Current progress and open challenges for applying deep learning across the biosciences

N Sapoval, A Aghazadeh, MG Nute… - Nature …, 2022 - nature.com
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …

Deep learning in bioinformatics: Introduction, application, and perspective in the big data era

Y Li, C Huang, L Ding, Z Li, Y Pan, X Gao - Methods, 2019 - Elsevier
Deep learning, which is especially formidable in handling big data, has achieved great
success in various fields, including bioinformatics. With the advances of the big data era in …

Machine‐Learning‐Assisted Nanozyme Design: Lessons from Materials and Engineered Enzymes

J Zhuang, AC Midgley, Y Wei, Q Liu, D Kong… - Advanced …, 2024 - Wiley Online Library
Nanozymes are nanomaterials that exhibit enzyme‐like biomimicry. In combination with
intrinsic characteristics of nanomaterials, nanozymes have broad applicability in materials …

Using deep learning to annotate the protein universe

ML Bileschi, D Belanger, DH Bryant, T Sanderson… - Nature …, 2022 - nature.com
Understanding the relationship between amino acid sequence and protein function is a long-
standing challenge with far-reaching scientific and translational implications. State-of-the-art …

DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism

D Wang, Z Zhang, Y Jiang, Z Mao, D Wang… - Nucleic acids …, 2021 - academic.oup.com
Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives
precise and efficient control for the translation process. There is mounting evidence for the …

UDSMProt: universal deep sequence models for protein classification

N Strodthoff, P Wagner, M Wenzel, W Samek - Bioinformatics, 2020 - academic.oup.com
Motivation Inferring the properties of a protein from its amino acid sequence is one of the key
problems in bioinformatics. Most state-of-the-art approaches for protein classification are …

Deep learning with logical constraints

E Giunchiglia, MC Stoian, T Lukasiewicz - arxiv preprint arxiv:2205.00523, 2022 - arxiv.org
In recent years, there has been an increasing interest in exploiting logically specified
background knowledge in order to obtain neural models (i) with a better performance,(ii) …

Coherent hierarchical multi-label classification networks

E Giunchiglia, T Lukasiewicz - Advances in neural …, 2020 - proceedings.neurips.cc
Hierarchical multi-label classification (HMC) is a challenging classification task extending
standard multi-label classification problems by imposing a hierarchy constraint on the …

Detrac: Transfer learning of class decomposed medical images in convolutional neural networks

A Abbas, MM Abdelsamea, MM Gaber - IEEE Access, 2020 - ieeexplore.ieee.org
Due to the high availability of large-scale annotated image datasets, paramount progress
has been made in deep convolutional neural networks (CNNs) for image classification tasks …

Protein–RNA interaction prediction with deep learning: structure matters

J Wei, S Chen, L Zong, X Gao, Y Li - Briefings in bioinformatics, 2022 - academic.oup.com
Protein–RNA interactions are of vital importance to a variety of cellular activities. Both
experimental and computational techniques have been developed to study the interactions …