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Software & Tools
KGsim-benchmark
KGsim-benchmark is a collection of 21 benchmark data sets for large biomedical knowledge graphs similarity evaluation. Team @ LASIGE: Catia Pesquita; Rita Sousa; Carlota CardosoProject
SMiLax
Publication
Rita T. Sousa,Sara Silva,Catia Pesquita. Evolving knowledge graph similarity for supervised learning in complex biomedical domains. BMC Bioinformatics, 21(1), Springer Science and Business Media LLC, 2020 [Biblios]Publication
Carlota Cardoso, Rita T. Sousa, Sebastian Köhler, Catia Pesquita. A Collection of Benchmark data sets for Knowledge Graph-based Similarity in the Biomedical Domain. In Extended Semantic Web Conference, 2020 [Biblios]Publication
Carlota Cardoso,Rita T Sousa,Sebastian Köhler,Catia Pesquita. A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. Database, 2020, Oxford University Press (OUP), 2020 [Biblios]Publication
Rita Isabel Torres de Sousa, Pesquita, Cátia, Silva, Sara Guilherme Oliveira da. Evolving meaning: using Genetic Programming to learn similarity perspectives for mining biomedical data. Master's dissertation, 2019 [Biblios]Publication
Rita T. Sousa, Sara Silva, Catia Pesquita. Explaining Protein-Protein Interaction Predictions with Genetic Programming. In Evo* 2022 -- Late-Breaking Abstracts Volume, pages 30-33, 2022 [Biblios]Publication
Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Susana Nunes, Filipa Serrano, Rita T. Sousa, Catia Pesquita, Sara C. Madeira, Helena Aidos. Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events. In Intelligent Disease Progression Prediction (iDPP) at CLEF, pages 1211-1227. CEUR-WS.org, 2022 [Biblios]Publication
Susana Nunes, Rita T. Sousa, Filipa Serrano, Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Sara C. Madeira, Helena Aidos, Catia Pesquita. Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity. In Intelligent Disease Progression Prediction (iDPP) at CLEF 2022. CEUR-WS.org, 2022 [Biblios]Publication
Rita T. Sousa, Sara Silva, Catia Pesquita. The Supervised Semantic Similarity Toolkit, In The Semantic Web: ESWC 2022 Satellite Events,Lecture Notes in Computer Science, pages 42-46. Springer International Publishing, 2022 [Biblios]Publication
Susana Nunes, Rita Sousa, Catia Pesquita. Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies. In European Conference on Computational Biology, 2021 [Biblios]Publication
Rita T Sousa, Sara Silva, Catia Pesquita. evoKGsim+: a framework for tailoring Knowledge Graph-based similarity for supervised learning. In Extended Semantic Web Conference, 2021 [Biblios]Publication
Rita T. Sousa,Sara Silva,Catia Pesquita. Supervised Biomedical Semantic Similarity. IEEE Access, 11, Institute of Electrical and Electronics Engineers (IEEE), 2023 [Biblios]Publication
Rita T. Sousa, Sara Silva, Heiko Paulheim, Catia Pesquita. Biomedical Knowledge Graph Embeddings with Negative Statements. In The Semantic Web – ISWC 2023,Lecture Notes in Computer Science, pages 428-446. Springer Nature Switzerland, 2023 [Biblios]Publication
Rita T. Sousa, Sara Silva, Catia Pesquita. Explainable Representations for Relation Prediction in Knowledge Graphs. In Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning. International Joint Conferences on Artificial Intelligence Organization, 2023 [Biblios]Publication
Susana Nunes,Rita T. Sousa,Catia Pesquita. Multi-domain knowledge graph embeddings for gene-disease association prediction. Journal of Biomedical Semantics, 14(1), Springer Science and Business Media LLC, 2023 [Biblios]Publication
Rita T. Sousa,Sara Silva,Catia Pesquita. Explaining protein–protein interactions with knowledge graph-based semantic similarity. Computers in Biology and Medicine, 170, Elsevier BV, 2024 [Biblios]News
LASIGE Workshop 2025
The 10th edition of the LASIGE Workshop took place on Wednesday, May 21, 2025, celebrating the vibrant and diverse research within the unit. This annual event once again provided a platform for sharing ongoing work and fostering collaboration among LASIGE members....News
FCiências.ID Awards Rita Sousa’s PhD thesis
Rita Sousa, a former PhD student at LASIGE, and current PhD collaborator, has been awarded by FCiências.ID for the excellence of her PhD thesis in Computer Science and Engineering. Her thesis, “Semantic perspectives for learning over biomedical knowledge...News
LASIGE members honoured on the 114th anniversary of Ciências ULisboa
LASIGE members among those distinguished by Ciências ULisboa (CIÊNCIAS) on its 114th anniversary, 29 April 2025. The event was dedicated to the recognition of excellence at CIÊNCIAS and, once again, several LASIGE students and teachers were recognized for their work...News
LASIGE’s 2024 PhD graduations
LASIGE is very proud and honored to congratulate its seven recent PhD graduates: Diogo Lima, “A Geographical-Aware State Deployment Service for Fog Computing”, supervised by Hugo Miranda; Diogo Soares, “Triclustering Three-way Temporal and...News
LASIGE Workshop 2024
The 9th edition of the LASIGE workshop took place last Wednesday, April 10, 2024, showcasing the vibrant research activities within the unit. This year, the event featured four insightful talks delivered by distinguished members of LASIGE, drawing attention to the...News
LASIGE team publishes in Computers for Biology and Medicine journal
LASIGE researchers Rita Sousa, Sara Silva, and Catia Pesquita have published a study in Computers for Biology and Medicine, a top 10% journal, introducing KGsim2vec, a method that enhances the explainability of AI models for protein–protein interaction prediction....News
LASIGE @ Ciências Research & Innovation Day 2023
As part of the Ciências ULisboa community, LASIGE took the opportunity to present to its peers the science that is produced in the unit in 5th edition of Ciências Research & Innovation Day! The event, a public showcase of the best science made in the centenary...News
LASIGE @ Encontro Ciência 2023
LASIGE participated in the annual science meeting organized by Fundação para a Ciência e Tecnologia (FCT), the Foundation that supports Science and Technology in Portugal, held in Aveiro, Portugal, on July 5-7, 2023, and some of our students could present their...News
LASIGE publishes in IEEE Access
LASIGE’s researchers Rita Sousa, Sara Silva and Cátia Pesquita have successfully published the paper “Supervised biomedical semantic similarity” in IEEE Access, a multidisciplinary, fully open-access journal. This work addresses the challenge of...News
Rita Sousa, Sara Silva and Cátia Pesquita accepted @ KR 2023
The paper “Explainable representations for relation prediction in knowledge graphs”, co-authored by LASIGE’s researchers Rita Sousa, Sara Silva, and Cátia Pesquita, has been accepted at the 20th International Conference on Principles of Knowledge...News
Girls in ICT 2023 @ Ciências
The 2023 edition of Girls in ICT, held May 3, 2023, at Ciências ULisboa, dedicated to the theme of Digital Skills for Life, promoted the following lectures: Computer Engineering: an open door to the Future (Susana Ferreira, Nokia, Graduated in Computer Engineering)...News
LASIGE @ the Ciências’s Open Day for Masters and Doctorates
LASIGE once again was present at the Ciências’s Open Day for Masters and Doctorates that took place at the campus of Ciências of ULisboa, held on April 20, 2023. An event to promote the Ciências’ ULisboa Master’s and PhD programmes, aimed at...News
8th LASIGE Workshop (2023)
The 8th LASIGE Workshop was held on March 22, 2023. The event included an award ceremony in which LASIGE researchers were distinguished for their research output for the previous year. The two best posters presented in the workshop were also awarded and… the winners...News
LASIGE Winter Forum
The LASIGE Winter Forum, organised by the PhD Student Commission, took place today, the 16th of December 2022. The program was diverse and ambitious. Among other activities, it included: a keynote speech by Luís Duarte, researcher at Sony Interactive Entertainment; a...News
LASIGE @ University of Mannheim
Lasige’s PhD student Rita Sousa was invited for a three-month stay with the Data and Web Science (DWS) Group of the University of Mannheim, Germany, that started in September, 2022. During the research stay, Rita collaborated with Prof. Heiko Paulheim, the data...News
Keynote speaker @ SeWeBMeDA
Cátia Pesquita was the keynote speaker at the 5th Workshop on Semantic Web solutions for large-scale biomedical data analytics (SeWeBMeDA) co-located with ESWC 2022. The talk, titled “Powering Biomedical Artificial Intelligence with a Holistic Knowledge Graph”,...News
LASIGE at Encontro Ciência 2022
The latest edition of Encontro Ciência 2022, promoted by Fundação para a Ciência e Tecnologia (FCT), the Foundation that supports Science and Technology in Portugal, was in person and was held on May 16-18, 2022. LASIGE took the opportunity to present some of its work...News
Best Poster Award at ESWC2021
Rita Sousa, LASIGE researcher and PhD Student, and the LASIGE integrated members, Sara Silva and Cátia Pesquita received the Best Poster Award at the 2021 Extended Semantic Web Conference (ESWC2021), June,10th, for their work “evoKGsim+ A framework for tailoring...News
6th LASIGE Workshop (2021)
The 6th LASIGE Workshop was held yesterday, May 10. The event took place online and it was very well received by LASIGE members and invitees. As usual, the event included an award ceremony in which LASIGE researchers were distinguished for their research output for...News
LASIGE researchers Carlota Cardoso, Rita Sousa and Cátia Pesquita published in Database
Carlota Cardoso, Rita Sousa and Cátia Pesquita, LASIGE researchers, in a collaboration with Sebastian Khöler (Monarch Initiative), present a collection of 21 benchmark data sets that aim at circumventing the difficulties in building benchmarks for large biomedical...News
LASIGE @ Encontro Ciência’ 20
Last week, November 3-4, 2020, LASIGE participated at the annual science meeting organized by Fundação para a Ciência e Tecnologia (FCT), the Foundation that supports Science and Technology in Portugal. Some of our researchers submitted their communications and were...News
LASIGE’s MSc students awarded merit scholarships by Ciências ULisboa
Three of LASIGE students are among the ten Ciências ULisboa students awarded with a merit scholarship for their work in 2018/2019 academic year. Diana Sousa, Robin Vassantlal and Rita Sousa curricular classifications were among the best of the Ciências ULisboa student...News
Best Poster Award at ESWC 2020
LASIGE researchers Carlota Cardoso, Rita Sousa and Cátia Pesquita (integrated researcher) were co-awarded the Best Poster Award at the 2020 Extended Semantic Web Conference. Their work, “ A Collection of Benchmark data sets for Knowledge Graph-based Similarity...News
LASIGE researchers publish in BMC Bioinformatics Special Issue in Machine learning for computational and systems biology
Rita Sousa, Sara Silva and Cátia Pesquita have published a paper about evolving semantic similarity representations to support supervised learning in the biomedical domain in BMC Bioinformatics. This is a top-ranked journal in Bioinformatics and Computational Biology...News
6 PhD grants for LASIGE students
Six Ph.D. students at LASIGE were granted, by FCT (2019), a four-year scholarship (including tuition) to do research under the supervision of a LASIGE senior member. Congratulations to Bernardo Almeida, Diana Sousa, Diogo Branco, João Batista, Rita Sousa and Sérgio...News
4th LASIGE Workshop (2019)
The 4th edition of LASIGE workshop was held at February 12, 2019. It had two main goals: Create synergies between LASIGE and other research labs by disseminating scientific works and sharing research impressions; Bring together all LASIGE members to discuss the...Talks
Summer of Research: Pitch Talks
The Summer of Research program aims to enrich the training experience of early-stage students and support the development of future researchers through hands-on and mentored research projects. When: July 21, 10:30-15:30 Where: Ciências ULisboa, Room 6.3.27 Agenda:...Talks
PHD in Informatics Seminar #3 2022/2023 | DI Ciências ULisboa
Title: Biomedical Knowledge Graph Embeddings with Negative Statements Speaker: Rita Sousa, LASIGE/DI-FCUL Date: March 2, 2023, 12h Where: Room 6.3.27 Abstract: A knowledge graph is a powerful representation of real-world entities and their relations. The vast majority...Talks
LASIGE Winter Forum
Date: December 16, 2022, 09h30 Where: FCUL, C6.2.56 Agenda: 09:30 Registration desk and coffee 09:50 Welcome Session 10:00 Introduction to LASIGE – Catia Pesquita [LASIGE] 10:20 LASIGE PhD Student Commission 10:30 Coffee Break 11:00 PhD Thesis Defense –...Talks
PhD in Informatics Seminar #8 2021/2022 | DI Ciências ULisboa
Title: Explainable semantic similarity for biomedical supervised learning Speaker: Rita Sousa, LASIGE/DI-FCUL Date: May 26, 12h Where: Room 6.3.27 Abstract: Explainable artificial intelligence approaches ensure algorithmic fairness, identify potential bias in the...Talks
Ten Minutes Talk with the PhD students in Informatics
Title: Evolving Meaning for supervised learning in complex biomedical domains using knowledge graphs Speaker: Rita Sousa, LASIGE – DI/FCUL When: Wednesday, May 19th, 17h45 Where: https://videoconf-colibri.zoom.us/j/87137996435 Short summary: Knowledge graphs...Talks
PhD in Informatics Seminar #2 2020/2021 | DI Ciências ULisboa
Title: Evolving meaning for supervised learning in complex biomedical domains using knowledge graphs Speaker: Rita Sousa When: March 18 (Thursday) at 12:00 Where: https://videoconf-colibri.zoom.us/j/83154248622 Abstract: In recent years, the explosion in complexity...Talks