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PubMed2002

Karyotyping of comparative genomic hybridization human metaphases by using support vector machines.

BACKGROUND: Comparative genomic hybridization (CGH) is a relatively new molecular cytogenetic method for detecting chromosomal imbalance. Karyotyping of human metaphases is an important step to assign each chromosome to one of 23 or 24 classes (22 autosomes and two sex chromosomes). Automatic karyotyping in CGH analysis is needed. However, conventional karyotyping approaches based on DAPI images require complex image enhancement procedures. METHODS: This paper proposes a simple feature extraction method, one that generates density profiles from original true color CGH images and uses normalized profiles as feature vectors without quantization. A classifier is developed by using support vector machine (SVM). It has good generalization ability and needs only limited training samples. RESULTS: Experiment results show that the feature extraction method of using color information in CGH images can improve greatly the classification success rate. The SVM classifier is able to acquire knowledge about human chromosomes from relatively few samples and has good generalization ability. A success rate of moe than 90% has been achieved and the time for training and testing is very short. CONCLUSIONS: The feature extraction method proposed here and the SVM-based classifier offer a promising computerized intelligent system for automatic karyotyping of CGH human chromosomes.

Chromosomes, Human↗

PubMed2002

Karyotyping of comparative genomic hybridization human metaphases using kernel nearest-neighbor algorithm.

BACKGROUND: Comparative genomic hybridization (CGH) is a relatively new molecular cytogenetic method that detects chromosomal imbalances. Automatic karyotyping is an important step in CGH analysis because the precise position of the chromosome abnormality must be located and manual karyotyping is tedious and time-consuming. In the past, computer-aided karyotyping was done by using the 4',6-diamidino-2-phenylindole, dihydrochloride (DAPI)-inverse images, which required complex image enhancement procedures. METHODS: An innovative method, kernel nearest-neighbor (K-NN) algorithm, is proposed to accomplish automatic karyotyping. The algorithm is an application of the "kernel approach," which offers an alternative solution to linear learning machines by mapping data into a high dimensional feature space. By implicitly calculating Euclidean or Mahalanobis distance in a high dimensional image feature space, two kinds of K-NN algorithms are obtained. New feature extraction methods concerning multicolor information in CGH images are used for the first time. RESULTS: Experiment results show that the feature extraction method of using multicolor information in CGH images improves greatly the classification success rate. A high success rate of about 91.5% has been achieved, which shows that the K-NN classifier efficiently accomplishes automatic chromosome classification from relatively few samples. CONCLUSIONS: The feature extraction method proposed here and K-NN classifiers offer a promising computerized intelligent system for automatic karyotyping of CGH human chromosomes.

Algorithms↗

PubMed1994

Suitability of artificial neural networks for feature extraction from cardiotocogram during labour.

Fetal condition during labour is inferred from a continuous display of fetal heart rate and uterine contractions called the cardiotocogram (CTG). The CTG requires a considerable expertise for correct interpretation, which is not always available. We are developing an intelligent system to support clinical decision-making during labour. The system's performance depends on its ability to classify features from the CTG similarly to experts. Artificial neural networks (NNs) can be taught by experts for such tasks, and so may be particularly suitable. We found NNs suitable for feature extraction when the problem was reduced to small well defined tasks, and numerical algorithms were used to pre-process the raw data before application to the NNs. A NN with optimised dimensions was used in this way to classify the magnitude of decelerations, a feature clinicians find particularly difficult. The NN was compared with the algorithm used in a commercial antenatal monitor and six reviewers which included two CTG experts. The experts were consistent (89.7% and 97.0%) and agreed well with each other (81.0%), whereas the non-experts were less consistent and agreed less well. The NN agreed well with the experts (75.0% and 81.9%) but the algorithm agreed poorly (56.5% and 68.9%). It was found that the algorithm's performance could be improved (72.1% and 76.7%) when modified to use additional information. Our earlier attempts to fully classify the raw CTG using a single NN were unsuccessful because of the large number of data patterns. A simplified approach to classify the magnitude and timing of decelerations was also unsuitable when contraction data was of poor quality or absent.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed1989

Artificial intelligence techniques for the control of cancer cells.

NEWCHEM, an artificial intelligence system for the control of cancer cell growth, is described. This system takes into account the most recent advances in molecular and cellular biology and in cell-drug interaction, and aims to develop optimal strategies for the selective control of cancer cell through qualitative reasoning from first principles at cellular level.

Computer Simulation↗

PubMed1989

Structure characteristics of QMSOC and the relevant operators.

This article presents a further description on the background, significance, and structure characteristics of Quantitative Medicine Simulation and Operation by Computer (QMSOC). Also some basic operators were recommended for calculations of biomedical events such as estimation of substance concentrations, exploration of etiology, evaluation of biomedical effects, etc. At last some differences of QMSOC from other artificial intelligent systems in the medical field were discussed.

Computer Simulation↗

PubMed2000

[Blindness caused by an airbag in a minor accident].

PURPOSE: Installation of airbags has reduced the rate of fatal injuries in severe automobile accidents. We report, however, severe ocular injuries in a minor accident as the result of an airbag. CASE REPORT: A front passenger suffered a blunt ocular trauma of her right eye during a collision. The approaching speed was about 31 km/h. The maximum change of velocity in direction of the impact was 19 km/h. Color traces were found on the upper rim of the airbag, apparently from the patient's eye shadow. RESULTS: In the emergency room, visual acuity was reduced to light perception. There was endothelial contusion, traumatic mydriasis, and lens subluxation. A sclopetarian retinopathy developed with a chorioretinal scar. Eight months after the accident visual acuity remained at light projection only. CONCLUSIONS: The eye injuries had very probably been caused by the deploying airbag. Improvements are a better geometry of deployment (e.g., tethered airbags), release at higher impacts only, and "intelligent systems" with additional sensors to avoid potentially hazardous airbag inflation in minor accidents.

Accidents, Traffic↗

PubMed1993

Carotenoid content of fruits and vegetables: an evaluation of analytic data.

The test of the association between dietary intake of specific carotenoids and disease incidence requires the availability of accurate and current food composition data for individual carotenoids. To generate a carotenoid database, an artificial intelligence system was developed to evaluate data for carotenoid content of food in five general categories, namely, number of samples, analytic method, sample handling, sampling plan, and analytic quality control. Within these categories, criteria have been created to rate analytic data for beta-carotene, alpha-carotene, lutein, lycopene, and beta-cryptoxanthin in fruits and vegetables. These carotenoids are also found in human blood. Following the evaluation of data, acceptable values for each carotenoid in the foods were combined to generate a database of 120 foods. The database includes the food description; median, minimum, and maximum values for the specific carotenoids in each food; the number of acceptable values and their references; and a confidence code, which is an indicator of the reliability of a specific carotenoid value for a food. The carotenoid database can be used to estimate the intake of specific carotenoids in order to examine the association between dietary carotenoids and disease incidence.

Carotenoids↗

PubMedDate not supplied

Artificial intelligence and Bayesian decision theory in the prediction of chemical carcinogens.

Two procedures for predicting the carcinogenicity of chemicals are described. One of these (CASE) is a self-learning artificial intelligence system that automatically recognizes activating and/or deactivating structural subunits of candidate chemicals and uses this to determine the probability that the test chemical is or is not a carcinogen. If the chemical is predicted to be carcinogen, CASE also projects its probable potency. The second procedure (CPBS) uses Bayesian decision theory to predict the potential carcinogenicity of chemicals based upon the results of batteries of short-term assays. CPBS is useful even if the test results are mixed (i.e. both positive and negative responses are obtained in different genotoxic assays). CPBS can also be used to identify highly predictive as well as cost-effective batteries of assays. For illustrative purposes the ability of CASE and CPBS to predict the carcinogenicity of a carcinogenic and a non-carcinogenic polycyclic aromatic hydrocarbon is shown. The potential for using the two methods in tandem to increase reliability and decrease cost is presented.

Animals↗

PubMed1988

CASE, the computer-automated structure evaluation method, correctly predicts the low mutagenicity for Salmonella of nitrated cyclopenta-fused polycyclic aromatic hydrocarbons.

Recently Goldring et al. [Mutation Res., 187 (1987) 67-77] reported the synthesis and purification of a series of nitro-substituted cyclopenta-fused polycyclic aromatic hydrocarbons. On the basis of expected charge distributions, these chemicals were predicted to be potent mutagens and, yet, contrary to expectation, they were found to be only weakly mutagenic for Salmonella. In their discussion, the authors suggest that application of CASE, an artificial intelligence system recently developed in these laboratories, would also not predict the low mutagenicity of this group of chemicals. In the present report, it is shown that CASE, in fact, correctly predicts the low mutagenicity of nitro-substituted cyclopenta-fused polycyclic aromatic hydrocarbons.

Mutagenicity Tests↗

PubMed1986

In vivo probes: problems and perspectives.

Devices constructed for potential use as invasive bioprobes incorporate a selective receiving site for molecular or ionic recognition, and a transducer which is capable of translating a perturbation of physical chemistry of the determinant-site reaction (interaction) into a usable signal. Four types are envisioned--implants for general hospital use, transient-use probes to replace classical blood tests, short-term implantable probes and the long-term variety. Performance criteria are selectivity, sensitivity, fast response, site-reversible, small, rugged, inexpensive, biocompatible, calibratible, facile use by non-expert personnel and ease of telemetry. These demands, not surprisingly, create enormous challenges to the sensor specialist. With respect to biocompatibility the sensor must not be involved in infection, clot formation or antigenic response, and, furthermore, protein adsorption, etc., which can affect the sensor response should be avoided. Calibration remains a problem of monumental proportions. Many devices drift from calibrated levels even in in vitro experiments, let alone in the implanted milieu. One solution has been to carry out on-line switching between patient blood and standard solutions. However, this type of approach leaves a lot to be desired with respect to portability. Another method which is attracting increasing attention is the chemometric or artificial intelligence system involving compensation by multi-sensor array configurations. Sensitivity and limit-of-detection have attracted little research due to the overwhelming nature of other difficulties. In the present paper we evaluate a number of these technical problems and discuss the architecture of devices that are currently available. Finally, some thoughts as to priorities for re-directing sensor research in the bioprobe area are presented.

Biocompatible Materials↗

PubMed1993

A neural network to analyze fertility data.

OBJECTIVE: To program an artificial intelligence system, a neural network, and use it to predict results of sperm penetration in bovine cervical mucus (Penetrak assay; Serono Laboratories, Norwell, MA) and zona-free hamster egg penetration from the semen analysis. DESIGN: Results of 139 Penetrak assays, 1,416 zona-free hamster egg penetration assays, and the corresponding semen analyses were retrospectively analyzed by an artificial neural network. MAIN OUTCOME MEASURES: Classification errors of the neural network were compared with those of linear and quadratic discriminant function analyses. RESULTS: Data were separated into training and test sets. For the Penetrak result, linear and quadratic discriminant function analysis correctly predicted 58% and 74% of the training set results and only 64.1% and 69.2% of the test data, respectively. The neural network correctly predicted 92% of training set results and 80% of test set results. For the zona-free hamster egg penetration assay outcome, linear and quadratic discriminant function analysis correctly classified 66.3% and 46.0% of the training set and 64.9% and 44.7% of the test set, respectively. The neural network correctly classified 75.7% of the training data and 67.8% of the test data. CONCLUSIONS: Using the semen analysis, the neural network correctly classified 67.8% of zona-free hamster egg penetration assay results and 80% of Penetrak results it had not encountered previously, suggesting that this method of data analysis may be successfully employed to predict fertility potential.

Animals↗

PubMed2003

[Techniques and current practice of urodynamics. Problems and traps].

Development of urodynamics particularly during the past decade are highlighted, as well as a number of issues to be faced in the near future: research into the etiopathogenesis of different conditions, finding more sensitive and specific diagnostic procedures to overcome the current ones, establishing more comprehensive indications for urodynamics examinations and, as a result of all the above achieving greater improvement of certain surgical procedures. Both the technique and interpretation of the different urodynamic examinations, as well as the more recent innovations, implementation issues and controversies are detailed to a highly up-to-date level. Neuromodulation and ambulatory urodynamics deserve thoughtful consideration in this paper. Finally, attention is given to the controversies and future challenges such as urodynamic research providing accurate diagnosis of lower urinary tract obstruction in women, establishing the indication of urodynamic studies in women with urinary exertional incontinence, outlining the indications of neuromodulation and ambulatory urodynamics, applicability of artificial intelligence systems, improvement of artificial sphincter materials, tissue growth for bladder enlargement and actual prevention of myelodysplasia.

Adult↗

PubMedDate not supplied

Reinforcement learning with internal expectation in the random neural networks for cascaded decisions.

The reinforcement learning scheme proposed in Halici (J. Biosystems 40 (1997) 83) for the random neural network (RNN) (Neural Computation 1 (1989) 502) is based on reward and performs well for stationary environments. However, when the environment is not stationary it suffers from getting stuck to the previously learned action and extinction is not possible. To overcome the problem, the reinforcement scheme is extended in Halici (Eur. J. Oper. Res., 126(2000) 288) by introducing a new weight update rule (E-rule) which takes into consideration the internal expectation of reinforcement. Although the E-rule is proposed for the RNN, it can be used for training learning automata or other intelligent systems based on reinforcement learning. This paper looks into the behavior of the learning scheme with internal expectation for the environments where the reinforcement is obtained after a sequence of cascaded decisions. The simulation results have shown that the RNN learns well and extinction is possible even for the cases with several decision steps and with hundreds of possible decision paths.

Computer Simulation↗

PubMed2002

Language plasticity revealed by electroencephalogram mapping.

Reasoning is the result of the computations made by intelligent systems, for instance those in the brain. It is not an abstract concept because calculations performed by computations are very concrete transactions among the different central processing unit components. Entropy measurements are proposed here to disclose the plasticity of the cerebral processing associated with language comprehension in video game playing. It is also assumed that entropy may be evaluated from the correlation coefficients obtained for the game event-related activity calculated for the different electroencephalogram derivations in the 10/20 system. The brain mapping derived from these entropy measurements clearly demonstrates the reallocation of speech functions to right brain areas when the classic left language circuits are damaged during prenatal life.

Brain Damage, Chronic↗

PubMed2025

Integrating explainable artificial intelligence with multiomics systems biology and electronic health record data mining for personalized drug repurposing in Alzheimer's disease.

Alzheimer's disease (AD) is characterized by region- and patient-specific molecular heterogeneity, which hinders therapeutic design. In this study, we introduce PRISM-ML (PRecision-medicine using Interpretable Systems and Multiomics with Machine Learning), an open-source integrated analysis pipeline that combines interpretable machine learning with systems biology and electronic health records data mining to elucidate the molecular diversity of AD and predict promising drug repurposing opportunities. First, we integrated and harmonized transcriptomic (bulk RNA-seq) and genomic (genome-wide association study) data from 2105 brain samples, each with matched data from the same individual (1363 AD patients, 742 controls; 9 tissues), sourced from three independent studies. Random forest classifiers with SHapley Additive exPlanations identified patient-specific biomarkers; unsupervised clustering resolved 36 molecularly distinct subtissues (defined as clusters of samples within a brain tissue that share a specific expression pattern); and gene-gene coexpression networks prioritized 262 high-centrality bottleneck genes as putative regulators of dysregulated pathways. Next, knowledge graph-based drug repurposing predicted six Food and Drug Administration (FDA)-approved drugs that simultaneously target multiple bottleneck genes and multiple AD-relevant pathways. Notably, in a large US de-identified insurance-claims database (n = 364 733), exposure to promethazine, one of the candidate drugs, was associated with a 57%-62% lower incidence of AD versus an active antihistamine comparator (adjusted hazard ratio 0.38; inverse-probability weighted 0.43; both P < .001), providing real-world support for its repurposing potential. In summary, PRISM-ML, as an explainable multiomics analysis pipeline, is readily transferable to other complex diseases, advancing precision medicine.

Alzheimer Disease↗

PubMed1998

An RNA folding method capable of identifying pseudoknots and base triples.

MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) method for RNA structure prediction. The MWM method is capable of detecting pseudoknots and other tertiary base-pairing interactions in a computationally efficient manner (Cary and Stormo, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 75-80, 1995). Here we report on the results of our efforts to improve the MWM method's predictive accuracy, and show how the method can be extended to detect base interactions formerly inaccessible to automated RNA modeling techniques. RESULTS: Improved performance in MWM structure prediction was achieved in two ways. First, new ways of calculating base pair likelihoods have been developed. These allow experimental data and combined statistical and thermodynamic information to be used by the program. Second, accuracy was improved by developing techniques for filtering out spurious base pairs predicted by the MWM program. We also demonstrate here a means by which the MWM folding method may be used to detect the presence of base triples in RNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. html CONTACT: tabaska@cshl.org

Algorithms↗

PubMed1986

Computer-automated prediction of the mutagenicity of benzidine, 4,4"-diaminoterphenyl, 4-dimethylaminoazobenzene and 4-cyanodimethylaniline: comparison with the results of the Second UKEMS Collaborative Study.

There was agreement between the experimental results, obtained in the course of the Second UKEMS Collaborative Study, for the mutagenicity in Salmonella typhimurium of benzidine, 4,4"-diaminoterphenyl, 4-dimethylaminoazobenzene and 4-cyanodimethylaniline and the mutagenicity predicted by CASE (Computer Automated Structure Evaluation), a recently developed artificial intelligence system.

Aniline Compounds↗

PubMed1998

Application of Kohonen neural networks for the non-morphological distinction between glomerular and tubular renal disease.

BACKGROUND: A Kohonen topological map is an artificial intelligence system of the connectionist school (neural networks). The map learns the typical features of the subclasses in the learning set by means of a shortest Euclidean distance algorithm, after which self-adaptation of the neurons occurs. By its ability of self-organization and generalization, a Kohonen map is useful for pattern recognition, and its application in the medical field as an aid for decision making seems promising. This study describes the use of a Kohonen topological mapping system in the classification of renal diseases as being glomerular or tubular on basis of clinical characteristics and laboratory results. METHODS: Forty-one parameters from 75 patients were retrospectively retrieved and used to train four different Kohonen maps of 10 x 10 neurons. For reference diagnostic classification, we referred to the results of the light-microscopic examination. The classification of the patients by the four different Kohonen networks was compared to the classification by a rule-based system and by three nephrologists. We also developed a 'hybrid' decision system that makes a classification on basis of the opinion of the four networks and that of the rule-based system. RESULTS: The results show that a Kohonen map is capable of classifying the patients as having glomerular or tubular disease with a higher sensitivity and predictive value than the nephrologists and the rule-based system, and that the best classification was performed by the hybrid system: sensitivity and predictive value for the diagnosis 'glomerular' respectively 100 and 88% for the network with the most adequate results, 90 and 83% for the nephrologists, 90 and 95% for the rule-based system, and 95 and 96% for the hybrid system; sensitivity and predictive value for the diagnosis 'tubular' respectively 50 and 100% for the neural networks, 31 and 45% for the nephrologists, 81 and 68% for the rule-based system, and 87 and 82% for the hybrid system). CONCLUSION: We conclude that a Kohonen map is capable of classifying the patients as having glomerular or tubular disease with a high sensitivity and predictive value. The rule-based system performs worse than the neural networks. The most adequate results were obtained with the hybrid system.

Adult↗