MLatom 2: An Integrative Platform for Atomistic Machine Learning.

Topics in Current Chemistry
Pavlo O. DralMario Barbatti

Abstract

Atomistic machine learning (AML) simulations are used in chemistry at an ever-increasing pace. A large number of AML models has been developed, but their implementations are scattered among different packages, each with its own conventions for input and output. Thus, here we give an overview of our MLatom 2 software package, which provides an integrative platform for a wide variety of AML simulations by implementing from scratch and interfacing existing software for a range of state-of-the-art models. These include kernel method-based model types such as KREG (native implementation), sGDML, and GAP-SOAP as well as neural-network-based model types such as ANI, DeepPot-SE, and PhysNet. The theoretical foundations behind these methods are overviewed too. The modular structure of MLatom allows for easy extension to more AML model types. MLatom 2 also has many other capabilities useful for AML simulations, such as the support of custom descriptors, farthest-point and structure-based sampling, hyperparameter optimization, model evaluation, and automatic learning curve generation. It can also be used for such multi-step tasks as Δ-learning, self-correction approaches, and absorption spectrum simulation within the machine-learning nucl...Continue Reading

References

May 16, 2007·Physical Review Letters·Jörg Behler, Michele Parrinello
Nov 8, 2008·Physical Chemistry Chemical Physics : PCCP·Jeng-Da Chai, Martin Head-Gordon
May 21, 2010·Physical Review Letters·Albert P BartókGábor Csányi
Sep 15, 2011·Physical Chemistry Chemical Physics : PCCP·Jörg Behler
Mar 10, 2012·Physical Review Letters·Matthias RuppO Anatole von Lilienfeld
Jul 7, 2015·Journal of Chemical Theory and Computation·Pavlo O DralWalter Thiel
Nov 18, 2015·Journal of Chemical Theory and Computation·Raghunathan RamakrishnanO Anatole von Lilienfeld
Aug 13, 2013·Journal of Chemical Theory and Computation·Katja HansenKlaus-Robert Müller
Feb 4, 2016·Journal of Computational Chemistry·Jan Řezáč
Nov 9, 2016·The Journal of Chemical Physics·Jörg Behler
May 17, 2017·Science Advances·Stefan ChmielaKlaus-Robert Müller
Apr 26, 2018·Physical Review Letters·Linfeng ZhangWeinan E
Jul 27, 2018·Nature·Keith T ButlerAron Walsh
Sep 12, 2018·The Journal of Physical Chemistry Letters·Pavlo O DralWalter Thiel
Sep 27, 2018·Nature Communications·Stefan ChmielaAlexandre Tkatchenko
May 3, 2019·Journal of Chemical Theory and Computation·Oliver T Unke, Markus Meuwly
Jun 21, 2019·Journal of Computational Chemistry·Pavlo O Dral
Feb 10, 2020·The Journal of Chemical Physics·Tim MuellerChuhong Wang
Mar 4, 2020·The Journal of Physical Chemistry Letters·Pavlo O Dral
Apr 23, 2020·Journal of Molecular Modeling·Shuming BaiMario Barbatti
Jun 4, 2020·The Journal of Chemical Physics·Pavlo O DralGábor Csányi
Jun 23, 2020·Journal of Chemical Information and Modeling·Xiang GaoAdrian E Roitberg
Sep 18, 2020·Nature·Charles R HarrisTravis E Oliphant
Oct 7, 2020·Chemical Reviews·Sergei Manzhos, Tucker Carrington
Jan 1, 2021·Journal of Chemical Theory and Computation·Ignacio Fdez GalvánRoland Lindh

❮ Previous
Next ❯

Software Mentioned

ME
NumPy
MLatom
MLatomF
MLatomPy
Hyperopt
GAP suite
ANAKIN
Newton
TensorFlow

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.