-FID), and zero-shot intersectional generalization (up to 21% FID improvement on held-out intersections). Downstream classifiers trained on CompDiff-generated data also show improved AUROC and reduced demographic bias, suggesting that architectural design of demographic conditioning is an important and underexplored factor in fair medical image generation. Code is available at https://anonymous.4open.science/r/CompDiff-6FE6.

Rishabh Jakhar, Michel Dumontier, Remzi Celebi

Extracting multi-step explanations from knowledge graphs poses a combinatorial challenge requiring both heuristic guidance (as candidates proliferate with depth) and credit assignment (as path quality emerges over extended sequences). Frontier LLMs, strong on knowledge/reasoning benchmarks, offer a compelling source of such heuristics, yet their knowledge comes sans guarantees and compositional performance degrades as chains lengthen. We thus present TESSERA, a 3-part neuro-symbolic framework that uses LLMs in a circumscribed role: for local discriminative judgement rather than autonomous multi-step generation; the knowledge graph then defines the hypothesis space enforcing hard structural constraints, and MCTS coordinates the long-horizon search with principled credit assignment via backpropagation. LLMs perform dual roles as a prior policy biasing exploration and a comparative state evaluator supplying reward signals. Evaluation on drug mechanism elucidation across two complementary knowledge graphs demonstrates fidelity to curated biology while surfacing coherent alternative mechanisms, with ablations confirming discriminative contribution from both LLM components. Beyond its current application, our framework offers a general paradigm for compositional reasoning over structured knowledge.

N'Dah Jean Kouagou, Arif Yilmaz, Michel Dumontier et al.

Rule mining on knowledge graphs allows for explainable link prediction. Contrarily, embedding-based methods for link prediction are well known for their generalization capabilities, but their predictions are not interpretable. Several approaches combining the two families have been proposed in recent years. The majority of the resulting hybrid approaches are usually trained within a unified learning framework, which often leads to convergence issues due to the complexity of the learning task. In this work, we propose a new way to combine the two families of approaches. Specifically, we enrich a given knowledge graph by means of its pre-trained entity and relation embeddings before applying rule mining systems on the enriched knowledge graph. To validate our approach, we conduct extensive experiments on seven benchmark datasets. An analysis of the results generated by our approach suggests that we discover new valuable rules on the enriched graphs. We provide an open source implementation of our approach as well as pretrained models and datasets at https://github.com/Jean-KOUAGOU/EnhancedRuleLearning

Raia Abu Ahmad, Reham Alharbi, Roberto Barile et al.

The International Semantic Web Research School (ISWS) is a week-long intensive program designed to immerse participants in the field. This document reports a collaborative effort performed by ten teams of students, each guided by a senior researcher as their mentor, attending ISWS 2023. Each team provided a different perspective to the topic of creative AI, substantiated by a set of research questions as the main subject of their investigation. The 2023 edition of ISWS focuses on the intersection of Semantic Web technologies and Creative AI. ISWS 2023 explored various intersections between Semantic Web technologies and creative AI. A key area of focus was the potential of LLMs as support tools for knowledge engineering. Participants also delved into the multifaceted applications of LLMs, including legal aspects of creative content production, humans in the loop, decentralised approaches to multimodal generative AI models, nanopublications and AI for personal scientific knowledge graphs, commonsense knowledge in automatic story and narrative completion, generative AI for art critique, prompt engineering, automatic music composition, commonsense prototyping and conceptual blending, and elicitation of tacit knowledge. As Large Language Models and semantic technologies continue to evolve, new exciting prospects are emerging: a future where the boundaries between creative expression and factual knowledge become increasingly permeable and porous, leading to a world of knowledge that is both informative and inspiring.

Mahmoud Ibrahim, Bart Elen, Chang Sun et al.

We present a novel framework for leveraging synthetic ICU time-series data not only to train but also to rigorously and trustworthily evaluate predictive models, both at the population level and within fine-grained demographic subgroups. Building on prior diffusion and VAE-based generators (TimeDiff, HealthGen, TimeAutoDiff), we introduce \textit{Enhanced TimeAutoDiff}, which augments the latent diffusion objective with distribution-alignment penalties. We extensively benchmark all models on MIMIC-III and eICU, on 24-hour mortality and binary length-of-stay tasks. Our results show that Enhanced TimeAutoDiff reduces the gap between real-on-synthetic and real-on-real evaluation (``TRTS gap'') by over 70\%, achieving $Δ_{TRTS} \leq 0.014$ AUROC, while preserving training utility ($Δ_{TSTR} \approx 0.01$). Crucially, for 32 intersectional subgroups, large synthetic cohorts cut subgroup-level AUROC estimation error by up to 50\% relative to small real test sets, and outperform them in 72--84\% of subgroups. This work provides a practical, privacy-preserving roadmap for trustworthy, granular model evaluation in critical care, enabling robust and reliable performance analysis across diverse patient populations without exposing sensitive EHR data, contributing to the overall trustworthiness of Medical AI.

Aditya Shourya, Michel Dumontier, Chang Sun

Recent advancements in vision-language systems have improved the accuracy of Radiological Visual Question Answering (VQA) Models. However, some challenges remain across each stage of model development: limited expert-labeled images hinders data procurement at scale; the intricate and nuanced patterns of radiological images make modeling inherently difficult; and the lack of evaluation evaluation efforts makes it difficult to identify cases where the model might be ill-conditioned. In this study, we fine-tune a lightweight 3B parameter vision-language model for Radiological VQA, demonstrating that small models, when appropriately tuned with curated data, can achieve robust performance across both open- and closed-ended questions. We propose a cost-effective training pipeline from synthetic question-answer pair generation to multi-stage fine-tuning on specialised radiological domain-targeted datasets (e.g., ROCO v2.0, MedPix v2.0). Our results show that despite operating at a fraction of the scale of state-of-the-art models such as LLaVA-Med, our model achieves promising performance given its small parameter size and the limited scale of training data. We introduce a lightweight saliency-based diagnostic tool that enables domain experts to inspect VQA model performance and identify ill-conditioned failure modes through saliency analysis.

Mahmoud Ibrahim, Yasmina Al Khalil, Sina Amirrajab et al.

This paper presents a comprehensive systematic review of generative models (GANs, VAEs, DMs, and LLMs) used to synthesize various medical data types, including imaging (dermoscopic, mammographic, ultrasound, CT, MRI, and X-ray), text, time-series, and tabular data (EHR). Unlike previous narrowly focused reviews, our study encompasses a broad array of medical data modalities and explores various generative models. Our search strategy queries databases such as Scopus, PubMed, and ArXiv, focusing on recent works from January 2021 to November 2023, excluding reviews and perspectives. This period emphasizes recent advancements beyond GANs, which have been extensively covered previously. The survey reveals insights from three key aspects: (1) Synthesis applications and purpose of synthesis, (2) generation techniques, and (3) evaluation methods. It highlights clinically valid synthesis applications, demonstrating the potential of synthetic data to tackle diverse clinical requirements. While conditional models incorporating class labels, segmentation masks and image translations are prevalent, there is a gap in utilizing prior clinical knowledge and patient-specific context, suggesting a need for more personalized synthesis approaches and emphasizing the importance of tailoring generative approaches to the unique characteristics of medical data. Additionally, there is a significant gap in using synthetic data beyond augmentation, such as for validation and evaluation of downstream medical AI models. The survey uncovers that the lack of standardized evaluation methodologies tailored to medical images is a barrier to clinical application, underscoring the need for in-depth evaluation approaches, benchmarking, and comparative studies to promote openness and collaboration.

Robin A Richardson, Remzi Celebi, Sven van der Burg et al.

There has been a large focus in recent years on making assets in scientific research findable, accessible, interoperable and reusable, collectively known as the FAIR principles. A particular area of focus lies in applying these principles to scientific computational workflows. Jupyter notebooks are a very popular medium by which to program and communicate computational scientific analyses. However, they present unique challenges when it comes to reuse of only particular steps of an analysis without disrupting the usual flow and benefits of the notebook approach, making it difficult to fully comply with the FAIR principles. Here we present an approach and toolset for adding the power of semantic technologies to Python-encoded scientific workflows in a simple, automated and minimally intrusive manner. The semantic descriptions are published as a series of nanopublications that can be searched and used in other notebooks by means of a Jupyter Lab plugin. We describe the implementation of the proposed approach and toolset, and provide the results of a user study with 15 participants, designed around image processing workflows, to evaluate the usability of the system and its perceived effect on FAIRness. Our results show that our approach is feasible and perceived as user-friendly. Our system received an overall score of 78.75 on the System Usability Scale, which is above the average score reported in the literature.

Nacira Abbas, Kholoud Alghamdi, Mortaza Alinam et al.

One of the grand challenges discussed during the Dagstuhl Seminar "Knowledge Graphs: New Directions for Knowledge Representation on the Semantic Web" and described in its report is that of a: "Public FAIR Knowledge Graph of Everything: We increasingly see the creation of knowledge graphs that capture information about the entirety of a class of entities. [...] This grand challenge extends this further by asking if we can create a knowledge graph of "everything" ranging from common sense concepts to location based entities. This knowledge graph should be "open to the public" in a FAIR manner democratizing this mass amount of knowledge." Although linked open data (LOD) is one knowledge graph, it is the closest realisation (and probably the only one) to a public FAIR Knowledge Graph (KG) of everything. Surely, LOD provides a unique testbed for experimenting and evaluating research hypotheses on open and FAIR KG. One of the most neglected FAIR issues about KGs is their ongoing evolution and long term preservation. We want to investigate this problem, that is to understand what preserving and supporting the evolution of KGs means and how these problems can be addressed. Clearly, the problem can be approached from different perspectives and may require the development of different approaches, including new theories, ontologies, metrics, strategies, procedures, etc. This document reports a collaborative effort performed by 9 teams of students, each guided by a senior researcher as their mentor, attending the International Semantic Web Research School (ISWS 2019). Each team provides a different perspective to the problem of knowledge graph evolution substantiated by a set of research questions as the main subject of their investigation. In addition, they provide their working definition for KG preservation and evolution.

Remzi Celebi, Joao Rebelo Moreira, Ahmed A. Hassan et al.

It is essential for the advancement of science that scientists and researchers share, reuse and reproduce workflows and protocols used by others. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize a number of important points regarding the means by which digital objects are found and reused by others. The question of how to apply these principles not just to the static input and output data but also to the dynamic workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe our inclusive and overarching approach to apply the FAIR principles to workflows and protocols and demonstrate its benefits. We apply and evaluate our approach on a case study that consists of making the PREDICT workflow, a highly cited drug repurposing workflow, open and FAIR. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. A semantic model was proposed to better address these specific requirements and were evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

Erik-Jan van Kesteren, Chang Sun, Daniel L. Oberski et al.

Combining data from varied sources has considerable potential for knowledge discovery: collaborating data parties can mine data in an expanded feature space, allowing them to explore a larger range of scientific questions. However, data sharing among different parties is highly restricted by legal conditions, ethical concerns, and / or data volume. Fueled by these concerns, the fields of cryptography and distributed learning have made great progress towards privacy-preserving and distributed data mining. However, practical implementations have been hampered by the limited scope or computational complexity of these methods. In this paper, we greatly extend the range of analyses available for vertically partitioned data, i.e., data collected by separate parties with different features on the same subjects. To this end, we present a novel approach for privacy-preserving generalized linear models, a fundamental and powerful framework underlying many prediction and classification procedures. We base our method on a distributed block coordinate descent algorithm to obtain parameter estimates, and we develop an extension to compute accurate standard errors without additional communication cost. We critically evaluate the information transfer for semi-honest collaborators and show that our protocol is secure against data reconstruction. Through both simulated and real-world examples we illustrate the functionality of our proposed algorithm. Without leaking information, our method performs as well on vertically partitioned data as existing methods on combined data -- all within mere minutes of computation time. We conclude that our method is a viable approach for vertically partitioned data analysis with a wide range of real-world applications.

Ruben Verborgh, Michel Dumontier

The fast-growing Web API landscape brings clients more options than ever before---in theory. In practice, they cannot easily switch between different providers offering similar functionality. We discuss a vision for developing Web APIs based on reuse of interface parts called features. Through the introduction of 5 design principles, we investigate the impact of feature-based reuse on Web APIs. Applying these principles enables a granular reuse of client and server code, documentation, and tools. Together, they can foster a measurable ecosystem with cross-API compatibility, opening the door to a more flexible generation of Web clients.

Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan et al.

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties.

Tobias Kuhn, Michel Dumontier

The current Web has no general mechanisms to make digital artifacts --- such as datasets, code, texts, and images --- verifiable and permanent. For digital artifacts that are supposed to be immutable, there is moreover no commonly accepted method to enforce this immutability. These shortcomings have a serious negative impact on the ability to reproduce the results of processes that rely on Web resources, which in turn heavily impacts areas such as science where reproducibility is important. To solve this problem, we propose trusty URIs containing cryptographic hash values. We show how trusty URIs can be used for the verification of digital artifacts, in a manner that is independent of the serialization format in the case of structured data files such as nanopublications. We demonstrate how the contents of these files become immutable, including dependencies to external digital artifacts and thereby extending the range of verifiability to the entire reference tree. Our approach sticks to the core principles of the Web, namely openness and decentralized architecture, and is fully compatible with existing standards and protocols. Evaluation of our reference implementations shows that these design goals are indeed accomplished by our approach, and that it remains practical even for very large files.

Tobias Kuhn, Michel Dumontier

To make digital resources on the web verifiable, immutable, and permanent, we propose a technique to include cryptographic hash values in URIs. We call them trusty URIs and we show how they can be used for approaches like nanopublications to make not only specific resources but their entire reference trees verifiable. Digital artifacts can be identified not only on the byte level but on more abstract levels such as RDF graphs, which means that resources keep their hash values even when presented in a different format. Our approach sticks to the core principles of the web, namely openness and decentralized architecture, is fully compatible with existing standards and protocols, and can therefore be used right away. Evaluation of our reference implementations shows that these desired properties are indeed accomplished by our approach, and that it remains practical even for very large files.

Robert Hoehndorf, Michel Dumontier, Georgios V. Gkoutos

Applied ontology is a relatively new field which aims to apply theories and methods from diverse disciplines such as philosophy, cognitive science, linguistics and formal logics to perform or improve domain-specific tasks. To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated. We propose that results in applied ontology must be evaluated within their domain of application, based on some ontology-based task within the domain, and discuss quantitative measures which would facilitate the objective evaluation and comparison of research results in applied ontology.