Multi-omic and multi-view clustering algorithms: review and cancer benchmark

N Rappoport, R Shamir - Nucleic acids research, 2018 - academic.oup.com
Recent high throughput experimental methods have been used to collect large biomedical
omics datasets. Clustering of single omic datasets has proven invaluable for biological and …

Constructing neural network based models for simulating dynamical systems

C Legaard, T Schranz, G Schweiger, J Drgoňa… - ACM Computing …, 2023 - dl.acm.org
Dynamical systems see widespread use in natural sciences like physics, biology, and
chemistry, as well as engineering disciplines such as circuit analysis, computational fluid …

[책][B] Synthetic data for deep learning

SI Nikolenko - 2021 - Springer
You are holding in your hands… oh, come on, who holds books like this in their hands
anymore? Anyway, you are reading this, and it means that I have managed to release one of …

Molecular sets (MOSES): a benchmarking platform for molecular generation models

D Polykovskiy, A Zhebrak… - Frontiers in …, 2020 - frontiersin.org
Generative models are becoming a tool of choice for exploring the molecular space. These
models learn on a large training dataset and produce novel molecular structures with similar …

Transforming the language of life: transformer neural networks for protein prediction tasks

A Nambiar, M Heflin, S Liu, S Maslov… - Proceedings of the 11th …, 2020 - dl.acm.org
The scientific community is rapidly generating protein sequence information, but only a
fraction of these proteins can be experimentally characterized. While promising deep …

Concept activation regions: A generalized framework for concept-based explanations

J Crabbé, M van der Schaar - Advances in Neural …, 2022 - proceedings.neurips.cc
Abstract Concept-based explanations permit to understand the predictions of a deep neural
network (DNN) through the lens of concepts specified by users. Existing methods assume …

Explaining latent representations with a corpus of examples

J Crabbé, Z Qian, F Imrie… - Advances in Neural …, 2021 - proceedings.neurips.cc
Modern machine learning models are complicated. Most of them rely on convoluted latent
representations of their input to issue a prediction. To achieve greater transparency than a …

Classification of human white blood cells using machine learning for stain‐free imaging flow cytometry

M Lippeveld, C Knill, E Ladlow, A Fuller… - Cytometry Part …, 2020 - Wiley Online Library
Imaging flow cytometry (IFC) produces up to 12 spectrally distinct, information‐rich images of
single cells at a throughput of 5,000 cells per second. Yet often, cell populations are still …

Angiodysplasia detection and localization using deep convolutional neural networks

AA Shvets, VI Iglovikov, A Rakhlin… - 2018 17th IEEE …, 2018 - ieeexplore.ieee.org
Accurate detection and localization for angiodysplasia lesions is an important problem in
early stage diagnostics of gastrointestinal bleeding and anemia. Gold standard for …

Deep in the bowel: highly interpretable neural encoder-decoder networks predict gut metabolites from gut microbiome

V Le, TP Quinn, T Tran, S Venkatesh - BMC genomics, 2020 - Springer
Background Technological advances in next-generation sequencing (NGS) and
chromatographic assays [eg, liquid chromatography mass spectrometry (LC-MS)] have …