The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules
Open accessAbstract
Shallow machine learning methods have been applied to chemoinformatics problems with some success. As more data becomes available and more complex problems are tackled, deep machine learning methods may also become useful. Here, we present a brief overview of deep learning methods and show in particular how recursive neural network approaches can be applied to the problem of predicting molecular properties. However, molecules are typically described by undirected cyclic graphs, while recursive approaches typically use directed acyclic graphs. Thus, we develop methods to address this discrepancy, essentially by considering an ensemble of recursive neural networks associated with all possible vertex-centered acyclic orientations of the molecular graph. One advantage of this approach is that it relies only minimally on the identification of suitable molecular descriptors because suitable representations are learned automatically from the data. Several variants of this approach are applied to the problem of predicting aqueous solubility and tested on four benchmark data sets. Experimental results show that the performance of the deep learning methods matches or exceeds the performance of other state-of-the-art methods according to several evaluation metrics and expose the fundamental limitations arising from training sets that are too small or too noisy. A Web-based predictor, AquaSol, is available online through the ChemDB portal ( cdb.ics.uci.edu ) together with additional material.
Overview
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.
Integrity signals
Registry
Cites
Statistics
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gradient-based learning applied to document recognition
Lecun, Y., Bottou, L., Bengio, Y., & Haffner, P. (1998) · Proceedings of the IEEE · doi:10.1109/5.726791 · Cited by 58,805
Learning representations by back-propagating errors
Rumelhart, D. E., Hinton, G. E., & Williams, R. J. (1986) · Nature · doi:10.1038/323533a0 · Cited by 31,892
Reducing the dimensionality of data with neural networks
Hinton, G. E., & Salakhutdinov, R. R. (2006) · Science · doi:10.1126/science.1127647 · Cited by 20,928
A fast learning algorithm for deep belief nets
Hinton, G. E., Osindero, S., & Teh, Y.-W. (2006) · Neural Computation · doi:10.1162/neco.2006.18.7.1527 · Cited by 16,336
Advances in Neural Information Processing Systems 25
Zhang, Y., Sutton, C. A., Storkey, A., & Zoubin Ghahramani, A. (2012) · Cited by 12,653
Learning long-term dependencies with gradient descent is difficult
Bengio, Y., Simard, P., & Frasconi, P. (1994) · IEEE Transactions on Neural Networks · doi:10.1109/72.279181 · Cited by 8,542
Improving neural networks by preventing co-adaptation of feature detectors
Hinton, G. E., Srivastava, N., Krizhevsky, A., Sutskever, I., & Salakhutdinov, R. R. (2012) · arXiv · doi:10.48550/arxiv.1207.0580 · Cited by 6,382
(2009) · Cited by 6,153
Greedy layer-wise training of deep networks
Bengio, Y., Lamblin, P., Popovici, D., & Larochelle, H. (2007) · Advances in Neural Information Processing Systems 19 · doi:10.7551/mitpress/7503.003.0024 · Cited by 4,841
Partition coefficients and their uses
Leo, A., Hansch, C., & Elkins, D. (1971) · Chemical Reviews · doi:10.1021/cr60274a001 · Cited by 4,540
Cited by
Deep learning in neural networks: an overview
Schmidhuber, J. (2015) · Neural Networks · doi:10.1016/j.neunet.2014.09.003 · Cited by 18,570
MoleculeNet: a benchmark for molecular machine learning
Wu, Z., Ramsundar, B., Feinberg, E. N., Gomes, J., Geniesse, C., Pappu, A. S., Leswing, K., & Pande, V. (2018) · Chemical Science · doi:10.1039/c7sc02664a · Cited by 3,107
Convolutional Networks on Graphs for Learning Molecular Fingerprints
Duvenaud, D., Maclaurin, D., Aguilera-Iparraguirre, J., Gómez-Bombarelli, R., Hirzel, T., Aspuru-Guzik, A., & Adams, R. P. (2015) · arXiv · doi:10.48550/arxiv.1509.09292 · Cited by 2,628
Opportunities and obstacles for deep learning in biology and medicine
Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Zietz, M., Hoffman, M. M., et al. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0387 · Cited by 2,310
Analyzing Learned Molecular Representations for Property Prediction
Yang, K., Swanson, K., Jin, W., Coley, C., Eiden, P., Gao, H., Guzman-Perez, A., Hopper, T., Kelley, B., Mathea, M., et al. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00237 · Cited by 1,923
Metadata
- Authors
- Lusci, A., Pollastri, G., & Baldi, P.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-07-02
- Volume
- 53
- Issue
- 7
- Pages
- 1563-1575
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2046589863
- Cited by
- 555
- References
- 52
- FWCI
- 15.58
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. https://app.cochat.ai/papers/10.1021/ci400187y
- The paper
- Lusci, A., Pollastri, G., & Baldi, P. (2013). Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. Journal of Chemical Information and Modeling. https://doi.org/10.1021/ci400187y
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
