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At least 19 recordsLinked to original sources
PubMed2001

Drug design by machine learning: support vector machines for pharmaceutical data analysis.

We show that the support vector machine (SVM) classification algorithm, a recent development from the machine learning community, proves its potential for structure-activity relationship analysis. In a benchmark test, the SVM is compared to several machine learning techniques currently used in the field. The classification task involves predicting the inhibition of dihydrofolate reductase by pyrimidines, using data obtained from the UCI machine learning repository. Three artificial neural networks, a radial basis function network, and a C5.0 decision tree are all outperformed by the SVM. The SVM is significantly better than all of these, bar a manually capacity-controlled neural network, which takes considerably longer to train.

Algorithms↗
PubMed2006

Classification of mental tasks from EEG signals using extreme learning machine.

In this paper, a recently developed machine learning algorithm referred to as Extreme Learning Machine (ELM) is used to classify five mental tasks from different subjects using electroencephalogram (EEG) signals available from a well-known database. Performance of ELM is compared in terms of training time and classification accuracy with a Backpropagation Neural Network (BPNN) classifier and also Support Vector Machines (SVMs). For SVMs, the comparisons have been made for both 1-against-1 and 1-against-all methods. Results show that ELM needs an order of magnitude less training time compared with SVMs and two orders of magnitude less compared with BPNN. The classification accuracy of ELM is similar to that of SVMs and BPNN. The study showed that smoothing of the classifiers' outputs can significantly improve their classification accuracies.

Algorithms↗
PubMed2001

Algebraic geometrical methods for hierarchical learning machines.

Hierarchical learning machines such as layered perceptrons, radial basis functions, Gaussian mixtures are non-identifiable learning machines, whose Fisher information matrices are not positive definite. This fact shows that conventional statistical asymptotic theory cannot be applied to neural network learning theory, for example either the Bayesian a posteriori probability distribution does not converge to the Gaussian distribution, or the generalization error is not in proportion to the number of parameters. The purpose of this paper is to overcome this problem and to clarify the relation between the learning curve of a hierarchical learning machine and the algebraic geometrical structure of the parameter space. We establish an algorithm to calculate the Bayesian stochastic complexity based on blowing-up technology in algebraic geometry and prove that the Bayesian generalization error of a hierarchical learning machine is smaller than that of a regular statistical model, even if the true distribution is not contained in the parametric model.

Algorithms↗
PubMed2025

Proteomics-enabled learning machine algorithms enhance the prediction of cardiovascular diseases in patients with type 2 diabetes mellitus.

BACKGROUND AND AIMS: Estimating the risk of cardiovascular disease (CVD) complications in type 2 diabetes mellitus (T2DM) patients is critical in the medical decision-making process. This study aimed to use a machine learning technique combined with proteomics to develop personalized models for predicting CVD in patients with T2DM. METHODS AND RESULTS: In total, 874 patients with T2DM and 2,920 Olink proteins obtained from the UK Biobank were used in this study. Proteins were screened using Cox regression and LASSO regression. A basic model containing clinical features and a full model combining proteome and clinical features were constructed using the random survival forest algorithm. The area under the receiver operating characteristic (ROC) curve (AUC) was used to evaluate the predictive performance of the models and compare them with other CVD predictive models. Compared with the basic model, the full model performed better in predicting CVD, with time-dependent AUCs of 0.81 (3 years), 0.74 (5 years) and 0.74 (10 years) (0.77, 0.69 and 0.67). We calculated the risk scores of the Framingham, ASCVD and Score2-Diabetes models. The results revealed that the prediction performance of the full model was also better than that of the abovementioned models. In terms of differentiation accuracy, the results of the net reclassification improvement index and integrated discrimination improvement index showed that the full model can identify high-risk individuals more accurately (accuracy rate: 79% vs. 69%). CONCLUSIONS: Proteomics can be used to predict cardiovascular complications in diabetic patients. It is also necessary to consider the applicability of the model due to the limitations of the sample size and the constraints of proteomics in clinical applications.

Humans↗
PubMed2006

Weighted quality estimates in machine learning.

MOTIVATION: Machine learning methods such as neural networks, support vector machines, and other classification and regression methods rely on iterative optimization of the model quality in the space of the parameters of the method. Model quality measures (accuracies, correlations, etc.) are frequently overly optimistic because the training sets are dominated by particular families and subfamilies. To overcome the bias, the dataset is usually reduced by filtering out closely related objects. However, such filtering uses fixed similarity thresholds and ignores a part of the training information. RESULTS: We suggested a novel approach to calculate prediction model quality based on assigning to each data point inverse density weights derived from the postulated distance metric. We demonstrated that our new weighted measures estimate the model generalization better and are consistent with the machine learning theory. The Vapnik-Chervonenkis theorem was reformulated and applied to derive the space-uniform error estimates. Two examples were used to illustrate the advantages of the inverse density weighting. First, we demonstrated on a set with a built-in bias that the unweighted cross-validation procedure leads to an overly optimistic quality estimate, while the density-weighted quality estimates are more realistic. Second, an analytical equation for weighted quality estimates was used to derive an SVM model for signal peptide prediction using a full set of known signal peptides, instead of the usual filtered subset.

Algorithms↗
PubMed2002

Consistency and reproducibility of attribute extraction by different machine learning systems.

Machine learning systems as tools for intelligent data analysis are used for extracting attributes relevant for prediction of defined outcomes. The aim of the paper was to compare two machine learning (ML) systems and propose method for intra- and inter-testing of consistency and reproducibility in attributes extracted from real dataset. See5 and FMLS extracted relevant attributes from real medical dataset. Comparison of results of both systems shows that: accuracy and sensitivity are nearly the same for both FMLS and See5 when FMLS was forced by attributes extracted by See5, and little bit lower when FMLS used its own extracted attributes; specificity is nearly the same for both FMLS and See5 when FMLS was forced by attributes extracted by See5, and much more higher when FMLS used its own extracted attributes; both of ML systems show intra-testing consistency and does not show any inter-testing consistency.

Artificial Intelligence↗
PubMed2002

Incremental learning in biological and machine learning systems.

Incremental learning concepts are reviewed in machine learning and neurobiology. They are identified in evolution, neurodevelopment and learning. A timeline of qualitative axon, neuron and synapse development summarizes the review on neurodevelopment. A discussion of experimental results on data incremental learning with recurrent artificial neural networks reveals that incremental learning often seems to be more efficient or powerful than standard learning but can produce unexpected side effects. A characterization of incremental learning is proposed which takes the elaborated biological and machine learning concepts into account.

Algorithms↗
PubMed1992

Modelling the structure and function of enzymes by machine learning.

A machine learning program, GOLEM, has been applied to two problems: (1) the prediction of protein secondary structure from sequence and (2) modelling a quantitative structure-activity relationship in drug design. GOLEM takes as input observations and combines them with background knowledge of chemistry to yield rules expressed as stereochemical principles for prediction. The secondary structure prediction was explored on the alpha/alpha class of proteins; on an unrelated test set it yielded 81% accuracy. The rules from GOLEM defined patterns of residues forming alpha-helices. The system studied for drug design was the activities of trimethoprim analogues binding to E. coli dihydrofolate reductase. The GOLEM rules were a better model than standard regression approaches. More importantly, these rules described the chemical properties of the enzyme-binding site that were in broad agreement with the crystallographic structure.

Amino Acid Sequence↗
PubMed2000

Detecting predictors of new-born survival by fuzzy sets based machine learning system.

Machine learning system based on fuzzy sets was used for detecting predictors of new-born survival within the first 15 days after birth. The system processed real-life medical data of 566 new-borns; 528 survived and were classified as "alive", the remaining 38 did not survive and were classified as "died". The state of each new-born was described by values of 112 attributes. The system detected five of the attributes as the best predictors for survival (asphyxia, apnoea, birth weight, reanimation and gestation age). To evaluate are the selected attributes relevant for prediction, the following procedure was used: 566 new-borns were divided into two groups by random selection; 396 (70%) randomly selected new-borns formed the learning group, the remaining 170 new-borns formed the test group. The system acquired prediction knowledge by processing data of the learning group new-borns. Using the knowledge thus acquired, the system predicted survival for each new-born from the test group several times, each time using another set of attributes: once, using all 112 attributes; once, using attributes detected by the system as the best predictors; once, using remaining attributes without the best predictors. After the predictions for all new-borns from the test group had been finished, classification accuracy, sensitivity (accuracy for "alive") and specificity (accuracy for "died") were calculated as measures of prediction success with particular sets of attributes. The results have shown that the best prognostic accuracies were achieved when prediction was done using those attributes which the system detected as the best predictors for new-born survival.

Artificial Intelligence↗
PubMed2026

Prediction of antimicrobial minimum inhibitory concentration from bacterial genomes using a scalable and interpretable machine learning approach.

Although machine learning models can predict antimicrobial susceptibility from bacterial whole genome sequencing (WGS), state-of-the-art approaches are computationally demanding or dependent on knowledge of genetic resistance determinants. Here, we describe an efficient data-driven approach to predicting minimum inhibitory concentration (MIC) by progressively extending and refining predictive genome segments, independent of prior knowledge of resistance determinants. Resultant models had high interpretability - known and potentially novel resistance determinants were captured. Using 762 clinical E. coli strains, 71.6% of predictions were within one dilution of the measured MIC. Models trained with this algorithm generalised better onto external data (F1 score = 0.85) compared with alternative models trained on annotated resistance determinants (F1 = 0.82) or k-mer counts (F1 = 0.74). Computational demands were low (RAM usage 23.6GB vs 38.8GB for k-mer model). These advantages represent an important advance in predicting antimicrobial susceptibility from WGS, with potential applications for clinical diagnostics, drug development, and surveillance.

Journal Article↗
PubMed2006

A Protein Classification Benchmark collection for machine learning.

Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods can be compared. It is primarily meant for method developers and users interested in comparing methods under standardized conditions. The collection contains datasets of sequences and structures, and each set is subdivided into positive/negative, training/test sets in several ways. There is a total of 6405 classification tasks, 3297 on protein sequences, 3095 on protein structures and 10 on protein coding regions in DNA. Typical tasks include the classification of structural domains in the SCOP and CATH databases based on their sequences or structures, as well as various functional and taxonomic classification problems. In the case of hierarchical classification schemes, the classification tasks can be defined at various levels of the hierarchy (such as classes, folds, superfamilies, etc.). For each dataset there are distance matrices available that contain all vs. all comparison of the data, based on various sequence or structure comparison methods, as well as a set of classification performance measures computed with various classifier algorithms.

Algorithms↗
PubMedDate not supplied

Analysis of respiratory pressure-volume curves in intensive care medicine using inductive machine learning.

We present a case study of machine learning and data mining in intensive care medicine. In the study, we compared different methods of measuring pressure-volume curves in artificially ventilated patients suffering from the adult respiratory distress syndrome (ARDS). Our aim was to show that inductive machine learning can be used to gain insights into differences and similarities among these methods. We defined two tasks: the first one was to recognize the measurement method producing a given pressure-volume curve. This was defined as the task of classifying pressure-volume curves (the classes being the measurement methods). The second was to model the curves themselves, that is, to predict the volume given the pressure, the measurement method and the patient data. Clearly, this can be defined as a regression task. For these two tasks, we applied C5.0 and CUBIST, two inductive machine learning tools, respectively. Apart from medical findings regarding the characteristics of the measurement methods, we found some evidence showing the value of an abstract representation for classifying curves: normalization and high-level descriptors from curve fitting played a crucial role in obtaining reasonably accurate models. Another useful feature of algorithms for inductive machine learning is the possibility of incorporating background knowledge. In our study, the incorporation of patient data helped to improve regression results dramatically, which might open the door for the individual respiratory treatment of patients in the future.

Adult↗
PubMed2004

A primer on gene expression and microarrays for machine learning researchers.

Data originating from biomedical experiments has provided machine learning researchers with an important source of motivation for developing and evaluating new algorithms. A new wave of algorithmic development has been initiated with the publication of gene expression data derived from microarrays. Microarray data analysis is particularly challenging given the large number of measurements (typically in the order of thousands) that are reported for relatively few samples (typically in the order of dozens). Many data sets are now available on the web. It is important that machine learning researchers understand how data are obtained and which assumptions are necessary in the analysis. Microarray data have the potential to cause significant impact in machine learning research, not just as a rich and realistic source of cases for testing new algorithms, as has been the UCI machine learning repository in the past decades, but also as a main motivation for their development. In this article, we briefly review the biology underlying microarrays, the process of obtaining gene expression measurements, and the rationale behind the common types of analyses involved in a microarray experiment. We outline the main challenges and reiterate critical considerations regarding the construction of supervised learning models that use this type of data. The goal of this article is to familiarize machine learning researchers with data originated from gene expression microarrays.

Algorithms↗
PubMed2005

Machine learning in bioinformatics: a brief survey and recommendations for practitioners.

Machine learning is used in a large number of bioinformatics applications and studies. The application of machine learning techniques in other areas such as pattern recognition has resulted in accumulated experience as to correct and principled approaches for their use. The aim of this paper is to give an account of issues affecting the application of machine learning tools, focusing primarily on general aspects of feature and model parameter selection, rather than any single specific algorithm. These aspects are discussed in the context of published bioinformatics studies in leading journals over the last 5 years. We assess to what degree the experience gained by the pattern recognition research community pervades these bioinformatics studies. We finally discuss various critical issues relating to bioinformatic data sets and make a number of recommendations on the proper use of machine learning techniques for bioinformatics research based upon previously published research on machine learning.

Algorithms↗
PubMed2002

Using machine learning classifiers to identify glaucomatous change earlier in standard visual fields.

PURPOSE: To compare the ability of several machine learning classifiers to predict development of abnormal fields at follow-up in ocular hypertensive (OHT) eyes that had normal visual fields in baseline examination. METHODS: The visual fields of 114 eyes of 114 patients with OHT with four or more visual field tests with standard automated perimetry over three or more years and for whom stereophotographs were available were assessed. The mean (+/-SD) number of visual field tests was 7.89 +/- 3.04. The mean number of years covered (+/-SD) was 5.92 +/- 2.34 (range, 2.81-11.77). Fields were classified as normal or abnormal based on Statpac-like methods (Humphrey Instruments, Dublin, CA) and by several machine learning classifiers. The machine learning classifiers were two types of support vector machine (SVM), a mixture of Gaussian (MoG) classifier, a constrained MoG, and a mixture of generalized Gaussian (MGG). Specificity was set to 96% for all classifiers, using data from 94 normal eyes evaluated longitudinally. Specificity cutoffs required confirmation of abnormality. RESULTS: Thirty-two percent (36/114) of the eyes converted to abnormal fields during follow-up based on the Statpac-like methods. All 36 were identified by at least one machine classifier. In nearly all cases, the machine learning classifiers predicted the confirmed abnormality, on average, 3.92 +/- 0.55 years earlier than traditional Statpac-like methods. CONCLUSIONS: Machine learning classifiers can learn complex patterns and trends in data and adapt to create a decision surface without the constraints imposed by statistical classifiers. This adaptation allowed the machine learning classifiers to identify abnormality in visual field converts much earlier than the traditional methods.

Algorithms↗
PubMed2005

Modeling clinical judgment and implicit guideline compliance in the diagnosis of melanomas using machine learning.

We explore several machine learning techniques to model clinical decision making of 6 dermatologists in the clinical task of melanoma diagnosis of 177 pigmented skin lesions (76 malignant, 101 benign). In particular we apply Support Vector Machine (SVM) classifiers to model clinician judgments, Markov Blanket and SVM feature selection to eliminate clinical features that are effectively ignored by the dermatologists, and a novel explanation technique whereby regression tree induction is run on the reduced SVM model's output to explain the physicians' implicit patterns of decision making. Our main findings include: (a) clinician judgments can be accurately predicted, (b) subtle decision making rules are revealed enabling the explanation of differences of opinion among physicians, and (c) physician judgment is non-compliant with the diagnostic guidelines that physicians self-report as guiding their decision making.

Artificial Intelligence↗
PubMed2026

In silico screening of anti-atherosclerotic compounds from Morus alba leaves by machine learning and network pharmacology.

OBJECTIVE: This study integrates machine learning with network pharmacology, molecular docking, and molecular dynamics simulations to screen bioactive compounds from Mulberry leaves and elucidate their potential mechanisms against atherosclerosis (AS). METHODS: A training dataset of anti-AS active compounds was compiled and encoded as Morgan fingerprints. Three machine learning classifiers, specifically Random Forest (RF), Support Vector Machine (SVM), and Extreme Gradient Boosting (XG-Boost), were constructed and evaluated using multiple performance metrics. Potential active components from Mulberry leaves and AS-related targets were retrieved, followed by protein-protein interaction network construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Molecular docking was then performed to evaluate binding affinities between core targets and candidate compounds, and the most stable complex was subjected to molecular dynamics simulations using GROMACS (2025). RESULTS: The RF model achieved superior performance (accuracy= 0.8354, F1 = 0.8408, AUC = 0.9119) with 100% external validation accuracy. Thirteen anti-AS candidates were prioritized from mulberry leaves, four of which have been previously documented. Network pharmacology revealed AKT1 and IL6 as core targets, enriched in pathways such as endocrine resistance. Molecular docking and dynamics simulations confirmed strong binding between oxysanguinarine and AKT1, with the complex exhibiting high stability. CONCLUSION: The RF model provides a reliable computational tool for prioritizing anti-AS compounds from Mulberry leaves. The integrated analysis reveals that Mulberry leaves exert anti-atherosclerotic effects through multi-target (e.g., AKT1, IL6) and multi-pathway (e.g., PI3K-Akt) mechanisms, offering a framework for further experimental validation.

Morus↗
PubMed2005

Modelling of classification rules on metabolic patterns including machine learning and expert knowledge.

Machine learning has a great potential to mine potential markers from high-dimensional metabolic data without any a priori knowledge. Exemplarily, we investigated metabolic patterns of three severe metabolic disorders, PAHD, MCADD, and 3-MCCD, on which we constructed classification models for disease screening and diagnosis using a decision tree paradigm and logistic regression analysis (LRA). For the LRA model-building process we assessed the relevance of established diagnostic flags, which have been developed from the biochemical knowledge of newborn metabolism, and compared the models' error rates with those of the decision tree classifier. Both approaches yielded comparable classification accuracy in terms of sensitivity (>95.2%), while the LRA models built on flags showed significantly enhanced specificity. The number of false positive cases did not exceed 0.001%.

Algorithms↗