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Biology

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On the relationship between scientific theory and ontology in everything flows.

History and philosophy of the life sciences
In their anthology Everything Flows: Towards a Processual Philosophy of Biology, Daniel J. Nicholson and John Dupré argue that modern theories of biology imply that the fundamental structure of reality is processual at its core. In the present work, ...

Recent advances in generative biology for biotherapeutic discovery.

Trends in pharmacological sciences
Generative biology combines artificial intelligence (AI), advanced life sciences technologies, and automation to revolutionize the process of designing novel biomolecules with prescribed properties, giving drug discoverers the ability to escape the l...

Toward the novel AI tasks in infection biology.

mSphere
Machine learning and artificial intelligence (AI) are becoming more common in infection biology laboratories around the world. Yet, as they gain traction in research, novel frontiers arise. Novel artificial intelligence algorithms are capable of addr...

The principle of uncertainty in biology: Will machine learning/artificial intelligence lead to the end of mechanistic studies?

PLoS biology
Molecular Biology has long tried to discover mechanisms, considering that unless we understand the principles, we cannot develop applications. Now machine learning and artificial intelligence enable direct leaps to application without understanding t...

Animal-robot interaction-an emerging field at the intersection of biology and robotics.

Bioinspiration & biomimetics
The field of animal-robot and organism-robot interaction systems (ARIS, ORIS) is a currently rapidly emerging field in biorobotics. In this special issue we aim for providing a comprehensive overview of the cutting-edge advancements and pioneering br...

Multi-label classification with XGBoost for metabolic pathway prediction.

BMC bioinformatics
BACKGROUND: Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism's metabolic network from its genome sequence. Recently there have been developments in machine learning-based pat...

Deep learning in terrestrial conservation biology.

Biologia futura
Biodiversity is being lost at an unprecedented rate on Earth. As a first step to more effectively combat this process we need efficient methods to monitor biodiversity changes. Recent technological advance can provide powerful tools (e.g. camera trap...

Biology-guided deep learning predicts prognosis and cancer immunotherapy response.

Nature communications
Substantial progress has been made in using deep learning for cancer detection and diagnosis in medical images. Yet, there is limited success on prediction of treatment response and outcomes, which has important implications for personalized treatmen...

AlphaFold and the future of structural biology.

Acta crystallographica. Section D, Structural biology
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.

AlphaFold and the future of structural biology.

IUCrJ
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.