104 citations · 318 across the 19 of their papers we have counts for
19 papers
Sequence-Informed Geometric Evaluation of RNA 3D Structures
Andrea Zerio, Yighua Yao, Alessandro Micheli +5
Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry,…
How Well Do LLMs Simulate Survey Responses Following a Breast Cancer Screening Intervention?
Kenneth Koh, Ryan Jak Yang Lim, Alessandro Sparacio +5
Collecting survey data is laborious and limited by privacy constraints. Large language models (LLMs) have shown promise as predictive social simulations. It is unclear whether they…
Entropy, Disagreement, and the Limits of Foundation Models in Genomics
Maxime Rochkoulets, Lovro Vrček, Mile Šikić
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly…
RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks
Rafael Josip Penić, Tin Vlašić, Roland G. Huber +2
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the…
Finding Hamiltonian cycles with graph neural networks
Filip Bosnić, Mile Šikić
We train a small message-passing graph neural network to predict Hamiltonian cycles on Erdős-Rényi random graphs in a critical regime. It outperforms existing hand-crafted heuristi…
Learning to Untangle Genome Assembly with Graph Convolutional Networks
Lovro Vrček, Xavier Bresson, Thomas Laurent +2
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of…