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PubMed2005

Human microRNA prediction through a probabilistic co-learning model of sequence and structure.

MicroRNAs (miRNAs) are small regulatory RNAs of approximately 22 nt. Although hundreds of miRNAs have been identified through experimental complementary DNA cloning methods and computational efforts, previous approaches could detect only abundantly expressed miRNAs or close homologs of previously identified miRNAs. Here, we introduce a probabilistic co-learning model for miRNA gene finding, ProMiR, which simultaneously considers the structure and sequence of miRNA precursors (pre-miRNAs). On 5-fold cross-validation with 136 referenced human datasets, the efficiency of the classification shows 73% sensitivity and 96% specificity. When applied to genome screening for novel miRNAs on human chromosomes 16, 17, 18 and 19, ProMiR effectively searches distantly homologous patterns over diverse pre-miRNAs, detecting at least 23 novel miRNA gene candidates. Importantly, the miRNA gene candidates do not demonstrate clear sequence similarity to the known miRNA genes. By quantitative PCR followed by RNA interference against Drosha, we experimentally confirmed that 9 of the 23 representative candidate genes express transcripts that are processed by the miRNA biogenesis enzyme Drosha in HeLa cells, indicating that ProMiR may successfully predict miRNA genes with at least 40% accuracy. Our study suggests that the miRNA gene family may be more abundant than previously anticipated, and confer highly extensive regulatory networks on eukaryotic cells.

Algorithms↗

PubMed2002

Artificial neural network predictive model for allergic disease using single nucleotide polymorphisms data.

The purpose of this study was to develop a novel diagnostic prediction method for allergic diseases from the data of single nucleotide polymorphisms (SNPs) using an artificial neural network (ANN). We applied the prediction method to four allergic diseases, such as atopic dermatitis (AD), allergic conjunctivitis (AC), allergic rhinitis (AR) and bronchial asthma (BA), and verified its predictive ability. Almost all the learning data were precisely predicted. Regarding the evaluation data, the learned ANN model could correctly predict a diagnosis with more than 78% accuracy. We also analyzed the SNP data using multiple regression analysis (MRA). Using the MRA model, less than 10% of patients with the above allergic diseases were correctly diagnosed, while this figure was more than 75% for persons without allergic diseases. From these results, it was shown that the ANN model was superior to the MRA model with respect to predictive ability of allergic diseases. Moreover, we used two different methods to convert the genetic polymorphism data into numerical data. Using both methods, diagnostic predictions were quite precise and almost the same predictive abilities were observed. This is the first study showing the application and usefulness of an ANN for the prediction of allergic diseases based on SNP data.

Journal Article↗

PubMed2006

Predicting the effect of missense mutations on protein function: analysis with Bayesian networks.

BACKGROUND: A number of methods that use both protein structural and evolutionary information are available to predict the functional consequences of missense mutations. However, many of these methods break down if either one of the two types of data are missing. Furthermore, there is a lack of rigorous assessment of how important the different factors are to prediction. RESULTS: Here we use Bayesian networks to predict whether or not a missense mutation will affect the function of the protein. Bayesian networks provide a concise representation for inferring models from data, and are known to generalise well to new data. More importantly, they can handle the noisy, incomplete and uncertain nature of biological data. Our Bayesian network achieved comparable performance with previous machine learning methods. The predictive performance of learned model structures was no better than a naïve Bayes classifier. However, analysis of the posterior distribution of model structures allows biologically meaningful interpretation of relationships between the input variables. CONCLUSION: The ability of the Bayesian network to make predictions when only structural or evolutionary data was observed allowed us to conclude that structural information is a significantly better predictor of the functional consequences of a missense mutation than evolutionary information, for the dataset used. Analysis of the posterior distribution of model structures revealed that the top three strongest connections with the class node all involved structural nodes. With this in mind, we derived a simplified Bayesian network that used just these three structural descriptors, with comparable performance to that of an all node network.

Algorithms↗

PubMed1997

Modeling obesity using abductive networks.

This paper investigates the use of abductive-network machine learning for modeling and predicting outcome parameters in terms of input parameters in medical survey data. Here we consider modeling obesity as represented by the waist-to-hip ratio (WHR) risk factor to investigate the influence of various parameters. The same approach would be useful in predicting values of clinical parameters that are difficult or expensive to measure from others that are more readily available. The AIM abductive network machine learning tool was used to model the WHR from 13 other health parameters. Survey data were collected for a randomly selected sample of 1100 persons aged 20 yr and over attending nine primary health care centers at Al-Khobar, Saudi Arabia. Models were synthesized by training on a randomly selected set of 800 cases, using both continuous and categorical representations of the parameters, and evaluated by predicting the WHR value for the remaining 300 cases. Models for WHR as a continuous variable predict the actual values within an error of 7.5% at the 90% confidence limits. Categorical models predict the correct logical value of WHR with an error in only 2 of the 300 evaluation cases. Analytical relationships derived from simple categorical models explain global observations on the total survey population to an accuracy as high as 99%. Simple continuous models represented as analytical functions highlight global relationships and trends. Results confirm the strong correlation between WHR and diastolic blood pressure, cholesterol level, and family history of obesity. Compared to other statistical and neural network approaches, AIM abductive networks provide faster and more automated model synthesis. A review is given of other areas where the proposed modeling approach can be useful in clinical practice.

Adult↗

PubMed2026

Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.

MOTIVATION: Analysis of single cell ATAC-seq and RNA-seq data has allowed to gain unprecedented insights into gene regulation by allowing to define cell type-specific regulatory regions and their effects on gene expression. While powerful, such analysis is challenging due to the inherent sparsity of single cell data. RESULTS: We present a new approach, MetaFR, to learn gene-specific models that link open-chromatin variation from scATAC-seq data to gene expression from scRNA-seq. Using efficient regression trees, we illustrate that accurate expression prediction models can be learned on the single-cell or meta-cell level. Validation was done using fine-mapped eQTLs. Meta-cell models were found to outperform single-cell models for most genes. Comparison to the SOTA method SCARlink revealed advantages of MetaFR in terms of runtime and prediction performance. MetaFR thus allows time-efficient analysis and obtains reliable models of gene expression prediction, which can be used to study gene regulation in any organism for which scRNA-seq and scATAC-seq data is available. AVAILABILITY AND IMPLEMENTATION: MetaFR is available under https://github.com/SchulzLab/MetaFR.

Single-Cell Analysis↗

PubMed2002

What is learned in sequential learning? An associative model of reward magnitude serial-pattern learning.

A computational model of sequence learning is described that is based on pairwise associations and generalization. Simulations by the model predicted that rats should learn a long monotonic pattern of food quantities better than a nonmonotonic pattern, as predicted by rule-learning theory, and that they should learn a short nonmonotonic pattern with highly discriminable elements better than 1 with less discriminable elements, as predicted by interitem association theory. In 2 other studies, the model also simulated behavioral "rule generalization," "extrapolation," and associative transfer data motivated by both rule-learning and associative perspectives. Although these simulations do not rule out the possibility that rats can use rule induction to learn serial patterns, they show that a simple associative model can account for the classical behavioral studies implicating rule learning in reward magnitude serial-pattern learning.

Animals↗

PubMed1984

Global and local control of choice behavior by cyclically varying outcome probabilities.

Subjects asked to simulate decision makers in a competitive bidding situation chose repeatedly between two alternatives; reward probability varied according to a sine wave function of time for one alternative but was held constant over time for the other. Learning functions for choice probability exhibited the wavelike pattern predicted by a statistical learning model. However, on later transfer trials, when success probability was independent of subjects' choices, their choice behavior continued to follow a wavelike function rather than approaching the constant .5 level predicted by the learning model. A possible basis in memory for the transfer performance was revealed in subjects' sketches of the remembered pattern of variation in reward probabilities. It is concluded that choice performance is controlled by a mixture of local feedback, in a manner described by the learning model, and more global information encoded in an abstract memory representation, with the balance of the influence shifting toward the latter when local feedback becomes uninformative.

Adult↗

PubMed2026

Prediction of bacterial protein-compound interactions with only positive samples.

MOTIVATION: Prediction of Compound-Protein Interactions (CPI) in bacteria is crucial to advance various pharmaceutical and chemical engineering fields, including biocatalysis, drug discovery, and industrial processing. However, current CPI models cannot be applied for bacterial CPI prediction due to the lack of curated negative interaction samples. RESULTS: We propose a novel Positive-Unlabeled (PU) learning framework, named BIN-PU, to address this limitation. BIN-PU generates pseudo positive and negative labels from known positive interaction data, enabling effective training of deep learning models for CPI prediction. We also propose a weighted positive loss function that weights to truly positive samples. We have validated BIN-PU coupled with multiple CPI backbone models, comparing the performance with the existing PU models using bacterial cytochrome P450 (CYP) data. Extensive experiments demonstrate the superiority of BIN-PU over the benchmark models in predicting CPIs with only truly positive samples. Furthermore, we have validated BIN-PU on additional bacterial proteins obtained from literature review, human CYP datasets, and uncurated data for its reproducibility. We have also validated the CPI prediction for the uncurated CYP data with biological and biophysical experiments. BIN-PU represents a significant advancement in CPI prediction for bacterial proteins, opening new possibilities for improving predictive models in related biological interaction tasks. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/datax-lab/CYP.

Bacterial Proteins↗

PubMedDate not supplied

Adaptive rival penalized competitive learning and combined linear predictor model for financial forecast and investment.

We propose a prediction model called Rival Penalized Competitive Learning (RPCL) and Combined Linear Predictor method (CLP), which involves a set of local linear predictors such that a prediction is made by the combination of some activated predictors through a gating network (Xu et al., 1994). Furthermore, we present its improved variant named Adaptive RPCL-CLP that includes an adaptive learning mechanism as well as a data pre-and-post processing scheme. We compare them with some existing models by demonstrating their performance on two real-world financial time series--a China stock price and an exchange-rate series of US Dollar (USD) versus Deutschmark (DEM). Experiments have shown that Adaptive RPCL-CLP not only outperforms the other approaches with the smallest prediction error and training costs, but also brings in considerable high profits in the trading simulation of foreign exchange market.

Algorithms↗

PubMed2005

A comparison of forward blocking and reduced overshadowing in human causal learning.

In this study, we directly compared forward blocking with reduced overshadowing in a human causal learning study using an A+, B- (first learning stage), AX+, BY+, KL+ (second learning stage) design. The results showed that reduced overshadowing was significantly stronger than forward blocking. These results are problematic for at least some associative learning models but were predicted on the basis of higher order reasoning accounts of cue competition in human causal learning.

Association↗

PubMed2004

Distinguishing social and asocial learning using diffusion dynamics.

Theoretical models predict that the cumulative number of individuals displaying a socially learned novel behavior will follow an accelerating pattern over time, whereas asocial processes have been associated with linear or decelerating functions. This raises the possibility that the shape of the diffusion curve may reveal something about the learning processes involved. If true, this would be particularly useful for identifying social transmission in observational field studies. Published data are reviewed and are found to provide limited support for this view. The use of accelerating curves as a diagnostic is challenging because (1) alternative theoretical models make similar predictions, (2) clear supporting empirical data are lacking, and (3) practical considerations frequently make accurate construction of the diffusion curve difficult.

Adaptation, Psychological↗

PubMed2026

Investigating cross-organism prediction of prokaryotic essential proteins using unsupervised language model and ensemble strategy.

Cross-organism prediction of essential proteins is a critical task for drug discovery and microbial engineering, yet the generalizability of existing machine learning models across diverse species remains a significant challenge. In this study, we propose DeepPEP, a large language model-based framework designed to reliably transfer essential protein annotations between distantly related organisms. Utilizing 66 curated prokaryotic datasets, we systematically evaluated DeepPEP's cross-organism performance under various conditions. Initial pairwise predictions revealed a correlation between performance and evolutionary distance; however, further investigation demonstrated that integrating training data from multiple organisms yields superior predictive power. In a benchmark scenario designed to simulate real-world applications, DeepPEP outperformed the state-of-the-art tool Geptop 2.0, showcasing a robust ability to identify species-specific essential proteins. Finally, a case study on novel genomes confirmed the model's practical effectiveness. Our results suggest that DeepPEP is a powerful strategy for prokaryotic essential protein prediction, and the rigorous evaluation framework established in this study provides a new benchmark for the field.

Large Language Models↗

PubMed2002

Reward, motivation, and reinforcement learning.

There is substantial evidence that dopamine is involved in reward learning and appetitive conditioning. However, the major reinforcement learning-based theoretical models of classical conditioning (crudely, prediction learning) are actually based on rules designed to explain instrumental conditioning (action learning). Extensive anatomical, pharmacological, and psychological data, particularly concerning the impact of motivational manipulations, show that these models are unreasonable. We review the data and consider the involvement of a rich collection of different neural systems in various aspects of these forms of conditioning. Dopamine plays a pivotal, but complicated, role.

Animals↗

PubMed1994

Modeling perceptual learning with multiple interacting elements: a neural network model describing early visual perceptual learning.

We introduce a neural network model of an early visual cortical area, in order to understand better results of psychophysical experiments concerning perceptual learning during odd element (pop-out) detection tasks (Ahissar and Hochstein, 1993, 1994a). The model describes a network, composed of orientation selective units, arranged in a hypercolumn structure, with receptive field properties modeled from real monkey neurons. Odd element detection is a final pattern of activity with one (or a few) salient units active. The learning algorithm used was the Associative reward-penalty (Ar-p) algorithm of reinforcement learning (Barto and Anandan, 1985), following physiological data indicating the role of supervision in cortical plasticity. Simulations show that network performance improves dramatically as the weights of inter-unit connections reach a balance between lateral iso-orientation inhibition, and facilitation from neighboring neurons with different preferred orientations. The network is able to learn even from chance performance, and in the presence of a large amount of noise in the response function. As additional tests of the model, we conducted experiments with human subjects in order to examine learning strategy and test model predictions.

Humans↗

PubMed2003

Evolving spike-timing-dependent plasticity for single-trial learning in robots.

Single-trial learning is studied in an evolved robot model of synaptic spike-timing-dependent plasticity (STDP). Robots must perform positive phototaxis but must learn to perform negative phototaxis in the presence of a short-lived aversive sound stimulus. STDP acts at the millisecond range and depends asymmetrically on the relative timing of pre- and post-synaptic spikes. Although it has been involved in learning models of input prediction, these models require the iterated presentation of the input pattern, and it is hard to see how this mechanism could sustain single-trial learning over a time-scale of tens of seconds. An incremental evolutionary approach is used to answer this question. The evolved robots succeed in learning the appropriate behaviour, but learning does not depend on achieving the right synaptic configuration but rather the right pattern of neural activity. Robot performance during positive phototaxis is quite robust to loss of spike-timing information, but in contrast, this loss is catastrophic for learning negative phototaxis where entrained firing is common. Tests show that the final weight configuration carries no information about whether a robot is performing one behaviour or the other. Fixing weights, however, has the effect of degrading performance, thus demonstrating that plasticity is used to sustain the neural activity corresponding both to the normal phototaxis condition and to the learned behaviour. The implications and limitations of this result are discussed.

Action Potentials↗

PubMed2002

Feature subset selection for splice site prediction.

MOTIVATION: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a review and references). These algorithms need information sources or features from which the models can be computed. For splice site prediction, the features we consider in this study are the presence or absence of certain nucleotides in close proximity to the splice site. Since it is not known how many and which nucleotides are relevant for splice site prediction, the set of features is chosen large enough such that the probability that all relevant information sources are in the set is very high. Using only those features that are relevant for constructing a splice site prediction system might improve the system and might also provide us with useful biological knowledge. Using fewer features will of course also improve the prediction speed of the system. RESULTS: A wrapper-based feature subset selection algorithm using a support vector machine or a naive Bayes prediction method was evaluated against the traditional method for selecting features relevant for splice site prediction. Our results show that this wrapper approach selects features that improve the performance against the use of all features and against the use of the features selected by the traditional method. AVAILABILITY: The data and additional interactive graphs on the selected feature subsets are available at http://www.psb.rug.ac.be/gps

Arabidopsis↗

PubMed2006

Predictive neural coding of reward preference involves dissociable responses in human ventral midbrain and ventral striatum.

Food preferences are acquired through experience and can exert strong influence on choice behavior. In order to choose which food to consume, it is necessary to maintain a predictive representation of the subjective value of the associated food stimulus. Here, we explore the neural mechanisms by which such predictive representations are learned through classical conditioning. Human subjects were scanned using fMRI while learning associations between arbitrary visual stimuli and subsequent delivery of one of five different food flavors. Using a temporal difference algorithm to model learning, we found predictive responses in the ventral midbrain and a part of ventral striatum (ventral putamen) that were related directly to subjects' actual behavioral preferences. These brain structures demonstrated divergent response profiles, with the ventral midbrain showing a linear response profile with preference, and the ventral striatum a bivalent response. These results provide insight into the neural mechanisms underlying human preference behavior.

Adult↗

PubMed2003

Combining artificial neural networks and transrectal ultrasound in the diagnosis of prostate cancer.

Arguably the most important step in the prognosis of prostate cancer is early diagnosis. More than 1 million transrectal ultrasound (TRUS)-guided prostate needle biopsies are performed annually in the United States, resulting in the detection of 200,000 new cases per year. Unfortunately, the urologist's ability to diagnose prostate cancer has not kept pace with therapeutic advances; currently, many men are facing the need for prostate biopsy with the likelihood that the result will be inconclusive. This paper will focus on the tools available to assist the clinician in predicting the outcome of the prostate needle biopsy. We will examine the use of "machine learning" models (artificial intelligence), in the form of artificial neural networks (ANNs), to predict prostate biopsy outcomes using prebiopsy variables. Currently, six validated predictive models are available. Of these, five are machine learning models, and one is based on logistic regression. The role of ANNs in providing valuable predictive models to be used in conjunction with TRUS appears promising. In the few studies that have compared machine learning to traditional statistical methods, ANN and logistic regression appear to function equivalently when predicting biopsy outcome. With the introduction of more complex prebiopsy variables, ANNs are in a commanding position for use in predictive models. Easy and immediate physician access to these models will be imperative if their full potential is to be realized.

Biopsy↗