Cited by 43Computational Drug Discovery MethodsMachine Learning in Materials ScienceHistory and advancements in chemistry

Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy

Open access
Chavan, Swapnil, Friedman, Ran, Nicholls, Ian·2015·International Journal of Molecular Sciences

Abstract

A k-nearest neighbor (k-NN) classification model was constructed for 118 RDT NEDO (Repeated Dose Toxicity New Energy and industrial technology Development Organization; currently known as the Hazard Evaluation Support System (HESS)) database chemicals, employing two acute toxicity (LD50)-based classes as a response and using a series of eight PaDEL software-derived fingerprints as predictor variables. A model developed using Estate type fingerprints correctly predicted the LD50 classes for 70 of 94 training set chemicals and 19 of 24 test set chemicals. An individual category was formed for each of the chemicals by extracting its corresponding k-analogs that were identified by k-NN classification. These categories were used to perform the read-across study for prediction of the chronic toxicity, i.e., Lowest Observed Effect Levels (LOEL). We have successfully predicted the LOELs of 54 of 70 training set chemicals (77%) and 14 of 19 test set chemicals (74%) to within an order of magnitude from their experimental LOEL values. Given the success thus far, we conclude that if the k-NN model predicts LD50 classes correctly for a certain chemical, then the k-analogs of such a chemical can be successfully used for data gap filling for the LOEL. This model should support the in silico prediction of repeated dose toxicity.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3390/ijms160511659

Cites

43 of 43 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Chavan et al. classified LD50 values using k-NN and predicted LOEL to measure chronic toxicity, with R square of test set only 0.54.

    “Chavan et al. classified the LD50 values of compounds using k-NN. Based on the classification, they predicted the LOEL (lowest observed effect level), which was then used to measure chronic toxicity. The R square value of the test set was only 0.54, however [93].”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Chavan, S., Friedman, R., & Nicholls, I.
Affiliations
  • Linnaeus University (SE)
  • Uppsala University (SE)
Corresponding author
  • Chavan, Swapnil
  • Nicholls, Ian
Venue
International Journal of Molecular Sciences
Publisher
MDPI AG
Published
2015-05-21
Volume
16
Issue
5
Pages
11659-11677
ISSN
1422-0067 (ISSN-L)
OpenAlex
W2096810557
Cited by
43
References
43
Citations by year
2026: 5 · 2025: 5 · 2024: 13 · 2023: 6 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 4 · 2018: 1 · 2016: 1 · 2015: 1
FWCI
1.03
Type
journal article
Language
en
Open access
Locations
  • International Journal of Molecular Sciences (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Diva portal (Dalarna University Library) (submittedVersion, other-oa)
  • Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Università degli Studi di Milano
  • European Commission (238701)
  • KU Leuven
  • Linnéuniversitetet
Topics
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › History and advancements in chemistry
Keywords
acute toxicity prediction, k-nearest neighbors, read-across, lowest observed effect level, LD50, repeated-dose toxicity, chemical fingerprints, data gap filling, in silico toxicity prediction
MeSH terms
Computer Simulation, Dose-Response Relationship, Drug, Humans, Lethal Dose 50, Models, Biological, Software, Cluster Analysis, Quantitative Structure-Activity Relationship, Drug Discovery

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review