Dumontier, Michel
Semantic Web and Creative AI -- A Technical Report from ISWS 2023
Ahmad, Raia Abu, Alharbi, Reham, Barile, Roberto, Böckling, Martin, Bolanos, Francisco, Bonfitto, Sara, Bruns, Oleksandra, Celino, Irene, Chudasama, Yashrajsinh, Critelli, Martin, d'Amato, Claudia, D'Ippolito, Giada, Dasoulas, Ioannis, De Giorgis, Stefano, De Leo, Vincenzo, Di Bonaventura, Chiara, Di Panfilo, Marco, Dobriy, Daniil, Domingue, John, Duan, Xuemin, Dumontier, Michel, Efeoglu, Sefika, Eschauzier, Ruben, Ginwa, Fakih, Ferranti, Nicolas, Graciotti, Arianna, Hanisch, Philipp, Hannah, George, Heidari, Golsa, Hogan, Aidan, Hussein, Hassan, Jouglar, Alexane, Kalo, Jan-Christoph, Kieffer, Manoé, Klironomos, Antonis, Koch, Inês, Lajewska, Weronika, Lazzari, Nicolas, Lindekrans, Mikael, Lippolis, Anna Sofia, Llugiqi, Majlinda, Mancini, Eleonora, Marzi, Eleonora, Menotti, Laura, Flores, Daniela Milon, Nagowah, Soulakshmee, Neubert, Kerstin, Niazmand, Emetis, Norouzi, Ebrahim, Martinez, Beatriz Olarte, Oudshoorn, Anouk Michelle, Poltronieri, Andrea, Presutti, Valentina, Purohit, Disha, Raoufi, Ensiyeh, Ringwald, Celian, Rockstroh, Johanna, Rudolph, Sebastian, Sack, Harald, Saeed, Zafar, Saeedizade, Mohammad Javad, Sahbi, Aya, Santini, Cristian, Simic, Aleksandra, Sommer, Dennis, Sousa, Rita, Tan, Mary Ann, Tarikere, Vidyashree, Tietz, Tabea, Tirpitz, Liam, Tomasino, Arnaldo, van Harmelen, Frank, Vissoci, Joao, Woods, Caitlin, Zhang, Bohui, Zhang, Xinyue, Zheng, Heng
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.
Generative AI for Synthetic Data Across Multiple Medical Modalities: A Systematic Review of Recent Developments and Challenges
Ibrahim, Mahmoud, Khalil, Yasmina Al, Amirrajab, Sina, Sun, Chang, Breeuwer, Marcel, Pluim, Josien, Elen, Bart, Ertaylan, Gokhan, Dumontier, Michel
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.
Improving rule mining via embedding-based link prediction
Kouagou, N'Dah Jean, Yilmaz, Arif, Dumontier, Michel, Ngomo, Axel-Cyrille Ngonga
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
TAPS Responsibility Matrix: A tool for responsible data science by design
Urovi, Visara, Celebi, Remzi, Sun, Chang, Rieswijk, Linda, Erard, Michael, Yilmaz, Arif, Moodley, Kody, Kumar, Parveen, Dumontier, Michel
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.
Knowledge Graphs Evolution and Preservation -- A Technical Report from ISWS 2019
Abbas, Nacira, Alghamdi, Kholoud, Alinam, Mortaza, Alloatti, Francesca, Amaral, Glenda, d'Amato, Claudia, Asprino, Luigi, Beno, Martin, Bensmann, Felix, Biswas, Russa, Cai, Ling, Capshaw, Riley, Carriero, Valentina Anita, Celino, Irene, Dadoun, Amine, De Giorgis, Stefano, Delva, Harm, Domingue, John, Dumontier, Michel, Emonet, Vincent, van Erp, Marieke, Arias, Paola Espinoza, Fallatah, Omaima, Ferrada, Sebastián, Ocaña, Marc Gallofré, Georgiou, Michalis, Gesese, Genet Asefa, Gillis-Webber, Frances, Giovannetti, Francesca, Buey, Marìa Granados, Harrando, Ismail, Heibi, Ivan, Horta, Vitor, Huber, Laurine, Igne, Federico, Jaradeh, Mohamad Yaser, Keshan, Neha, Koleva, Aneta, Koteich, Bilal, Kurniawan, Kabul, Liu, Mengya, Ma, Chuangtao, Maas, Lientje, Mansfield, Martin, Mariani, Fabio, Marzi, Eleonora, Mesbah, Sepideh, Mistry, Maheshkumar, Tirado, Alba Catalina Morales, Nguyen, Anna, Nguyen, Viet Bach, Oelen, Allard, Pasqual, Valentina, Paulheim, Heiko, Polleres, Axel, Porena, Margherita, Portisch, Jan, Presutti, Valentina, Pustu-Iren, Kader, Mendez, Ariam Rivas, Roshankish, Soheil, Rudolph, Sebastian, Sack, Harald, Sakor, Ahmad, Salas, Jaime, Schleider, Thomas, Shi, Meilin, Spinaci, Gianmarco, Sun, Chang, Tietz, Tabea, Dhouib, Molka Tounsi, Umbrico, Alessandro, Berg, Wouter van den, Xu, Weiqin
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.
On Reasoning with RDF Statements about Statements using Singleton Property Triples
Nguyen, Vinh, Bodenreider, Olivier, Thirunarayan, Krishnaprasad, Fu, Gang, Bolton, Evan, Rosinach, Núria Queralt, Furlong, Laura I., Dumontier, Michel, Sheth, Amit
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.
Invited Talks
Doyle, Richard J. (NASA Jet Propulsion Laboratory) | Dumontier, Michel (Stanford University) | Hirsh, Haym (Cornell University) | Jensen, David (University of Massachusetts at Amherst) | Karp, Peter (SRI International) | Monteleoni, Claire (George Washington University) | Obradovic, Zoen (Temple University) | Re, Christopher (Stanford University) | Rzhetsky, Andrey (University of Chicago) | Wagstaff, Kiri L. (NASA Jet Propulsion Laboratory)
Abstracts of the invited talks presented at the AAAI Fall Symposium on Discovery Informatics: AI Takes a Science-Centered View on Big Data. Talks include A Data Lifecycle Approach to Discovery Informatics, Generating Biomedical Hypotheses Using Semantic Web Technologies, Socially Intelligent Science, Representing and Reasoning with Experimental and Quasi-Experimental Designs, Bioinformatics Computation of Metabolic Models from Sequenced Genomes, Climate Informatics: Recent Advances and Challenge Problems for Machine Learning in Climate Science, Predictive Modeling of Patient State and Therapy Optimization, Case Studies in Data-Driven Systems: Building Carbon Maps to Finding Neutrinos, Computational Analysis of Complex Human Disorders, and Look at This Gem: Automated Data Prioritization for Scientific Discovery of Exoplanets, Mineral Deposits, and More.