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Substructural Connectivity Fingerprint and Extreme Entropy Machines-A New Method of Compound Representation and Analysis.

ABSTRACT: Key-based substructural fingerprints are an important element of computer-aided drug design techniques. The usefulness of the fingerprints in filtering compound databases is invaluable, as they allow for the quick rejection of molecules with a low probability of being active. However, this method is flawed, as it does not consider the connections between substructures. After changing the connections between particular chemical moieties, the fingerprint representation of the compound remains the same, which leads to difficulties in distinguishing between active and inactive compounds. In this study, we present a new method of compound representation-substructural connectivity fingerprints (SCFP), providing information not only about the presence of particular substructures in the molecule but also additional data on substructure connections. Such representation was analyzed by the recently developed methodology-extreme entropy machines (EEM). The SCFP can be a valuable addition to virtual screening tools, as it represents compound structure with greater detail and more specificity, allowing for more accurate classification.

SUBMITTER: Rataj K

PROVIDER: S-EPMC6100401 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Substructural Connectivity Fingerprint and Extreme Entropy Machines-A New Method of Compound Representation and Analysis.

Rataj Krzysztof K Czarnecki Wojciech W Podlewska Sabina S Pocha Agnieszka A Bojarski Andrzej J AJ

Molecules (Basel, Switzerland) 20180523 6

Key-based substructural fingerprints are an important element of computer-aided drug design techniques. The usefulness of the fingerprints in filtering compound databases is invaluable, as they allow for the quick rejection of molecules with a low probability of being active. However, this method is flawed, as it does not consider the connections between substructures. After changing the connections between particular chemical moieties, the fingerprint representation of the compound remains the ...[more]

PMID: 29789513

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Project description:The Complexity-entropy causality plane (CECP) is a parsimonious representation space for time series. It has only two dimensions: normalized permutation entropy ([Formula: see text]) and Jensen-Shannon complexity ([Formula: see text]) of a time series. This two-dimensional representation allows for detection of slow or rapid drifts in the condition of mechanical components monitored through sensor measurements. The CECP representation can be used for both predictive analytics and visual monitoring of changes in component condition. This method requires minimal pre-processing of raw signals. Furthermore, it is insensitive to noise, stationarity, and trends. These desirable properties make CECP a good candidate for machine condition monitoring and fault diagnostics. In this work we study the effectiveness of CECP on three rotary component condition assessment applications. We use CECP representation of vibration signals to differentiate various machine component health conditions for rotary machine components, namely roller bearing and gears. The results confirm that the CECP representation is able to detect, with high accuracy, changes in underlying dynamics of machine component degradation states. From class separability perspective, the CECP representation is able to generate linearly separable classes for the classification of different fault states. This classification performance improves with increasing signal length. For signal length of 16,384 data points, the fault classification accuracy varies from 90% to 100% for bearing applications, and from 85% to 100% for gear applications. We observed that the optimum parameter for CECP representatino depends on the application. For bearing applications we found that embedding dimension D = 4, 5, 6, and embedding delay τ = 1, 2, 3 are suitable for good fault classification. For gear applications we find that embedding dimension D = 4, 5, and embedding delay τ = 1, 5 are suitable for fault classification.

Project description:BackgroundBiomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease, with genotype-phenotype associations still incompletely understood. We compared human- and machine-curated HCM molecular mechanisms' models and examined the performance of different machine approaches for that task.ResultsWe created six models representing HCM molecular mechanisms using different approaches and made them publicly available, analyzed them as networks, and tried to explain the models' differences by the analysis of factors that affect the quality of machine-curated models (query constraints and reading systems' performance). A result of this work is also the Interactive HCM map, the only publicly available knowledge resource dedicated to HCM. Sizes and topological parameters of the networks differed notably, and a low consensus was found in terms of centrality measures between networks. Consensus about the most important nodes was achieved only with respect to one element (calcium). Models with a reduced level of noise were generated and cooperatively working elements were detected. REACH and TRIPS reading systems showed much higher accuracy than Sparser, but at the cost of extraction performance. TRIPS proved to be the best single reading system for text segments about HCM, in terms of the compromise between accuracy and extraction performance.ConclusionsDifferent approaches in curation can produce models of the same disease with diverse characteristics, and they give rise to utterly different conclusions in subsequent analysis. The final purpose of the model should direct the choice of curation techniques. Manual curation represents the gold standard for information extraction in biomedical research and is most suitable when only high-quality elements for models are required. Automated curation provides more substance, but high level of noise is expected. Different curation strategies can reduce the level of human input needed. Biomedical knowledge would benefit overwhelmingly, especially as to its rapid growth, if computers were to be able to assist in analysis on a larger scale.

Project description:BackgroundEEG may be affected by artefacts hindering the analysis of brain signals. Data-driven methods like independent component analysis (ICA) are successful approaches to remove artefacts from the EEG. However, the ICA-based methods developed so far are often affected by limitations, such as: the need for visual inspection of the separated independent components (subjectivity problem) and, in some cases, for the independent and simultaneous recording of the inspected artefacts to identify the artefactual independent components; a potentially heavy manipulation of the EEG signals; the use of linear classification methods; the use of simulated artefacts to validate the methods; no testing in dry electrode or high-density EEG datasets; applications limited to specific conditions and electrode layouts.MethodsOur fingerprint method automatically identifies EEG ICs containing eyeblinks, eye movements, myogenic artefacts and cardiac interference by evaluating 14 temporal, spatial, spectral, and statistical features composing the IC fingerprint. Sixty-two real EEG datasets containing cued artefacts are recorded with wet and dry electrodes (128 wet and 97 dry channels). For each artefact, 10 nonlinear SVM classifiers are trained on fingerprints of expert-classified ICs. Training groups include randomly chosen wet and dry datasets decomposed in 80 ICs. The classifiers are tested on the IC-fingerprints of different datasets decomposed into 20, 50, or 80 ICs. The SVM performance is assessed in terms of accuracy, False Omission Rate (FOR), Hit Rate (HR), False Alarm Rate (FAR), and sensitivity (p). For each artefact, the quality of the artefact-free EEG reconstructed using the classification of the best SVM is assessed by visual inspection and SNR.ResultsThe best SVM classifier for each artefact type achieved average accuracy of 1 (eyeblink), 0.98 (cardiac interference), and 0.97 (eye movement and myogenic artefact). Average classification sensitivity (p) was 1 (eyeblink), 0.997 (myogenic artefact), 0.98 (eye movement), and 0.48 (cardiac interference). Average artefact reduction ranged from a maximum of 82% for eyeblinks to a minimum of 33% for cardiac interference, depending on the effectiveness of the proposed method and the amplitude of the removed artefact. The performance of the SVM classifiers did not depend on the electrode type, whereas it was better for lower decomposition levels (50 and 20 ICs).DiscussionApart from cardiac interference, SVM performance and average artefact reduction indicate that the fingerprint method has an excellent overall performance in the automatic detection of eyeblinks, eye movements and myogenic artefacts, which is comparable to that of existing methods. Being also independent from simultaneous artefact recording, electrode number, type and layout, and decomposition level, the proposed fingerprint method can have useful applications in clinical and experimental EEG settings.

Dataset Information

Substructural Connectivity Fingerprint and Extreme Entropy Machines-A New Method of Compound Representation and Analysis.

Publications

Substructural Connectivity Fingerprint and Extreme Entropy Machines-A New Method of Compound Representation and Analysis.

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