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PubMed1992

A practical application of neural network analysis for predicting outcome of individual breast cancer patients.

It has been previously shown that Neural Networks can be trained to recognize individual breast cancer patients at high and low risk for recurrent disease and death. This paper expands on the initial investigation and shows that by coding time as one of the prognostic variables, a Neural Network can use censored survival data to predict patient outcome over time. In this demonstration a Neural Network was trained, tested, and validated using censored survival data from a group of 1373 patients with node-positive breast cancer. The Neural Network method predicted patient outcome as accurately as Cox Regression modeling. The final Neural Network model can be presented with a patient's prognostic information and make a series of predictions about probability of relapse at different times of follow-up, allowing one to draw survival probability curves for individual patients.

Adult↗
PubMed1992

Review of neural network applications in medical imaging and signal processing.

The current applications of neural networks to in vivo medical imaging and signal processing are reviewed. As is evident from the literature neural networks have already been used for a wide variety of tasks within medicine. As this trend is expected to continue this review contains a description of recent studies to provide an appreciation of the problems associated with implementing neural networks for medical imaging and signal processing.

Diagnostic Imaging↗
PubMed1992

New method of automated sleep quantification.

Since its discovery some 50 years ago, the electro-encephalogram (EEG) has formed the basis for classification of sleep into several stages, either laboriously performed by visual examination of the EEG and related signals or, more recently, by automated techniques. Both visual scoring and most automated analyses are highly subjective and rely on application of a predefined set of rules. A method of analysing the EEG which requires no such application of rules and aims to give some indication of the dynamics of sleep in humans is proposed in the paper.

Adult↗
PubMed1992

Automated interictal EEG spike detection using artificial neural networks.

Feed-forward, error-back-propagation artificial neural networks were applied to recognition of epileptiform patterns in the EEG. The inherent network properties of generalization and variability tolerance were effective in identifying wave forms that differed from the training patterns but still maintained 'epileptiform' spatio-temporal characteristics. The certainty of recognition was measured as a continuous function with a range of 0-1. Two levels of certainty (0.825 and 0.900) were used to indicate recognition of spikes and sharp waves (SSW). An average 94.2% (+/- 7.3) of the SSW were recognized; 20.9% (+/- 22.9) of all recognized SSW were false-positive recognitions. The time required for pattern recognition was well within the time required for digitizing the analogue data. This study provides evidence that neural network technology is, in principle, an effective pattern recognition strategy for identification of epileptiform transients in the EEG. The analysis is sufficiently rapid to be of potential value as a strategy for data reduction of long recordings stored on bulk media.

Electroencephalography↗
PubMed1992

Prediction of the side of hand movements from single-trial multi-channel EEG data using neural networks.

Thirty channels of EEG data were recorded prior to voluntary right or left hand movements. Event-related desynchronization (ERD) was quantified in the 8-10 Hz and 10-12 Hz bands in single-trial data and used as training input for a neural network comprised of a learning vector quantizer (LVQ). After a training period, the network was able to predict the side of hand movement from single-trial EEG data recorded prior to movement onset.

Brain↗
PubMed1992

The use of artificial neural networks to estimate speech intelligibility from acoustic variables: a preliminary analysis.

Previous research has used regression analysis to attempt to predict the intelligibility of hearing-impaired speakers from acoustic speech parameters. Improvement of prediction may be achieved by the use of computerized artificial neural networks to process mathematically the acoustic input variables as part of the intelligibility process. A preliminary scheme for estimating speech intelligibility from acoustic parameters using a neural network is outlined and preliminary data illustrate its use.

Adult↗
PubMed2025

Comparative analysis of convolutional neural network models for the histopathological differentiation of acinic cell carcinoma and secretory carcinoma.

OBJECTIVE: Although artificial intelligence tools show promise for enhancing the diagnosis of head and neck lesions, few studies have tested these resources for the microscopic diagnosis of salivary gland tumors. Specifically, the microscopic differentiation between acinic cell carcinoma and secretory carcinoma has never been addressed in this context. Therefore, this exploratory study aimed to comparatively evaluate the feasibility of applying convolutional neural networks for the microscopic differentiation between acinic cell carcinomas and secretory carcinomas. METHODS: A cross-sectional study using whole-slide images from 46 patients with acinic cell carcinoma (n = 26) or secretory carcinoma (n = 20) was conducted. Eight CNNs (ResNet-50, InceptionV3, VGG16, Xception, MobileNet, DenseNet121, EfficientNetB0, and EfficientNetV2B0) were trained and evaluated for accuracy, sensitivity, specificity, F1-score, and AUC. Performance was measured in training, validation, and test subsets. Accuracy and loss curves were also presented. RESULTS: InceptionV3 demonstrated the best overall performance, with the lowest loss (1.39), highest accuracy (0.81), sensitivity (0.90), and F1-score (0.81). VGG16 achieved the highest AUC (0.86) and precision (0.77). DenseNet121 showed the lowest performance in terms of accuracy (0.65) and F1-Score (0.52), but the highest specificity (0.85). CONCLUSION: This proof-of-concept study suggests that convolutional neural networks may be feasible tools to support the microscopic differentiation between acinic cell carcinoma and secretory carcinoma. The performance of these models critically depends on the size of the dataset and the quality of annotations. The findings should be interpreted cautiously given the limited dataset and potential sources of bias. Further validation with larger, multicenter datasets is needed before any clinical application can be considered.

Humans↗
PubMed2025

A multi-modal transformer for cell type-agnostic regulatory predictions.

Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns generalizable representations of genomic sequence and cell type-specific chromatin accessibility through a masked accessibility-based pre-training objective. Following pre-training, EpiBERT can be fine-tuned for gene expression prediction, achieving accuracy comparable to the sequence-only Enformer model, while also being able to generalize to unobserved cell states. The learned representations are interpretable and useful for predicting chromatin accessibility quantitative trait loci (caQTLs), regulatory motifs, and enhancer-gene links. Our work represents a step toward improving the generalization of sequence-based deep neural networks in regulatory genomics.

Humans↗
PubMed1992

Analysis of the clinical variables driving decision in an artificial neural network trained to identify the presence of myocardial infarction.

STUDY OBJECTIVE: To determine which clinical variables drive the output of an artificial neural network trained to identify the presence of myocardial infarction. DESIGN: Partial output analysis. SETTING: Tertiary university teaching center. PARTICIPANTS: Seven hundred six patients more than 18 years old presenting with anterior chest pain. MEASUREMENTS: Differential network output analysis. MAIN RESULTS: A methodology was developed as the first step in measuring the impact input clinical variables have on the output (diagnosis) of an artificial neural network trained to identify the presence of acute myocardial infarction. The methodology revealed that the network used the presence of ECG findings, as well as the presence of rales, syncope, jugular venous distension, response to trinitroglycerin, and nausea and vomiting, as major predictive sources. Although this first-step analysis studied individual variables, it must be stated that the network comes to clinical closure based on the settings of all variables in a pattern and that the impact of a single variable cannot be taken out of the context of a pattern. CONCLUSION: An artificial neural network trained to recognize the presence of myocardial infarction appears to place diagnostic importance on clinical variables that have not been shown previously to be highly predictive for infarction.

Adolescent↗
PubMed1992

Relationships between secondary structure fractions for globular proteins. Neural network analyses of crystallographic data sets.

The relationship between the fractions of protein secondary structural components as determined from X-ray crystallographic data by the procedures of Kabsch and Sander (KS) and of Levitt and Greer (LG) is analyzed by neural network analysis of these two tabulations of literature data. A linear relationship between the KS and LG reductions of X-ray data to secondary structure descriptors is demonstrated by a regression analysis of the relationships between these sets of structural parameters. Back-propagation neural network analysis was then used to derive equations for determination of the most probable fractions of beta-sheet, bend, turn, and "other" conformations given the fraction of alpha-helix in a globular protein. The deviation of the X-ray values for beta-sheet from that determined with these equations was shown to have a variance that exponentially decreased with increasing fraction of alpha-helix. A second neural network analysis showed that knowledge of both the alpha-helical and beta-sheet fractions in a protein significantly reduces the uncertainty in prediction of the other components of the secondary structure. These analyses provide insight into the nature of the data sets derived from crystal structures. Since these complications of crystal structure data are commonly used as reference information for quantitative evaluation of spectra (for example, FTIR, Raman, and electronic or vibrational circular dichroism) in terms of secondary structure, such internal correlations in the reference sets may have significant effects on the stability of spectroscopic analyses derived from them.

Mathematics↗
PubMed2021

Deep generative neural network for accurate drug response imputation.

Drug response differs substantially in cancer patients due to inter- and intra-tumor heterogeneity. Particularly, transcriptome context, especially tumor microenvironment, has been shown playing a significant role in shaping the actual treatment outcome. In this study, we develop a deep variational autoencoder (VAE) model to compress thousands of genes into latent vectors in a low-dimensional space. We then demonstrate that these encoded vectors could accurately impute drug response, outperform standard signature-gene based approaches, and appropriately control the overfitting problem. We apply rigorous quality assessment and validation, including assessing the impact of cell line lineage, cross-validation, cross-panel evaluation, and application in independent clinical data sets, to warrant the accuracy of the imputed drug response in both cell lines and cancer samples. Specifically, the expression-regulated component (EReX) of the observed drug response achieves high correlation across panels. Using the well-trained models, we impute drug response of The Cancer Genome Atlas data and investigate the features and signatures associated with the imputed drug response, including cell line origins, somatic mutations and tumor mutation burdens, tumor microenvironment, and confounding factors. In summary, our deep learning method and the results are useful for the study of signatures and markers of drug response.

Antineoplastic Agents↗
PubMed2025

AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.

Humans↗
PubMed2025

Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.

MOTIVATION: The wide range of cellular complexity created by multicellular organisms is due in large part to the intricate and synergistic interplay of regulatory complexes throughout the eukaryotic genome. These regulatory elements "enhance" specific gene programs and have been shown to operate in diverse networks that are distinct across cell states of the same organism. Attempts to characterize and predict enhancers have typically focused on leveraging information-dense DNA sequence in parallel with epigenomic assays. We examined the viability of enhancer prediction using only a minimal set of epigenomic datasets without direct DNA information. RESULTS: We demonstrate that chromatin datasets are sufficient to identify enhancers genome-wide with high accuracy. By training networks leveraging data from multiple cell types simultaneously, we generated a cell-type invariant enhancer prediction platform that utilized only the patterns of protein binding for inference. We also showed the utility of swarm-based adversarial attacks [adversarial particle swarm optimization (APSO)] to deconvolute trained genomic neural networks for the first time. Critically, unlike saliency mapping or other game-theory based approaches, APSO is completely network-architecture independent and can be applied to any prediction engine to derive the features that drive inference. AVAILABILITY AND IMPLEMENTATION: All software and code for data downloading, processing, enhancer inference, eXplainable AI (XAI), and complete figure generation are publicly available on GitHub at https://github.com/EpiGenomicsCode/ChromEnhancer and Zenodo at https://doi.org/10.5281/zenodo.15652797.

Enhancer Elements, Genetic↗
PubMed2025

DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data.

MOTIVATION: The spatial organization of chromatin is fundamental to gene regulation and essential for proper cellular function. The Hi-C technique remains the leading method for unraveling 3D genome structures, but the limited availability of high-resolution (HR) Hi-C data poses significant challenges for comprehensive analysis. Deep learning models have been developed to predict HR Hi-C data from low-resolution counterparts. Early Convolutional Neural Network (CNN)-based models improved resolution but struggled with issues like blurring and capturing fine details. In contrast, Generative Adversarial Network (GAN)-based methods encountered difficulties in maintaining diversity and generalization. Additionally, most existing algorithms perform poorly in cross-cell line generalization, where a model trained on one cell type is used to enhance HR data in another cell type. RESULTS: In this work, we propose Dilated Cascading Residual Network (DiCARN) to overcome these challenges and improve Hi-C data resolution. DiCARN leverages dilated convolutions and cascading residuals to capture a broader context while preserving fine-grained genomic interactions. Additionally, we incorporate DNase-seq data into our model, providing a robust framework that demonstrates superior generalizability across cell lines in HR Hi-C data reconstruction. AVAILABILITY AND IMPLEMENTATION: DiCARN is publicly available at https://github.com/OluwadareLab/DiCARN.

Chromatin↗
PubMed2026

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset.

SUMMARY: Image-based spatial transcriptomics (iST) deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network (GNN) models are promising methods for capturing the complex molecular and cellular phenotypes in tissues at single-transcript and single-cell levels. A key application of GNNs is the detection of spatial domains or niches, that is, groups of molecules and/or cells that collaboratively work together to produce complex phenotypes. Due to the vast number of detected transcripts in (iST) dataset, applying GNNs on RNA molecule graphs is not trivial. We present a Python package, SpatialRNA, for easy (sub)graph generation from tissue samples and provide comprehensive tutorials for convenient and efficient application of Graph Neural Network models under the PyG framework. This highly scalable tool comprehensively segments tissue into spatial domains, aiding in biological interpretation of iST data and its underlying molecular microenvironments. AVAILABILITY AND IMPLEMENTATION: The SpatialRNA package is freely accessible from online repository https://github.com/ruqianl/spatialrna and can be installed via pip. Comprehensive tutorials, guidance on parameter selection, and complete workflows of case studies are available from the documentation website https://ruqianl.github.io/spatialrna_docs/, and uploaded on Zenodo with a DOI 10.5281/zenodo.17339575.

Neural Networks, Computer↗