@GoncalvesLab

Gonçalves Lab @TUDelft (CS @EEMCS_TUD). Research on Computational Molecular Biomedicine, Machine Learning, Oncology by @JoanaGoncalves et al.

 Delft, Netherlands
goncalveslab.tudelft.nl
Joined September 2022
  • Tweets16
  • Following577
  • Followers119
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Looking back on a most important event: @y_i_tepeli masterfully defended his PhD, 16 Jun 2025, on effective strategies for therapeutic target prediction & selection bias mitigation in ML edu.nl/hv4xt. Congratulations Dr. Tepeli! Looking for his next move, snatch him.
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Gonçalves Lab retweeted
Anshul Kundaje@anshulkundajeMar 21
Honestly feel kinda sad to see so many young scientists adopting and idolizing ultra hype culture. I think people don't really understand the medium and long term consequences to their own credibility and that of science as a whole.
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Replying to @GoncalvesLab @y_i_tepeli
@y_i_tepeli
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TL;DR Part I: anti-cancer therapy target discovery, synthetic lethality prediction (ELISL) & stratification of oncogene-addicted cohorts (Oncostratifier, collab Iorio's lab). Part II: mitigation of selection bias in ML via diversity-guided self-training (DCAST, Metric-DST).
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Thank you to everyone contributing to this great celebration! Promotor Marcel Reinders, paranymphs Kirti Biharie & Sander Goossens, the whole DBL lab ❤️, family+friends of Yasin, committee Aalt-Jan van Dijk, Boudewijn Lelieveldt, Jeroen de Ridder, Patrick Kemmeren, Wouter Kouw.
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Paper by our Sander Goossens! Shows we can learn tumor-relevant mutational signatures of DDR deficiency from gene perturbation screens with mutation profiling after DNA damage. Check out SNMF (supervised NMF)! doi.org/10.1101/2024.11.27.6… #DDR #DNARepair #MachineLearning @eemcs_tud
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Paper by our @y_i_tepeli: How to train fairer ML models from data affected by selection bias? Diversity! DCAST learns from diverse vs. most confident samples to avoid confirmation bias via semi-supervised learning. #MachineLearning #FairnessML @eemcs_tud arxiv.org/abs/2409.20126

DCAST: Diverse Class-Aware Self-Training Mitigates Selection Bias...

Fairness in machine learning seeks to mitigate model bias against individuals based on sensitive features such as sex or age, often caused by an uneven representation of the population in the...

arxiv.org
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Our graduated BSc students, Andrei Tociu & Emiel Witting, will present their theses at BNAIC/Benelearn'23: assessing domain adaptation for mitigating sample selection bias. Great supervision by @y_i_tepeli! #bnaic #benelearn #MachineLearning #fairnessML #responsibleAI @eemcs_tud
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Hiring twice, join us at @tudelft! See thread for details/links. - Postdoc/PhD: multimodal ML for molecular maps of human tissue in health & disease (@_hubmap). - PhD: computational analysis of individual diversity in complex disease using cell "villages" of human donors (iCELL).
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Postdoc/PhD: multimodal machine learning for molecular maps of human tissue in health & disease (@_hubmap): (spatial) (single-cell) multiomics integration, signatures, cross-modal prediction. academictransfer.com/en/3283… #Bioinformatics #MachineLearning #PhD #Postdoc #vacancy #job

PhD or Postdoc multimodal machine learning for molecular maps of human tissue

Are you interested in machine learning for multimodal molecular analysis of human tissue? Join the TU Delft team and be part of this exciting international HuBMAP consortium!

academictransfer.com
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PhD on computational methods to uncover genetic diversity in complex disease using large-scale cell "villages" and single-cell molecular profiling of human donors (iCELL Convergence Flagship). academictransfer.com/en/3283… #Bioinformatics #PhD #vacancy #job #genetics #MachineLearning

PhD position on iCELL: individualized CELLular models of disease diversity in the population

Excited about desigining computational methods to uncover genetic diversity in complex disease using large-scale cellular models of human donors? Read on and join us!

academictransfer.com
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Gonçalves Lab retweeted
Yasin Tepeli@y_i_tepeli20 Sep 2022
👋 Come visit the poster if you are interested in synthetic lethality. #ECCB2020
Gonçalves Lab@GoncalvesLab20 Sep 2022
Today @y_i_tepeli is presenting poster P209-T at #ECCB2022 on our effort to improve synthetic lethality prediction. Sequence homology <-> related function? We integrate it w/ cancer omics to predict SL pairs, showing effect on patient survival. Preprint: doi.org/10.1101/2022.09.19.5…
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Today @y_i_tepeli is presenting poster P209-T at #ECCB2022 on our effort to improve synthetic lethality prediction. Sequence homology <-> related function? We integrate it w/ cancer omics to predict SL pairs, showing effect on patient survival. Preprint: doi.org/10.1101/2022.09.19.5…
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@ECCBinfo @cancerSL #MachineLearning
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Latest by @y_i_tepeli in our quest to improve synthetic lethality prediction. Isn’t sequence homology indicative of related function? We integrate it with cancer omics to predict SL gene pairs. Differences in patient survival suggest therapeutic potential. @cancerSL w/ C. Seale
bioRxiv@biorxivpreprint19 Sep 2022
ELISL: Early-Late Integrated Synthetic Lethality Prediction in Cancer biorxiv.org/cgi/content/shor… #bioRxiv
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Colm Seale's MSc thesis in #OUP_Bioinformatics! On selection bias in synthetic lethality prediction. What's up with bias in SL data? Are published models robust? How to diagnose, build more resilient models? doi.org/10.1093/bioinformati… with Yasin Tepeli. #MachineLearning @cancerSL

Overcoming selection bias in synthetic lethality prediction

AbstractMotivation. Synthetic lethality (SL) between two genes occurs when simultaneous loss of function leads to cell death. This holds great promise for

academic.oup.com
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