Evidence map›Paper›PMID 40227432›Full record

ArticleJournal of chemical theory and computation2025

Calculating a Phase Diagram of a Simple Water Model Using Unsupervised Machine Learning on Simulation Data.

Peter Ogrin, Tomaz Urbic

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Peter OgrinFaculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 ljubljana, Slovenia.
Tomaz UrbicFaculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 ljubljana, Slovenia.ORCID 0000-0001-6440-0220

Funding

Solvation modeling for next-gen biomolecule simulationsRM1GM135136 · NIGMS · STATE UNIVERSITY NEW YORK STONY BROOK · PI COUTSIAS, EVANGELOS A., DILL, KEN A · 2020 to 2024
$6.0M
NIGMS NIH HHS RM1 GM135136
6 · The paper itself

Abstract

We use unsupervised machine learning to construct a phase diagram of a simple 2D rose water model. The machine learning method that we use is a combination of dimensionality reduction methods and clustering algorithms. Two different data sets from the same simulations are used as input data for machine learning. These are angular distribution functions and a set of different thermodynamic, dynamic, and structural properties. To evaluate the efficiency of the method, the machine learning results are compared to manually determined phase diagrams. We show that the methods successfully predict the phase diagram of the rose water model. Furthermore, the phase diagrams obtained from the two data sets are in semiquantitative agreement with each other. Four different solid phases, one liquid phase, and one gaseous phase were determined. The method we have presented is straightforward and easy to implement. It requires almost no prior knowledge of the system to obtain a phase diagram. The method can also be used to distinguish between the different parts of the same phase that have different properties or a sufficiently different structure, and in this way find local differences and anomalies.

Identifiers

PMID40227432
PMCPMC12020001

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.