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Results for “Predictive Learning Models”

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PubMed2004

Addiction as a computational process gone awry.

Addictive drugs have been hypothesized to access the same neurophysiological mechanisms as natural learning systems. These natural learning systems can be modeled through temporal-difference reinforcement learning (TDRL), which requires a reward-error signal that has been hypothesized to be carried by dopamine. TDRL learns to predict reward by driving that reward-error signal to zero. By adding a noncompensable drug-induced dopamine increase to a TDRL model, a computational model of addiction is constructed that over-selects actions leading to drug receipt. The model provides an explanation for important aspects of the addiction literature and provides a theoretic view-point with which to address other aspects.

Animals↗

PubMed1990

Empirical testing of a cognitive model to account for neuropsychological functioning underlying arithmetic problem solving.

The efficacy of a cognitive-based arithmetic problem-solving model (Dinnel, Glover, & Halpain, in press; Dinnel, Glover, & Ronning, 1984) was tested using 989 students with learning disabilities. Comprehensive neuropsychological test battery information was used to predict composite arithmetic test performance as a means of examining the utility of this model. Results of this study offer support for Dinnel et al.'s (Dinnel, Glover, & Halpain, in press; Dinnel, Glover, & Ronning, 1984) model in accounting for arithmetic performance under continuous visual stimulus conditions. However, these data indicate a more complex neuropsychological underpinning to arithmetic performance in both visual and aural stimulus conditions. The neuropsychological aspects of arithmetic problem solving were discussed in relationship to this cognitive-based model.

Adolescent↗

PubMed2004

Modeling and analysis of heterogeneous regulation in biological networks.

In this study, we propose a novel model for the representation of biological networks and provide algorithms for learning model parameters from experimental data. Our approach is to build an initial model based on extant biological knowledge and refine it to increase the consistency between model predictions and experimental data. Our model encompasses networks which contain heterogeneous biological entities (mRNA, proteins, metabolites) and aims to capture diverse regulatory circuitry on several levels (metabolism, transcription, translation, post-translation and feedback loops, among them). Algorithmically, the study raises two basic questions: how to use the model for predictions and inference of hidden variables states, and how to extend and rectify model components. We show that these problems are hard in the biologically relevant case where the network contains cycles. We provide a prediction methodology in the presence of cycles and a polynomial time, constant factor approximation for learning the regulation of a single entity. A key feature of our approach is the ability to utilize both high-throughput experimental data, which measure many model entities in a single experiment, as well as specific experimental measurements of few entities or even a single one. In particular, we use together gene expression, growth phenotypes, and proteomics data. We tested our strategy on the lysine biosynthesis pathway in yeast. We constructed a model of more than 150 variables based on an extensive literature survey and evaluated it with diverse experimental data. We used our learning algorithms to propose novel regulatory hypotheses in several cases where the literature-based model was inconsistent with the experiments. We showed that our approach has better accuracy than extant methods of learning regulation.

Algorithms↗

PubMed2005

On adaptation, maximization, and reinforcement learning among cognitive strategies.

Analysis of binary choice behavior in iterated tasks with immediate feedback reveals robust deviations from maximization that can be described as indications of 3 effects: (a) a payoff variability effect, in which high payoff variability seems to move choice behavior toward random choice; (b) underweighting of rare events, in which alternatives that yield the best payoffs most of the time are attractive even when they are associated with a lower expected return; and (c) loss aversion, in which alternatives that minimize the probability of losses can be more attractive than those that maximize expected payoffs. The results are closer to probability matching than to maximization. Best approximation is provided with a model of reinforcement learning among cognitive strategies (RELACS). This model captures the 3 deviations, the learning curves, and the effect of information on uncertainty avoidance. It outperforms other models in fitting the data and in predicting behavior in other experiments.

Adaptation, Psychological↗

PubMed1997

Computational neural networks for predictive microbiology: I. Methodology.

Artificial neural networks are mathematical tools inspired by what is known about the physical structure and mechanism of the biological cognition and learning. Neural networks have attracted considerable attention due to their efficacy to model wide spectrum of challenging problems. In this paper, we present one of the most popular networks, the backpropagation, and discuss its learning algorithm and analyze several issues necessary for designating optimal networks that can generalize after being trained on examples. As an application in the area of predictive microbiology, modeling of microorganism growth by neural networks will be presented in a second paper of this series.

Algorithms↗

PubMed2000

Competition among causes but not effects in predictive and diagnostic learning.

Causal asymmetry is one of the most fundamental features of the physical world: Causes produce effects, but not vice versa. This article is part of a debate between the view that, in principle, people are sensitive to causal directionality during learning (causal-model theory) and the view that learning primarily involves acquiring associations between cues and outcomes irrespective of their causal role (associative theories). Four experiments are presented that use asymmetries of cue competition to discriminate between these views. These experiments show that, contrary to associative accounts, cue competition interacts with causal status and that people are capable of differentiating between predictive and diagnostic inferences. Additional implications of causal-model theory are elaborated and empirically tested against alternative accounts. The results uniformly favor causal-model theory.

Adult↗

PubMed1998

Plasticity of directional place fields in a model of rodent CA3.

We propose a computational model of the CA3 region of the rat hippocampus that is able to reproduce the available experimental data concerning the dependence of directional selectivity of the place cell discharge on the environment and on the spatial task. The main feature of our model is a continuous, unsupervised Hebbian learning dynamics of recurrent connections, which is driven by the neuronal activities imposed upon the network by the environment-dependent external input. In our simulations, the environment and the movements of the rat are chosen to mimic those commonly observed in neurophysiological experiments. The environment is represented as local views that depend on both the position and the heading direction of the rat. We hypothesize that place cells are intrinsically directional, that is, they respond to local views. We show that the synaptic dynamics in the recurrent neural network rapidly modify the discharge correlates of the place cells: Cells tend to become omnidirectional place cells in open fields, while their directionality tends to get stronger in radial-arm mazes. We also find that the synaptic learning mechanisms account for other properties of place cell activity, such as an increase in the place cell peak firing rates as well as clustering of place fields during exploration. Our model makes several experimental predictions that can be tested using current techniques.

Animals↗

PubMed2005

Ambulatory teaching: do approaches to learning predict the site and preceptor characteristics valued by clerks and residents in the ambulatory setting?

BACKGROUND: In a study to determine the site and preceptor characteristics most valued by clerks and residents in the ambulatory setting we wished to confirm whether these would support effective learning. The deep approach to learning is thought to be more effective for learning than surface approaches. In this study we determined how the approaches to learning of clerks and residents predicted the valued site and preceptor characteristics in the ambulatory setting. METHODS: Postal survey of all medical residents and clerks in training in Ontario determining the site and preceptor characteristics most valued in the ambulatory setting. Participants also completed the Workplace Learning questionnaire that includes 3 approaches to learning scales and 3 workplace climate scales. Multiple regression analysis was used to predict the preferred site and preceptor characteristics as the dependent variables by the average scores of the approaches to learning and perception of workplace climate scales as the independent variables. RESULTS: There were 1642 respondents, yielding a 47.3% response rate. Factor analysis revealed 7 preceptor characteristics and 6 site characteristics valued in the ambulatory setting. The Deep approach to learning scale predicted all of the learners' preferred preceptor characteristics (beta = 0.076 to beta = 0.234, p < .001). Valuing preceptor Direction was more strongly associated with the Surface Rational approach (beta = .252, p < .001) and with the Surface Disorganized approach to learning (beta = .154, p < 001) than with the Deep approach. The Deep approach to learning scale predicted valued site characteristics of Office Management, Patient Logistics, Objectives and Preceptor Interaction (p < .001). The Surface Rational approach to learning predicted valuing Learning Resources and Clinic Set-up (beta = .09, p = .001; beta = .197, p < .001). The Surface Disorganized approach to learning weakly negatively predicted Patient Logistics (beta = -.082, p = .003) and positively the Learning Resources (beta = .088, p = .003). Climate factors were not strongly predictive for any studied characteristics. Role Modeling and Patient Logistics were predicted by Supportive Receptive climate (beta = .135, p < .001, beta = .118, p < .001). CONCLUSION: Most site and preceptor characteristics valued by clerks and residents were predicted by their Deep approach to learning scores. Some characteristics reflecting the need for good organization and clear direction are predicted by learners' scores on less effective approaches to learning.

Adult↗

PubMed2025

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome.

Predicting and deciphering the regulatory logic of enhancers is a challenging problem, due to the intricate sequence features and lack of consistent genetic or epigenetic signatures that can accurately discriminate enhancers from other genomic regions. Recent machine-learning based methods have spotlighted the importance of extracting nucleotide composition of enhancers but failed to learn the sequence context and perform suboptimally. Motivated by advances in genomic language models, we developed DNABERT-Enhancer, a novel enhancer prediction method, by applying DNABERT pre-trained language model on the human genome. We trained two different models, using large collection of enhancers curated from the ENCODE registry of candidate cis-Regulatory Elements. The best fine-tuned model achieved 88.05% accuracy with Matthews correlation coefficient of 76% on independent set aside data. Further, we present the analysis of the predicted enhancers for all chromosomes of the human genome by comparing with the enhancer regions reported in publicly available databases. Finally, we applied DNABERT-Enhancer along with other DNABERT based regulatory genomic region prediction models to predict candidate SNPs with allele-specific enhancer and transcription factor binding activity. The genome-wide enhancer annotations and candidate loss-of-function genetic variants predicted by DNABERT-Enhancer provide valuable resources for genome interpretation in functional and clinical genomics studies.

Journal Article↗

PubMed2000

Computational models of the basal ganglia.

Computer simulation studies and mathematical analysis of models of the basal ganglia are being used increasingly to explore theories of basal ganglia function. We review the implications of these new models for a general understanding of basal ganglia function in normal as well as in diseased brains. The focus is on their functional similarities rather than on the details of mathematical methodologies and simulation techniques. Most of the models suggest a vital role for the basal ganglia in learning. Although this interest in learning is partly driven by experimental results associating the acute firing of dopamine cells with reward prediction in monkeys, some of the models have preceded the electrophysiological results. Another common theme of the models is selection. In this case, the striatum is seen as detecting and selecting cortical contexts for access to basal ganglia output. Although the behavioral consequences of this selection are hard to define, the models provide frameworks within which to explore these ideas empirically. This provides a means of refining our understanding of basal ganglia function and to consider dysfunction within the new logical frameworks.

Animals↗

PubMed1998

Workshop overview: scientific and regulatory challenges for the reduction, refinement, and replacement of animals in toxicity testing.

Public concern for animal welfare has been expressed through legislative control of animal use for experimental purposes since the first legislation was introduced in 1876 in the United Kingdom. Legislative control of animal use has been introduced in virtually every developed country, with major initiatives in Europe (1986) and the United States (1966 and 1985). Advances in scientific thinking resulted in the development of the concept of the three Rs--refinement, reduction, and replacement--by Russell and Burch in 1959. The field has expanded substantially since, with specialist scientific journals dedicated to alternatives, World Congresses organized to discuss the scientific and philosophical issues, and European and U.S. validation organizations being launched. Current scientific attention is focused on validation of alternative methods. The underlying scientific principles of chemical toxicity are complicated and insufficiently understood for alternative methods for all toxicity endpoints of importance in protecting human health to be available. Important lessons have been learned about how to validate methods, including the need to have prediction models available before the validation is undertaken, the need to understand the variability of the animal-based data which is to be used as the validation standard, and the need to have well-managed validation programs. Future progress will depend on the development of novel methods, which can now be validated through international collaborative efforts.

Animal Testing Alternatives↗

PubMed2026

Linking MRI radiomics to transcriptomics-based radiosensitivity in lower-grade glioma: A radiogenomic framework.

BACKGROUND: RSI is a transcriptomics-based biomarker associated with radiotherapy outcomes, but its clinical application is constrained by the requirement for tumor tissue and RNA sequencing. This study investigates whether MRI-derived radiomic features can reflect RSI-defined intrinsic radiosensitivity in lower-grade glioma.This addresses a critical gap arising from the limited availability of matched imaging and genomic data in routine clinical practice. METHODS: MRI-derived radiomic features were extracted from FLAIR images of lower-grade glioma patients obtained from TCIA and matched with transcriptomic data from TCGA. A total of 107 patients with both MRI and RNA sequencing data were included in the radiogenomic analysis. Radiomic features were ranked using a Borda-based ensemble feature selection strategy. Five supervised machine-learning classifiers were trained to predict RSI-based radiosensitivity classification, and model interpretability was assessed using SHAP within radiogenomic framework. RESULTS: Classification performance increased with feature number and stabilized at compact subset of 13 radiomic features. Logistic regression showed stable performance with an AUC of 0.82 (95 % CI: 0.71-0.93). SHAP analysis indicated that heterogeneity-related texture features were dominant contributors to model predictions, with many associated with the RR phenotype, while others were linked to the RS phenotype. CONCLUSION: An MRI-based radiomic signature enables non-invasive prediction of RSI-defined radiosensitivity in lower-grade glioma. Rather than offering an immediately deployable clinical tool, this study establishes a proof-of-concept radiogenomic framework demonstrating that intrinsic radiosensitivity, traditionally assessed through invasive molecular assays, can be approximated using quantitative imaging features. These findings highlight the potential of imaging-based radiosensitivity assessment and provide a foundation for future radiogenomic investigations.

Lower-grade glioma↗

PubMed2005

Sample handling for mass spectrometric proteomic investigations of human sera.

Proteomic investigations of sera are potentially of value for diagnosis, prognosis, choice of therapy, and disease activity assessment by virtue of discovering new biomarkers and biomarker patterns. Much debate focuses on the biological relevance and the need for identification of such biomarkers while less effort has been invested in devising standard procedures for sample preparation and storage in relation to model building based on complex sets of mass spectrometric (MS) data. Thus, development of standardized methods for collection and storage of patient samples together with standards for transportation and handling of samples are needed. This requires knowledge about how sample processing affects MS-based proteome analyses and thereby how nonbiological biased classification errors are avoided. In this study, we characterize the effects of sample handling, including clotting conditions, storage temperature, storage time, and freeze/thaw cycles, on MS-based proteomics of human serum by using principal components analysis, support vector machine learning, and clustering methods based on genetic algorithms as class modeling and prediction methods. Using spiking to artificially create differentiable sample groups, this integrated approach yields data that--even when working with sample groups that differ more than may be expected in biological studies--clearly demonstrate the need for comparable sampling conditions for samples used for modeling and for the samples that are going into the test set group. Also, the study emphasizes the difference between class prediction and class comparison studies as well as the advantages and disadvantages of different modeling methods.

Humans↗

PubMedDate not supplied

Diagnosing anorexia based on partial least squares, back propagation neural network, and support vector machines.

Support vector machine (SVM), as a novel type of learning machine, for the first time, was used to develop a predictive model for early diagnosis of anorexia. It was based on the concentration of six elements (Zn, Fe, Mg, Cu, Ca, and Mn) and the age extracted from 90 cases. Compared with the results obtained from two other classifiers, partial least squares (PLS) and back-propagation neural network (BPNN), the SVM method exhibited the best whole performance. The accuracies for the test set by PLS, BPNN, and SVM methods were 52%, 65%, and 87%, respectively. Moreover, the models we proposed could also provide some insight into what factors were related to anorexia.

Anorexia↗

PubMed2006

Category dimensionality and feature knowledge: when more features are learned as easily as fewer.

Three experiments compared the learning of lower-dimensional family resemblance categories (4 dimensions) with the learning of higher-dimensional ones (8 dimensions). Category-learning models incorporating error-driven learning, hypothesis testing, or limited capacity attention predict that additional dimensions should either increase learning difficulty or decrease learning of individual features. Contrary to these predictions, the experiments showed no slower learning of high-dimensional categories; instead, subjects learned more features from high-dimensional categories than from low-dimensional categories. This result obtained both in standard learning with feedback and in noncontingent, observational learning. These results show that rather than interfering with learning, categories with more dimensions cause individuals to learn more. The authors contrast the learning of family resemblance categories with learning in classical conditioning and probability learning paradigms, in which competition among features is well documented.

Concept Formation↗

PubMed1985

Attributional style and depression.

The study aimed to test the prediction, arising out of Abramson et al.'s (1978) reformulated learned helplessness model of depression, that depressed individuals have significantly different attributions about the causes of events from non-depressed individuals. No support was found for this hypothesis when comparing a depressed psychiatric sample with a matched normal group. Several hypotheses are offered to account for the failure to agree with previous studies.

Adult↗

PubMed2006

A sensorimotor map: modulating lateral interactions for anticipation and planning.

Experimental studies of reasoning and planned behavior have provided evidence that nervous systems use internal models to perform predictive motor control, imagery, inference, and planning. Classical (model-free) reinforcement learning approaches omit such a model; standard sensorimotor models account for forward and backward functions of sensorimotor dependencies but do not provide a proper neural representation on which to realize planning. We propose a sensorimotor map to represent such an internal model. The map learns a state representation similar to self-organizing maps but is inherently coupled to sensor and motor signals. Motor activations modulate the lateral connection strengths and thereby induce anticipatory shifts of the activity peak on the sensorimotor map. This mechanism encodes a model of the change of stimuli depending on the current motor activities. The activation dynamics on the map are derived from neural field models. An additional dynamic process on the sensorimotor map (derived from dynamic programming) realizes planning and emits corresponding goal-directed motor sequences, for instance, to navigate through a maze.

Action Potentials↗

PubMed2006

Experiments with AdaBoost.RT, an improved boosting scheme for regression.

The application of boosting technique to regression problems has received relatively little attention in contrast to research aimed at classification problems. This letter describes a new boosting algorithm, AdaBoost.RT, for regression problems. Its idea is in filtering out the examples with the relative estimation error that is higher than the preset threshold value, and then following the AdaBoost procedure. Thus, it requires selecting the suboptimal value of the error threshold to demarcate examples as poorly or well predicted. Some experimental results using the M5 model tree as a weak learning machine for several benchmark data sets are reported. The results are compared to other boosting methods, bagging, artificial neural networks, and a single M5 model tree. The preliminary empirical comparisons show higher performance of AdaBoost.RT for most of the considered data sets.

Algorithms↗