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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&#x2009;=&#x2009;364&#xa0;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&#x2009;<&#x2009;.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↗
PubMed2003

Finding subtle motifs by branching from sample strings.

UNLABELLED: Many motif finding algorithms apply local search techniques to a set of seeds. For example, GibbsDNA (Lawrence et al. 1993, Science, 262, 208-214) applies Gibbs sampling to random seeds, and MEME (Bailey and Elkan, 1994, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB-94), 28-36) applies the EM algorithm to selected sample strings, i.e. substrings of the sample. In the case of subtle motifs, recent benchmarking efforts show that both random seeds and selected sample strings may never get close to the globally optimal motif. We propose a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings. Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms. AVAILABILITY: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Algorithms↗
PubMed2005

Mining sequence annotation databanks for association patterns.

MOTIVATION: Millions of protein sequences currently being deposited to sequence databanks will never be annotated manually. Similarity-based annotation generated by automatic software pipelines unavoidably contains spurious assignments due to the imperfection of bioinformatics methods. Examples of such annotation errors include over- and underpredictions caused by the use of fixed recognition thresholds and incorrect annotations caused by transitivity based information transfer to unrelated proteins or transfer of errors already accumulated in databases. One of the most difficult and timely challenges in bioinformatics is the development of intelligent systems aimed at improving the quality of automatically generated annotation. A possible approach to this problem is to detect anomalies in annotation items based on association rule mining. RESULTS: We present the first large-scale analysis of association rules derived from two large protein annotation databases-Swiss-Prot and PEDANT-and reveal novel, previously unknown tendencies of rule strength distributions. Most of the rules are either very strong or very weak, with rules in the medium strength range being relatively infrequent. Based on dynamics of error correction in subsequent Swiss-Prot releases and on our own manual analysis we demonstrate that exceptions from strong rules are, indeed, significantly enriched in annotation errors and can be used to automatically flag them. We identify different strength dependencies of rules derived from different fields in Swiss-Prot. A compositional breakdown of association rules generated from PEDANT in terms of their constituent items indicates that most of the errors that can be corrected are related to gene functional roles. Swiss-Prot errors are usually caused by under-annotation owing to its conservative approach, whereas automatically generated PEDANT annotation suffers from over-annotation. AVAILABILITY: All data generated in this study are available for download and browsing at http://pedant.gsf.de/ARIA/index.htm.

Conserved Sequence↗
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↗
PubMed2000

Genome annotation assessment in Drosophila melanogaster.

Computational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region of Drosophila melanogaster. This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools, contributed predictions for features including gene structure, protein homologies, promoter sites, and repeat elements. We evaluated these predictions using two standards, one based on previously unreleased high-quality full-length cDNA sequences and a second based on the set of annotations generated as part of an in-depth study of the region by a group of Drosophila experts. Although these standard sets only approximate the unknown distribution of features in this region, we believe that when taken in context the results of an evaluation based on them are meaningful. The results were presented as a tutorial at the conference on Intelligent Systems in Molecular Biology (ISMB-99) in August 1999. Over 95% of the coding nucleotides in the region were correctly identified by the majority of the gene finders, and the correct intron/exon structures were predicted for >40% of the genes. Homology-based annotation techniques recognized and associated functions with almost half of the genes in the region; the remainder were only identified by the ab initio techniques. This experiment also presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region. We discovered that the promoter predictors' high false-positive rates make their predictions difficult to use. Integrating gene finding and cDNA/EST alignments with promoter predictions decreases the number of false-positive classifications but discovers less than one-third of the promoters in the region. We believe that by establishing standards for evaluating genomic annotations and by assessing the performance of existing automated genome annotation tools, this experiment establishes a baseline that contributes to the value of ongoing large-scale annotation projects and should guide further research in genome informatics.

Alcohol Dehydrogenase↗
PubMed2004

Fuzzy branching temporal logic.

Intelligent systems require a systematic way to represent and handle temporal information containing uncertainty. In particular, a logical framework is needed that can represent uncertain temporal information and its relationships with logical formulae. Fuzzy linear temporal logic (FLTL), a generalization of propositional linear temporal logic (PLTL) with fuzzy temporal events and fuzzy temporal states defined on a linear time model, was previously proposed for this purpose. However, many systems are best represented by branching time models in which each state can have more than one possible future path. In this paper, fuzzy branching temporal logic (FBTL) is proposed to address this problem. FBTL adopts and generalizes concurrent tree logic (CTL*), which is a classical branching temporal logic. The temporal model of FBTL is capable of representing fuzzy temporal events and fuzzy temporal states, and the order relation among them is represented as a directed graph. The utility of FBTL is demonstrated using a fuzzy job shop scheduling problem as an example.

Journal Article↗
PubMed1996

Extracting 1/f fluctuation from the arterial blood pressure of an artificial heart.

We have studied the fluctuations of an artificial circulation for the analysis of the physiological aspects; however, the conventionally used fast Fourier transform (FFT) method cannot separate harmonic oscillations, such as respiratory and Mayer waves, from the 1/f fluctuation, which has been though to represent underlying fractal dynamics. Fractal structure was shown in the strange attractor with chaotic dynamics, which is thought to be a flexible and intelligent system. In this study, the coarse-graining spectral analyzing (CGSA) method was utilized to quantitatively evaluate the proportion of the 1/f fluctuation in the total power in the frequency domain and to analyze artificial circulation in the whole system. We implanted two pneumatically actuated ventricular assist devices as biventricular bypasses (BVBs) in chronic animal experiments using 4 healthy adult goats. To compare the natural and prosthetic circulation of each experimental animal, the BVB-type complete prosthetic circulation model with electrically induced ventricular fibrillation was adopted. All hemodynamic parameters of natural and prosthetic circulation were recorded under awake conditions and calculated with the use of a personal computer. With the use of the CGSA method, time-series data of the hemodynamics were analyzed and fractal percentages, extracting the 1/f fluctuation from a given time series, were calculated. Fractal percentages of the arterial blood pressure were 85.8 +/- 10.7% and 82.0 +/- 7.3% with natural and artificial circulation, respectively (not significant [NS]). 1/f fluctuation showed the characteristics of being fractal in a time series. The fractal structure showed robustness and error resistance in nonlinear dynamics. Therefore, our results suggest that the circulatory regulatory system of the artificial heart may have desirable characteristics such as error resistance.

Animals↗
PubMed1978

Uses of coronary heart attack registers.

By studying all coronary heart attacks presenting within defined communities it should be possible to avoid the distortions and omissions inherent in hospital-based case series. In practice the technique presents several problems. Measures of frequency and outcome are very sensitive to the diagnostic criteria used. Data of varying quality are mixed and specific attack rates can be calculated only for items for which the census provides a denominator. Patients presenting to different medical services have different outcomes, but probably less because of treatment than because the severity of the attack affects behaviour in it. Despite these problems, some such intelligence system is of value in any comprehensive strategy for coronary heart disease.

Adult↗
PubMed2005

Anatomical ontologies: names and places in biology.

Ontology has long been the preserve of philosophers and logicians. Recently, ideas from this field have been picked up by computer scientists as a basis for encoding knowledge and with the hope of achieving interoperability and intelligent system behavior. In bioinformatics, ontologies might allow hitherto impossible query and data-mining activities. We review the use of anatomy ontologies to represent space in biological organisms, specifically mouse and human.

Anatomy↗
PubMed2003

Mathematical modeling of decision making: a soft and fuzzy approach to capturing hard decisions.

This research focuses on a modeling approach and set of mathematical tools that were derived from research on intelligence systems, namely fuzzy system modeling. This study systematically evaluates these tools as an approach for modeling human decision making, contrasting the approach with more traditional methods based on regression. The research was conducted using experts and a simulated task environment related to allocating rewards in the form of merit pay. The results indicate that fuzzy system models generally perform as well as or better than both linear and nonlinear regression methods in terms of model fit. These results are discussed in terms of issues regarding modeling precision versus parsimony, the value of adaptive modeling techniques, empirical versus subjective approaches to model building, and individual differences in judgment strategies. Potential applications of this research include using the modeling approach studied to build higher-fidelity models that yield new insights and a better understanding of decision-making strategies and environments.

Decision Making↗
PubMedDate not supplied

Artificial intelligence techniques for cancer treatment planning.

An artificial intelligence system, NEWCHEM, for the development of new oncology therapies is described. This system takes into account the most recent advances in molecular and cellular biology and in cell-drug interaction, and aims to guide experimentation in the design of new optimal protocols. Further work is being carried out, aimed to embody in the system all the basic knowledge of biology, physiopathology and pharmacology, to reason qualitatively from first principles so as to be able to suggest cancer therapies.

Animals↗
PubMed1999

The power and limits of a rule-based morpho-semantic parser.

The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors.

Humans↗
PubMed2001

Agroterrorism, biological crimes, and biowarfare targeting animal agriculture. The clinical, pathologic, diagnostic, and epidemiologic features of some important animal diseases.

In the past 100 years, to our knowledge there have been approximately 12 events involving the intentional introduction of microbiologic agents into livestock and animal populations worldwide, of which three were World War I events in the United States. To the best of the authors' knowledge, there has been no recent intentional introduction of microbiologic agents (viruses or bacteria) into livestock and animal populations in the United States. The criminal or terrorist use of chemicals against animals and agriculture products have been more common. With the political, economic, and military new world order, however, the United States must maintain a vigilant posture. The framework for this vigilance must be an intelligence system sensitive to the needs of agriculture and a first-class animal disease diagnostic surveillance and response system.

Agriculture↗
PubMed2004

FREX: a query interface for biological processes with hierarchical and recursive structures.

An intelligent system for signal transduction pathways and other higher order functional knowledge is presented. Molecular mechanisms of biological processes are typically represented as diagrams ("pathways") that have a graph-analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and range from metal ion to protein to biological processes in general. In addition, the kinds of interactions that connect biological entities are likewise diverse. Consequently, current knowledge about pathways is highly heterogeneous both in the sense of the types of constituents and the granularity of descriptions. To cope with this problem, the proposed system adopts a recursive and hierarchical representation model that enables the annotation and query of pathways or sub-pathways of arbitral granularity. By combining the use of this hierarchical structure and biological ontologies, literature-based information regarding biological mechanisms becomes accessible by computer.

Computational Biology↗
PubMed2004

[Study on the effects of exposure to rare earth elements and health-responses in children aged 7-10 years].

OBJECTIVE: To study the effects of environmental exposure to rare earth elements (REEs) on health in children. METHODS: The level of physical growth and development, function of immune system, intelligence were chosen as the health-response indexes of children. Indicators for physical growth and development were measured. IgA, IgG, IgM and complement C3, C4 in blood serum were determined with turbidimeter measure, IgE were determined by chemiluminescence immunoassay (CLIA), lymphocyle subset CD3, CD4, CD8, CD4/CD8 and NK were determined by flowcytometry. Intelligence quotient (IQ) were examined with Drawing A Man Test in the children aged 7-10 years randomly sampled in the area containing rare earth (RE) ore and the control area in Xunwucounty, Jiangxi. Blood REEs were determined by inductively coupled plasma source mass pectrometry (ICP-MS). RESULTS: All 15 kinds of REEs were detected in each sample, the quantity of blood REEs of the children were lower in exposure group than in control group and in the rare earth area [(2.10 +/- 0.88)ng/g] was 1.73 times as that of the children in the control area [(1.26 +/- 1.35) ng/g]. The difference is significant (P < 0.01). The humoral immunity would be changed in the body of the children exposed to REEs, the quantity of IgM was lower in exposure group than in control group. The measuring result of T lymph subgroup of the children indicates: CD3, CD4, CD4/CD8 changed a lot. The percent of CD3, CD8 were significantly lower and CD4/CD8 was significantly higher in exposure group than in control group. The score of IQ was lower significantly in the exposure group than in the control. The percentage of high IQ decreased, the percentage of low IQ increased. Multiple regression analysis showed the variable of blood REEs in exposure to REEs group or those in the control group were introduced into the Vital capacity, blood pressure and IgM regression model. The distance from home to the RE area and either RE put in home influenced the score of children's IQ. CONCLUSION: The children aged 7-10 years in RE ore area may have higher REEs burden in the body, and exposure to REEs could have adverse influences in children.

CD4-CD8 Ratio↗