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Results for “Predictive Learning Models”

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At least 217 records · Page 12Linked to original sources

PubMed1995

Neural pattern formation via a competitive Hebbian mechanism.

In this contribution we investigate a simple pattern formation process [9,10] based on Hebbian learning and competitive interactions within cortex. This process generates spatial representations of afferent (sensory) information which strongly resemble patterns of response properties of neurons commonly called brain maps. For one of the most thoroughly studied phenomena in cortical development, the formation of topographic maps, orientation and ocular dominance columns in macaque striate cortex, the process, for example, generates the observed patterns of receptive field properties including the recently described correlations between orientation preference and ocular dominance. Competitive Hebbian learning has not only proven to be a useful concept in the understanding of development and plasticity in several brain areas, but the underlying principles have have been successfully applied to problems in machine learning [22]. The model's universality, simplicity, predictive power, and usefulness warrants a closer investigation.

Animals↗

PubMed1984

Influence of gender constancy and social power on sex-linked modeling.

Competing predictions derived from cognitive-developmental theory and social learning theory concerning sex-linked modeling were tested. In cognitive-developmental theory, gender constancy is considered a necessary prerequisite for the emulation of same-sex models, whereas according to social learning theory, sex-role development is promoted through a vast system of social influences with modeling serving as a major conveyor of sex role information. In accord with social learning theory, even children at a lower level of gender conception emulated same-sex models in preference to opposite-sex ones. Level of gender constancy was associated with higher emulation of both male and female models rather than operating as a selective determinant of modeling. This finding corroborates modeling as a basic mechanism in the sex-typing process. In a second experiment we explored the limits of same-sex modeling by pitting social power against the force of collective modeling of different patterns of behavior by male and female models. Social power over activities and rewarding resources produced cross-sex modeling in boys, but not in girls. This unexpected pattern of cross-sex modeling is explained by the differential sex-typing pressures that exist for boys and girls and socialization experiences that heighten the attractiveness of social power for boys.

Child Development↗

PubMed2025

Integrating Imaging-Derived Clinical Endotypes with Plasma Proteomics and External Polygenic Risk Scores Enhances Coronary Microvascular Disease Risk Prediction.

Coronary microvascular disease (CMVD) is an underdiagnosed but significant contributor to the burden of ischemic heart disease, characterized by angina and myocardial infarction. The development of risk prediction models such as polygenic risk scores (PRS) for CMVD has been limited by a lack of large-scale genome-wide association studies (GWAS). However, there is significant overlap between CMVD and enrollment criteria for coronary artery disease (CAD) GWAS. In this study, we developed CMVD PRS models by selecting variants identified in a CMVD GWAS and applying weights from an external CAD GWAS, using CMVD-associated loci as proxies for the genetic risk. We integrated plasma proteomics, clinical measures from perfusion PET imaging, and PRS to evaluate their contributions to CMVD risk prediction in comprehensive machine and deep learning models. We then developed a novel unsupervised endotyping framework for CMVD from perfusion PET-derived myocardial blood flow data, revealing distinct patient subgroups beyond traditional case-control definitions. This imaging-based stratification substantially improved classification performance alongside plasma proteomics and PRS, achieving AUROCs between 0.65 and 0.73 per class, significantly outperforming binary classifiers and existing clinical models, highlighting the potential of this stratification approach to enable more precise and personalized diagnosis by capturing the underlying heterogeneity of CMVD. This work represents the first application of imaging-based endotyping and the integration of genetic and proteomic data for CMVD risk prediction, establishing a framework for multimodal modeling in complex diseases.

Cardiovascular Disease↗

PubMed2026

Predicting food taste with bound-driven optimization.

The prediction of sensory attributes from ingredient-level formulations is an emerging challenge at the intersection of food science and artificial intelligence. We address the fundamental question of whether the taste of a food can be predicted from its ingredients by treating recipes as composite materials. We apply Hashin-Shtrikman (HS) and Reuss-Voigt (RV) bounds, techniques originally developed for elastic moduli, as a null-hypothesis additive baseline for five taste dimensions (sweetness, sourness, bitterness, umami, saltiness) on a curated dataset of 70 recipes decomposed into 115 distinct ingredients scored against a library of 209 ingredient-level taste references with trained-panel ground truth. This baseline systematically under-predicts perceived taste: 77% of actual taste values exceeded the HS upper bound, with the exceedance rate ranging from 26% (bitterness) to 97% (saltiness). We traced this gap to specific processing chemistry (Maillard reactions, caramelization, evaporative concentration, protein hydrolysis, and nucleotide synergy) and introduced a hybrid model that augments the HS baseline with eight chemistry-proxy features encoding these mechanisms. Our results show that our interpretable hybrid model eliminates the systematic bias and reduces mean absolute error by 27%-62% for sweetness, sourness, umami, and saltiness while using only 10 interpretable features, achieving performance comparable to a black-box Lasso regression on 115 per-ingredient features. We further demonstrate constrained inverse design via Differential Evolution, recovering ingredient formulations that match target taste profiles subject to compositional bounds. Our work demonstrates how key chemical processes during food preparation can inform and augment physics-based and machine learning models, providing a quantitative fingerprint of processing chemistry's contribution to taste perception and paving the way for model-driven food formulation with targeted sensory characteristics.

Composite material bounds↗

PubMed2000

Cerebellar learning of accurate predictive control for fast-reaching movements.

Long conduction delays in the nervous system prevent the accurate control of movements by feedback control alone. We present a new, biologically plausible cerebellar model to study how fast arm movements can be executed in spite of these delays. To provide a realistic test-bed of the cerebellar neural model, we embed the cerebellar network in a simulated biological motor system comprising a spinal cord model and a six-muscle two-dimensional arm model. We argue that if the trajectory errors are detected at the spinal cord level, memory traces in the cerebellum can solve the temporal mismatch problem between efferent motor commands and delayed error signals. Moreover, learning is made stable by the inclusion of the cerebello-nucleo-olivary loop in the model. It is shown that the cerebellar network implements a nonlinear predictive regulator by learning part of the inverse dynamics of the plant and spinal circuit. After learning, fast accurate reaching movements can be generated.

Arm↗

PubMedDate not supplied

Backward inhibitory learning in honeybees: a behavioral analysis of reinforcement processing.

One class of theoretical accounts of associative learning suggests that reinforcers are processed according to learning rules that minimize the predictive error between the expected strength of future reinforcement and its actual strength. The omission of reinforcement in a situation where it is expected leads to inhibitory learning of stimuli indicative for such a violation of the prediction. There are, however, results indicating that inhibitory learning can also be induced by other mechanisms. Here, we present data from olfactory reward conditioning in honeybees that show that (1) one- and multiple-trial backward conditioning results in conditioned inhibition (CI); (2) the inhibition is maximal for a 15-sec interval between US and CS; (3) there is a nonmonotonic dependency on the degree of CI from the US-CS interval during backward pairing; and (4) the prior association of context stimuli with reinforcement is not necessary for the development of CI. These results cannot be explained by models that only minimize a prediction error. Rather, they are consistent with models of associative learning that, in addition, assume that learning depends on the temporal overlap of a CS with two processes, a fast excitatory and a slow inhibitory one, both evoked by a reinforcer. The fmdings from this behavioral analysis of reinforcement processing are compared with the known properties of an individual, identified neuron involved in reinforcement processing in the bee brain, to further understand the mechanisms underlying predictive reward learning.

Animals↗

PubMed2026

The Use of Deep Learning in RNA Therapeutic Development.

Ribonucleic acid (RNA)-based therapeutics have emerged as promising methods of disease treatment due to their ability to target the human genome and influence protein production, their versatility, and their relative lack of toxicity compared to other gene therapies. However, the RNA therapeutic design space is extremely large, encompassing multiple variables, including codon identities, secondary structure, and design of specific regions. RNA therapeutic optimization is difficult due to the impracticality of exploring such a vast design space experimentally. To address this limitation, deep learning methods have been employed to optimize RNA therapeutic development. In this review, we examine the application of deep learning models across three key aspects of RNA therapeutic development (RNA structure prediction, CRISPR activity, and RNA delivery), highlighting major contributions in these fields and analyzing how deep learning model architectures could affect model performance. We then discuss challenges associated with using deep learning for RNA therapeutics, such as computational and data limitations. Finally, we offer perspectives on areas for future exploration, such as emerging model architectures and methods of integration with more advanced high-throughput screening techniques. Ultimately, this review provides an overview of how deep learning is used in RNA therapeutic development and how it can evolve in the future.

Deep Learning↗

PubMed1982

Role of affective assessment in modeling aggressive behavior.

This study examines the role of affective assessment, a self-generated influence in learning acquisition, in Bandura's original modeling-of-aggression procedure. Thirty-two first- and second-grade children (both sexes) rated toys and televised acts of aggression against an inflated doll according to their personal affective preference. A matched control group of 32 children was yoked to the affective preferences of the experimental subjects. Control subjects were not shown the televised aggression. All children were then introduced to a free-play situation in which toys and an inflated doll were present. In line with Bandura's findings, we predicted that observational learning would be demonstrated across experimental and control conditions. However, in line with the tenets and previous research findings in support of logical learning theory, we predicted that children would model affectively preferred aggressive acts and toys more readily than affectively dispreferred acts and toys. The experimental predictions were supported in the data collection. Boys and girls differed significantly only in their imitation of positively rated aggressive actions and not in their imitation of negatively rated aggressive actions. The broader theoretical implications of these results, as well as the ramifications of these findings for the televised violence and aggression issue, are discussed.

Affect↗

PubMed2025

The Mycobacterium tuberculosis Transposon Sequencing Database (MtbTnDB): A Large-Scale Guide to Genetic Conditional Essentiality.

Characterizing genetic essentiality across various conditions is fundamental for understanding gene function. Transposon sequencing (TnSeq) is a powerful technique to generate genome-wide essentiality profiles in bacteria and has been extensively applied to Mycobacterium tuberculosis (Mtb). Dozens of TnSeq screens have yielded valuable insights into the biology of Mtb in vitro, inside macrophages, and in model host organisms. Despite their value, these Mtb TnSeq profiles have not been standardized or collated into a single, easily searchable database. This results in significant challenges when attempting to query and compare these resources, limiting our ability to obtain a comprehensive and consistent understanding of genetic conditional essentiality in Mtb. We address this problem by building a central repository of publicly available Mtb TnSeq screens, the Mtb transposon sequencing database (MtbTnDB). The MtbTnDB is a living resource that encompasses to date ≈150 standardized TnSeq screens, enabling open access to data, visualizations, and functional predictions through an interactive web app (www.mtbtndb.app). We conduct several statistical analyses on the complete database, such as demonstrating that (i) genes in the same genomic neighborhood have similar TnSeq profiles, and (ii) clusters of genes with similar TnSeq profiles are enriched for genes from similar functional categories. We further analyze the performance of machine learning models trained on TnSeq profiles to predict the functional annotation of orphan genes in Mtb. By facilitating the comparison of TnSeq screens across conditions, the MtbTnDB will accelerate the exploration of conditional genetic essentiality, provide insights into the functional organization of Mtb genes, and help predict gene function in this important human pathogen.

DNA Transposable Elements↗

PubMedDate not supplied

Selectional constraints: an information-theoretic model and its computational realization.

A new, information-theoretic model of selectional constraints is proposed. The strategy adopted here is a minimalist one: how far can one get making as few assumptions as possible? In keeping with that strategy, the proposed model consists of only two components: first, a fairly generic taxonomic representation of concepts, and, second, a probabilistic formalization of selectional constraints defined in terms of that taxonomy, computed on the basis of simple, observable frequencies of co-occurrence between predicates and their arguments. Unlike traditional selection restrictions, the information-theoretic approach avoids empirical problems associated with definitional theories of word meaning, accommodates the observation that semantic anomaly often appears to be a matter of degree, and provides an account of how selectional constraints can be learned. A computational implementation of the model "learns" selectional constraints from collections of naturally occurring text; the predictions of the implemented model are evaluated against judgments elicited from adult subjects, and used to explore the way that arguments are syntactically realized for a class of English verbs. The paper concludes with a discussion of the role of selectional constraints in the acquisition of verb meaning.

Adult↗

PubMed1986

Validation criteria for animal models of human mental disorders: learned helplessness as a paradigm case.

Three sets of criteria are proposed for assessing animal models of human mental disorders: predictive validity (performance in the test predicts performance in the condition being modelled), face validity (phenomenological similarity) and construct validity (theoretical rationale). The problems inherent in each of these validation procedures are discussed, and their application to the learned helplessness model of depression is examined. It is concluded that whilst the model has good predictive validity, important questions about face validity remain unanswered, and construct validity has not yet been established. The distinctions between animal models and some related experimental procedures are also discussed.

Animals↗

PubMed2000

Disparity tuning as simulated by a neural net.

Previous research has suggested that the processing of binocular disparity in complex cells may be described with an energy formalism. The energy formalism allows for a representation of disparity by differences in the position or in the phase of monocular receptive subfields of binocular cells, or by combination of these two types. We studied the coding of disparities with an approach complementary to previous algorithmic investigations. Since realization of these representations is probably not genetically determined but learned during ontogeny, we used backpropagation networks to study which of these three possibilities were realized within neural nets. Three types of networks were trained with noise patterns in analogy to the three types of energy models. The networks learned the task and generalized to untrained correlated noise pattern input. Outputs were broadly tuned to spatial frequency and did not respond to anti-correlated noise patterns. Although the energy model was not explicitly implemented, we could analyze the outputs of the networks using predictions of the energy formalism. After learning was completed, the model neurons preferred position shifts over phase shifts in representing disparity. We discuss the general meaning of these findings and the correspondences and deviations between the energy model, V1 neurons, and our networks.

Computer Simulation↗

PubMed2025

Deep Learning on Histologic Slides Accurately Predicts Consensus Molecular Subtypes and Spatial Heterogeneity in Colon Cancer.

Colon cancer (CC) is the third most prevalent cancer type. It is highly heterogeneous, particularly in terms of molecular profiles, which have both prognostic and predictive impacts on the treatment efficacy. However, CC treatment in adjuvant situations is currently guided solely by T and N staging. In this context, consensus molecular subtypes (CMSs) were introduced to stratify patients with CC based on molecular profiles. Recent studies have shown that CMS can be heterogeneous in CC, leading to a worse prognosis. This study focused on predicting CMS and its heterogeneity in CC using deep learning on digitized hematoxylin and eosin ± saffron-stained whole-slide images. Data and whole-slide images of 1996 patients from the PETACC-8, The Cancer Genome Atlas-COAD, and PRODIGE-13 cohorts were used. The model is trained to predict a 4-dimensional CMS vector, reflecting intratumor heterogeneity (ITH). It comprises a self-supervised model for embedding image patches into vectors and a weakly supervised model predicting CMS calls. Ground-truth CMS scores are obtained with the CMSclassifier package. Interpretability analyses are performed at the slide and patch levels. For homogeneous tumors, the model trained on PETACC-8 achieves 93.0% (±1.4%) macroaverage area under the curve in internal cross-validation and 94.4% macroaverage area under the curve in external validation over PRODIGE-13, whereas the The Cancer Genome Atlas-COAD model reaches 85.4% (±3.0%) in cross-validation and 92.4% over PRODIGE-13. The trained models also provide spatial distributions of CMS across tumor slides and associate specific histologic features with each CMS. Finally, the models are able to predict ITH. The results show that a deep learning model trained on routine histology slides is capable of providing an efficient and robust method for predicting CMS and characterizing a patient's ITH, paving the way for the routine consideration of CMS/ITH in clinical decision making in the adjuvant setting.

Humans↗

PubMed2000

Machine learning for survival analysis: a case study on recurrence of prostate cancer.

Machine learning techniques have recently received considerable attention, especially when used for the construction of prediction models from data. Despite their potential advantages over standard statistical methods, like their ability to model non-linear relationships and construct symbolic and interpretable models, their applications to survival analysis are at best rare, primarily because of the difficulty to appropriately handle censored data. In this paper we propose a schema that enables the use of classification methods--including machine learning classifiers--for survival analysis. To appropriately consider the follow-up time and censoring, we propose a technique that, for the patients for which the event did not occur and have short follow-up times, estimates their probability of event and assigns them a distribution of outcome accordingly. Since most machine learning techniques do not deal with outcome distributions, the schema is implemented using weighted examples. To show the utility of the proposed technique, we investigate a particular problem of building prognostic models for prostate cancer recurrence, where the sole prediction of the probability of event (and not its probability dependency on time) is of interest. A case study on preoperative and postoperative prostate cancer recurrence prediction shows that by incorporating this weighting technique the machine learning tools stand beside modern statistical methods and may, by inducing symbolic recurrence models, provide further insight to relationships within the modeled data.

Artificial Intelligence↗

PubMed2025

Automated Machine Learning Tools to Build Regression Models for Schizosaccharomyces pombe Omics Data.

Machine learning is a powerful tool for analyzing biological data and making useful predictions. The surge of biological data from high-throughput omics technologies has raised the need for modeling approaches capable of tackling such amounts of data, which is pivotal to understanding the nature of complex molecular systems. Here, we show how to construct a simple model using automated machine learning (AutoML) to predict protein abundance in Schizosaccharomyces pombe, using data obtained from codon usage bias and quantitative proteomics.

Machine Learning↗

PubMed2025

The signed two-space proximity model for learning representations in protein-protein interaction networks.

MOTIVATION: Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally expensive. Thus, attention has been recently drawn to machine learning approaches. Furthermore, insufficient effort has been made toward analyzing signed PPI networks, which capture both activating (positive) and inhibitory (negative) interactions. To accurately represent biological relationships, we present the Signed Two-Space Proximity Model (S2-SPM) for signed PPI networks, which explicitly incorporates both types of interactions, reflecting the complex regulatory mechanisms within biological systems. This is achieved by leveraging two independent latent spaces to differentiate between positive and negative interactions while representing protein similarity through proximity in these spaces. Our approach also enables the identification of archetypes representing extreme protein profiles. RESULTS: S2-SPM's superior performance in predicting the presence and sign of interactions in SPPI networks is demonstrated in link prediction tasks against relevant baseline methods. Additionally, the biological prevalence of the identified archetypes is confirmed by an enrichment analysis of Gene Ontology (GO) terms, which reveals that distinct biological tasks are associated with archetypal groups formed by both interactions. This study is also validated regarding statistical significance and sensitivity analysis, providing insights into the functional roles of different interaction types. Finally, the robustness and consistency of the extracted archetype structures are confirmed using the Bayesian Normalized Mutual Information (BNMI) metric, proving the model's reliability in capturing meaningful SPPI patterns. AVAILABILITY: S2-SPM is implemented and freely available under the MIT license at https://github.com/Nicknakis/S2SPM.

Protein Interaction Mapping↗

PubMed1989

Causal explanations and emotional health of women during divorce.

This study investigated (a) relationships between women's causal explanations for divorce and their present emotional health, and (b) the clinical usefulness of the Personal Stress Inventory (Ireton, 1980) as a stress assessment tool. The convenience sample consisted of 36 women ending a first marriage. Subjects were interviewed using the Tennessee Self-Concept Scale (Fitts, 1965), the Personal Stress Inventory, and a causal explanations questionnaire. Results indicated that causal explanations did predict self-esteem and emotional distress under conditions suggested by the reformulated learned helplessness model. The Personal Stress Inventory includes an emotional distress subscale that predicted self-esteem, self-perceptions of coping ability, and overall concerns about wellness/energy.

Adaptation, Psychological↗

PubMed2025

Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques.

Individualized prediction of cancer drug sensitivity is of vital importance in precision medicine. While numerous predictive methodologies for cancer drug response have been proposed, the precise prediction of an individual patient's response to drug and a thorough understanding of differences in drug responses among individuals continue to pose significant challenges. This study introduced a deep learning model PASO, which integrated transformer encoder, multi-scale convolutional networks and attention mechanisms to predict the sensitivity of cell lines to anticancer drugs, based on the omics data of cell lines and the SMILES representations of drug molecules. First, we use statistical methods to compute the differences in gene expression, gene mutation, and gene copy number variations between within and outside biological pathways, and utilized these pathway difference values as cell line features, combined with the drugs' SMILES chemical structure information as inputs to the model. Then the model integrates various deep learning technologies multi-scale convolutional networks and transformer encoder to extract the properties of drug molecules from different perspectives, while an attention network is devoted to learning complex interactions between the omics features of cell lines and the aforementioned properties of drug molecules. Finally, a multilayer perceptron (MLP) outputs the final predictions of drug response. Our model exhibits higher accuracy in predicting the sensitivity to anticancer drugs comparing with other methods proposed recently. It is found that PARP inhibitors, and Topoisomerase I inhibitors were particularly sensitive to SCLC when analyzing the drug response predictions for lung cancer cell lines. Additionally, the model is capable of highlighting biological pathways related to cancer and accurately capturing critical parts of the drug's chemical structure. We also validated the model's clinical utility using clinical data from The Cancer Genome Atlas. In summary, the PASO model suggests potential as a robust support in individualized cancer treatment. Our methods are implemented in Python and are freely available from GitHub (https://github.com/queryang/PASO).

Deep Learning↗