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At least 19 recordsLinked to original sources
PubMed2025

Comparing artificial and convolutional neural networks with traditional models for Genomic prediction in wheat.

With the rapid development of sequencing technology, the application of genomic prediction has become more and more common in breeding schemes of livestocks and crops. Selecting an appropriate statistical model is of central importance to achieve high prediction accuracy. Recently, machine learning models have been expected to upgrade genomic prediction into a new era. However, the perspective still suffers from lack of evidence that machine learning models can generally outperform the traditional ones on empirical data sets. In this study, we compared two machine learning models based on artificial neural network (ANN) and convolutional neural network (CNN) with four traditional models, including genomic best linear unbiased prediction (GBLUP), Bayesian ridge regression (BRR), BayesA and BayesB, using three published data sets for grain yield in wheat. For each model, we considered two variants: modeling and ignoring the genotype-by-environment ([Formula: see text]) interaction. In the comparison, we considered two strategies of cross-validation: predicting genotypes that have not been evaluated in any environment (CV1) and predicting genotypes that have been tested in other environments (CV2). Our results showed that traditional Bayesian models (BayesA, BayesB, and BRR) outperformed GBLUP, ANN and CNN when considering [Formula: see text] interaction. The accuracies of ANN and CNN were higher than traditional models only in CV1 and when [Formula: see text] interaction was ignored. It was also found that the performance of the two machine learning models was significantly affected by the interaction between the CV strategy and the way of treating the [Formula: see text] interaction, while that of the four traditional models was only influenced by whether the [Formula: see text] interaction was considered or not. Thus, machine learning models can be a powerful complementary to the traditional ones and their superiority may depend on the prediction scenario. Among the two machine learning models, we observed that the accuracy of ANN was higher than CNN in most cases, indicating that it is still challenging to adapt complex machine learning models such as CNN to genomic prediction.

ANN↗
PubMed2002

A multiple circular path convolution neural network system for detection of mammographic masses.

A multiple circular path convolution neural network (MCPCNN) architecture specifically designed for the analysis of tumor and tumor-like structures has been constructed. We first divided each suspected tumor area into sectors and computed the defined mass features for each sector independently. These sector features were used on the input layer and were coordinated by convolution kernels of different sizes that propagated signals to the second layer in the neural network system. The convolution kernels were trained, as required, by presenting the training cases to the neural network. In this study, randomly selected mammograms were processed by a dual morphological enhancement technique. Radiodense areas were isolated and were delineated using a region growing algorithm. The boundary of each region of interest was then divided into 36 sectors using 36 equi-angular dividers radiated from the center of the region. A total of 144 Breast Imaging-Reporting and Data System-based features (i.e., four features per sector for 36 sectors) were computed as input values for the evaluation of this newly invented neural network system. The overall performance was 0.78-0.80 for the areas (Az) under the receiver operating characteristic curves using the conventional feed-forward neural network in the detection of mammographic masses. The performance was markedly improved with Az values ranging from 0.84 to 0.89 using the MCPCNN. This paper does not intend to claim the best mass detection system. Instead it reports a potentially better neural network structure for analyzing a set of the mass features defined by an investigator.

Breast Neoplasms↗
PubMed2005

Efficient training algorithms for a class of shunting inhibitory convolutional neural networks.

This article presents some efficient training algorithms, based on first-order, second-order, and conjugate gradient optimization methods, for a class of convolutional neural networks (CoNNs), known as shunting inhibitory convolution neural networks. Furthermore, a new hybrid method is proposed, which is derived from the principles of Quickprop, Rprop, SuperSAB, and least squares (LS). Experimental results show that the new hybrid method can perform as well as the Levenberg-Marquardt (LM) algorithm, but at a much lower computational cost and less memory storage. For comparison sake, the visual pattern recognition task of face/nonface discrimination is chosen as a classification problem to evaluate the performance of the training algorithms. Sixteen training algorithms are implemented for the three different variants of the proposed CoNN architecture: binary-, Toeplitz- and fully connected architectures. All implemented algorithms can train the three network architectures successfully, but their convergence speed vary markedly. In particular, the combination of LS with the new hybrid method and LS with the LM method achieve the best convergence rates in terms of number of training epochs. In addition, the classification accuracies of all three architectures are assessed using ten-fold cross validation. The results show that the binary- and Toeplitz-connected architectures outperform slightly the fully connected architecture: the lowest error rates across all training algorithms are 1.95% for Toeplitz-connected, 2.10% for the binary-connected, and 2.20% for the fully connected network. In general, the modified Broyden-Fletcher-Goldfarb-Shanno (BFGS) methods, the three variants of LM algorithm, and the new hybrid/LS method perform consistently well, achieving error rates of less than 3% averaged across all three architectures.

Algorithms↗
PubMed2025

Detecting Interspecific Positive Selection Using Convolutional Neural Networks.

Traditional statistical methods using maximum likelihood and Bayesian inference can detect positive selection from an interspecific phylogeny and a codon sequence alignment based on model assumptions, but they are prone to false positives due to alignment errors and can lack power. These problems are particularly pronounced when faced with high levels of indels and divergence. To address these issues, we trained and tested convolutional neural network models on simulated data and achieved higher accuracy in detecting selection across a specific range of phylogenetic scenarios and evolutionary modes. This advantage is particularly evident when performing inference on noisy data prone to misalignments. Our method shows some ability to account for these errors, where most statistical frameworks fail to do so in a tractable manner. We explore the generalizability of our convolutional neural network models to unseen evolutionary scenarios and identify future avenues to achieve broader utility. Once trained, our convolutional neural network model is faster at test time, making it a scalable alternative to traditional statistical methods for large-scale, multigene analyses. In addition to binary classification (inference of the presence or absence of positive selection during the evolution of the sequences), we use saliency maps to understand what the model learns and observe how this could be leveraged for sitewise inference of positive selection.

Neural Networks, Computer↗
PubMed2006

A convolutional neural network approach for objective video quality assessment.

This paper describes an application of neural networks in the field of objective measurement method designed to automatically assess the perceived quality of digital videos. This challenging issue aims to emulate human judgment and to replace very complex and time consuming subjective quality assessment. Several metrics have been proposed in literature to tackle this issue. They are based on a general framework that combines different stages, each of them addressing complex problems. The ambition of this paper is not to present a global perfect quality metric but rather to focus on an original way to use neural networks in such a framework in the context of reduced reference (RR) quality metric. Especially, we point out the interest of such a tool for combining features and pooling them in order to compute quality scores. The proposed approach solves some problems inherent to objective metrics that should predict subjective quality score obtained using the single stimulus continuous quality evaluation (SSCQE) method. This latter has been adopted by video quality expert group (VQEG) in its recently finalized reduced referenced and no reference (RRNR-TV) test plan. The originality of such approach compared to previous attempts to use neural networks for quality assessment, relies on the use of a convolutional neural network (CNN) that allows a continuous time scoring of the video. Objective features are extracted on a frame-by-frame basis on both the reference and the distorted sequences; they are derived from a perceptual-based representation and integrated along the temporal axis using a time-delay neural network (TDNN). Experiments conducted on different MPEG-2 videos, with bit rates ranging 2-6 Mb/s, show the effectiveness of the proposed approach to get a plausible model of temporal pooling from the human vision system (HVS) point of view. More specifically, a linear correlation criteria, between objective and subjective scoring, up to 0.92 has been obtained on a set of typical TV videos.

Algorithms↗
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

Development and validation of a deep learning model based on cascade mask regional convolutional neural network to noninvasively and accurately identify human round spermatids.

INTRODUCTION: The difficulty of identifying human round spermatids (hRSs) has impeded applications of the human round spermatid injection (ROSI) technique. RSs can be accurately screened through flow cytometric analysis utilizing the Hoechst fluorescence profile reflecting DNA, but this method is not suitable for isolating hRSs due to the toxicity associated with Hoechst staining. OBJECTIVE: To evaluate the capacity of a deep learning model grounded in a cascade mask region-based convolutional neural network (R-CNN) for the noninvasive and accurate identification of hRSs. METHODS: In this study, we presented the development and validation of a deep learning model for identifying hRSs through the analysis of 3457 optical light microscope images of sorted hRSs obtained via flow cytometric analysis. The model's accuracy and specificity were evaluated by calculating the mean average precision (mAP). Furthermore, a double-blind experiment was conducted to access the reliability of the proposed model in accurately identifying hRSs. It detected the expression of protamine (PRM1) and/or peanut lectin (PNA), which are established markers for RSs. RESULTS: Our deep learning-based model demonstrated a high precision, achieving a mAP of over 0.80 for isolating hRSs in test datasets. The expression of PRM1 and/or PNA was observed in all cells noninvasively selected by our AI model during an independent double-blind test. This phenomenon confirmed the accuracy and effectiveness of the proposed model. The model's capability for noninvasive and accurate isolation of hRSs among spermatogenic cells highlighted its robustness and generalizability for clinical applications. CONCLUSION: The deep learning AI model based on a cascade R-CNN has the ability to accurately identify hRSs among spermatogenic cells. The application of this noninvasive method, which requires no additional procedures in clinical practice, is able to facilitate the widespread implementation of ROSI technique. Therefore, it can provide patients with spermatogenic arrest the opportunity to become biological fathers.

Humans↗
PubMedDate not supplied

Subject independent facial expression recognition with robust face detection using a convolutional neural network.

Reliable detection of ordinary facial expressions (e.g. smile) despite the variability among individuals as well as face appearance is an important step toward the realization of perceptual user interface with autonomous perception of persons. We describe a rule-based algorithm for robust facial expression recognition combined with robust face detection using a convolutional neural network. In this study, we address the problem of subject independence as well as translation, rotation, and scale invariance in the recognition of facial expression. The result shows reliable detection of smiles with recognition rate of 97.6% for 5600 still images of more than 10 subjects. The proposed algorithm demonstrated the ability to discriminate smiling from talking based on the saliency score obtained from voting visual cues. To the best of our knowledge, it is the first facial expression recognition model with the property of subject independence combined with robustness to variability in facial appearance.

Discrimination, Psychological↗
PubMed1995

Differentiation between nodules and end-on vessels using a convolution neural network architecture.

In recent years, many computer-aided diagnosis schemes have been proposed to assist radiologists in detecting lung nodules. The research efforts have been aimed at increasing the sensitivity while decreasing the false-positive detections on digital chest radiographs. Among the problems of reducing the number of false positives, the differentiation between nodules and end-on vessels is one of the most challenging tasks performed by computer. Most investigators have used a conventional two-stage pattern recognition approach, ie, feature extraction followed by feature classification. The performance of this approach depends totally on good feature definition in the feature extraction stage. Unfortunately, suitable feature definition and corresponding extraction implementation algorithms proved to be very difficult to define and specify. A convolution neural network (CNN) architecture, trained by direct connection to the raw image is proposed to tackle the problem. The CNN, which uses locally responsive activation function, is directly and locally connected to the raw image. The performance of the CNN is evaluated in comparison to an expert radiologist. We used the receiver operating characteristics (ROC) method with area under the curve (Az) as the performance index to evaluate all the simulation results. The CNN showed superior performance (Az = 0.99) to the radiologist's (Az = 0.83). The CNN approach can potentially be applied to other applications, such as the differentiation of film defects and microcalcifications in mammography, in which the image features are difficult to define or not known a priori.

Algorithms↗
PubMed2023

Towards mechanistic models of mutational effects: Deep learning on Alzheimer's Aβ peptide.

Deep Mutational Scanning (DMS) has enabled multiplexed measurement of mutational effects on protein properties, including kinematics and self-organization, with unprecedented resolution. However, potential bottlenecks of DMS characterization include experimental design, data quality, and depth of mutational coverage. Here, we apply deep learning to comprehensively model the mutational effect of the Alzheimer's Disease associated peptide Aβ42 on aggregation-related biochemical traits from DMS measurements. Among tested neural network architectures, Convolutional Neural Networks and Recurrent Neural Networks are found to be the most cost-effective models with high performance even under insufficiently-sampled DMS studies. While sequence features are essential for satisfactory prediction from neural networks, geometric-structural features further enhance the prediction performance. Notably, we demonstrate how mechanistic insights into phenotype may be extracted from the neural networks themselves suitably designed. This methodological benefit is particularly relevant for biochemical systems displaying a strong coupling between structure and phenotype such as the conformation of Aβ42 aggregate and nucleation, as shown here using a Graph Convolutional Neural Network (GCN) developed from the protein atomic structure input. In addition to accurate imputation of missing values (which here ranged up to 55% of all phenotype values at key residues), the mutationally-defined nucleation phenotype generated from a GCN shows improved resolution for identifying known disease-causing mutations relative to the original DMS phenotype. Our study suggests that neural network derived sequence-phenotype mapping can be exploited not only to provide direct support for protein engineering or genome editing but also to facilitate therapeutic design with the gained perspectives from biological modeling.

Alzheimer's disease↗
PubMed2025

Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.

Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data have been developed to uncover these adaptive signatures. Convolutional neural networks (CNNs) are particularly effective for this task, as they handle large data arrays while maintaining element correlations. However, shallow CNNs may miss complex patterns due to their limited capacity, while deep CNNs can capture these patterns but require extensive data and computational power. Transfer learning addresses these challenges by utilizing a deep CNN pretrained on a large dataset as a feature extraction tool for downstream classification and evolutionary parameter prediction. This approach reduces extensive training data generation requirements and computational needs while maintaining high performance. In this study, we developed TrIdent, a tool that uses transfer learning to enhance detection of adaptive genomic regions from image representations of multilocus variation. We evaluated TrIdent across various genetic, demographic, and adaptive settings, in addition to unphased data and other confounding factors. TrIdent demonstrated improved detection of adaptive regions compared to recent methods using similar data representations. We further explored model interpretability through class activation maps and adapted TrIdent to infer selection parameters for identified adaptive candidates. Using whole-genome haplotype data from European and African populations, TrIdent effectively recapitulated known sweep candidates and identified novel cancer, and other disease-associated genes as potential sweeps.

Selection, Genetic↗
PubMed2026

Non-destructive prediction of lead content in oilseed rape leaves by fluorescence hyperspectral technology based on neural network.

Based on fluorescence hyperspectral imaging (FHSI), this study targeted rapid, non-destructive quantification of lead (Pb) content in oilseed rape leaves treated with varying silicon (Si) concentrations, acquiring fluorescence spectra over the 484.43-1001.61 nm wavelength range. To optimize spectral data quality, preprocessing methods (Savitzky-Golay smoothing, first derivative, detrending) were comprehensively compared. Characteristic wavelengths were then selected via interval variable iterative shrinkage, which effectively compressed data dimensionality and reduced computational load. A hybrid SE-CL1DA model, fusing a 1D convolutional neural network, a long short-term memory network and SE attention mechanism was constructed, with Bayesian optimization tuning hyperparameters to boost stability. The BO-SE-CL1DA outperformed both traditional machine learning and insufficiently optimized deep learning model (Rp2=0.9609, RMSE = 0.0377 mg/kg, RPD = 5.1736), thus enabling accurate Pb estimation, supporting Si-regulated heavy metal stress management and facilitating agricultural contamination monitoring.

Plant Leaves↗
PubMed2026

Automated Classification of Lymphoma Subtypes From Histopathological Images Using a U-Net Deep Learning Model: Comparative Evaluation Study.

BACKGROUND: Accurate classification and grading of lymphoma subtypes are essential for treatment planning. Traditional diagnostic methods face challenges of subjectivity and inefficiency, highlighting the need for automated solutions based on deep learning techniques. OBJECTIVE: This study aimed to investigate the application of deep learning technology, specifically the U-Net model, in classifying and grading lymphoma subtypes to enhance diagnostic precision and efficiency. METHODS: In this study, the U-Net model was used as the primary tool for image segmentation integrated with attention mechanisms and residual networks for feature extraction and classification. A total of 620 high-quality histopathological images representing 3 major lymphoma subtypes were collected from The Cancer Genome Atlas and the Cancer Imaging Archive. All images underwent standardized preprocessing, including Gaussian filtering for noise reduction, histogram equalization, and normalization. Data augmentation techniques such as rotation, flipping, and scaling were applied to improve the model's generalization capability. The dataset was divided into training (70%), validation (15%), and test (15%) subsets. Five-fold cross-validation was used to assess model robustness. Performance was benchmarked against mainstream convolutional neural network architectures, including fully convolutional network, SegNet, and DeepLabv3+. RESULTS: The U-Net model achieved high segmentation accuracy, effectively delineating lesion regions and improving the quality of input for classification and grading. The incorporation of attention mechanisms further improved the model's ability to extract key features, whereas the residual structure of the residual network enhanced classification accuracy for complex images. In the test set (N=1250), the proposed fusion model achieved an accuracy of 92% (1150/1250), a sensitivity of 91.04% (1138/1250), a specificity of 89.04% (1113/1250), and an F1-score of 90% (1125/1250) for the classification of the 3 lymphoma subtypes, with an area under the receiver operating characteristic curve of 0.95 (95% CI 0.93-0.97). The high sensitivity and specificity of the model indicate strong clinical applicability, particularly as an assistive diagnostic tool. CONCLUSIONS: Deep learning techniques based on the U-Net architecture offer considerable advantages in the automated classification and grading of lymphoma subtypes. The proposed model significantly improved diagnostic accuracy and accelerated pathological evaluation, providing efficient and precise support for clinical decision-making. Future work may focus on enhancing model robustness through integration with advanced algorithms and validating performance across multicenter clinical datasets. The model also holds promise for deployment in digital pathology platforms and artificial intelligence-assisted diagnostic workflows, improving screening efficiency and promoting consistency in pathological classification.

Humans↗
PubMed2026

Deep learning-assisted, pathogenesis-informed lung histopathology scoring in preclinical mouse models of SARS-CoV-2 and influenza A infection.

INTRODUCTION: SARS-CoV-2 and influenza A virus (IAV) cause viral pneumonia, yet their lung lesions evolve with distinct spatial organization and resolution-phase architecture. In preclinical murine studies, H&E histopathology is a primary endpoint, but burden-focused semiquantitative scoring can miss pathogen- and phase-specific differences in lesion topology, compartmental involvement, inflammatory organization, and repair. We aimed to define virus- and phase-specific morphologic signatures and translate them into a practical, pathogenesis-informed scoring guide, supported by whole-slide convolutional neural network (CNN) analysis with class activation mapping (CAM). METHODS: Mice were infected under standardized conditions and evaluated during the early, peak-injury, and late phases of infection, corresponding to 2~3, 5~8, and 14 days post-infection (dpi), respectively. Lungs were assessed by H&E with semiquantitative scoring and by immunostaining to map viral antigen distribution and epithelial tropism. Whole-slide CNN models were trained for virus- and phase-specific classification, and CAM localized discriminative regions. RESULTS: Dose titration established reproducible lethal and sublethal infection conditions for both viruses. Viral antigen kinetics diverged, with SARS-CoV-2 peaking early and declining toward clearance by the resolution phase, whereas IAV peaked later and declined by the resolution phase, paralleling distinct injury-repair trajectories. CNN/CAM analysis distinguished virus- and phase-specific histologic patterns across the early, peak-injury, and resolution phases of infection and highlighted spatial signatures consistent with expert review. At the peak-injury phase, SARS-CoV-2 lungs showed broad alveolar/interstitial involvement, whereas IAV exhibited bronchocentric inflammatory organization. During the resolution phase, IAV showed prominent epithelial regeneration with remodeling-forward architecture, while SARS-CoV-2 more often retained localized residual inflammatory foci. Across both infections, tissue inflammatory composition shifted over time, with higher neutrophil representation during the peak-injury phase and a relative increase in lymphocytic representation during the resolution phase. Integrating lesion topology/distribution, edema, epithelial injury-regeneration, remodeling features, and lymphocyte predominance, we proposed a pathogen-resolved, phase-informed histopathology scoring guide with recommended evaluation windows for each model. CONCLUSION: Together, these findings define virus- and phase-specific morphologic programs that inform respiratory virus pathogenesis in mice and can be translated into practical scoring criteria for preclinical respiratory virus studies.

Animals↗
PubMed2026

[Applications and Challenges of Deep Learning in Human Genome Research].

In recent years, the advent of high-throughput omics technologies has fueled an explosive growth in human genomic data. Uncovering the latent functions within this vast data has become a significant challenge in functional genomics research. While traditional statistical methods have proved successful for analyzing smaller-scale datasets in the past, they exhibit clear limitations in analytical efficiency and integrating multi-dimensional data, struggling to meet the escalating demands of contemporary genomic analysis. The introduction of deep learning (DL) technologies offers a novel paradigm for this field. This review systematically examines the advances in applying deep learning to human genomics research. Studies demonstrate that when ample labeled data is available, discriminative DL computational methods-such as Convolutional Neural Networks (CNNs) and Long Short-Term Memory networks (LSTMs)-achieve high accuracy and efficiency in genomic variant discovery tasks. Furthermore, generative DL methods, particularly Large Language Models (LLMs) leveraging self-supervised pre-training strategies, effectively integrate complex genomic information and exhibit superior performance in functional genomic sequence annotation and gene regulation studies. This review also explores the application of LLMs in multi-omics data integration and prediction. Looking ahead, the continued accumulation of long-read sequencing and high-dimensional data is expected to enable DL technologies to integrate increasingly complex and heterogeneous genomic information, playing an increasingly crucial role in human genomics research.

Deep Learning↗
PubMed2026

Whole-Genome Deep Learning Predicts Chemotherapy Response in Colorectal Cancer.

Chemotherapy response in colorectal cancer (CRC) exhibits significant heterogeneity, with current clinical predictors failing to capture complex genomic determinants of resistance. We developed a hybrid deep learning framework integrating convolutional neural networks (CNNs) and bidirectional long short-term memory (BiLSTM) networks to analyze whole-genome somatic mutations, evolutionary conservation, chromatin accessibility, and 3D genome architecture in 2,546 TCGA patients. An attention mechanism identified predictive genomic regions. The model achieved an AUC of 0.92 (95% CI: 0.89-0.94) in cross-validation and 0.88 (95% CI: 0.85-0.91) in independent validation, outperforming clinical models (&#x394;AUC = +0.18, p < 0.001). Key predictors included non-coding variants in TP53, KRAS, and PIK3CA regulatory regions. Triple-positive patients (mutations in all 3 regions) had significantly worse progression-free survival (HR = 4.7, p < 0.001). Our framework enables accurate chemotherapy response prediction and reveals novel non-coding resistance mechanisms, advancing precision oncology in CRC.

Humans↗
PubMed2026

Predictive design of tissue-specific mammalian enhancers that function in the mouse embryo.

Enhancers control tissue-specific gene expression across animals1. Although deep learning2,3 has enabled enhancer prediction and design in mammalian cell lines and non-mammalian model organisms4-10 (reviewed in a previous publication11), it remains unclear whether such approaches can operate within the regulatory complexity of mammalian genomes and tissues in vivo. Here we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks on curated chromatin accessibility data and fine-tune them by transfer learning on validated human and mouse enhancers. Guided by these models, we design 15 synthetic enhancers for the heart, limb and central nervous system in mouse embryos, all of which are active in their intended target tissue. These results demonstrate that mammalian enhancer function can be reliably inferred from DNA sequence alone, enabling the predictive de novo design of tissue-specific synthetic enhancers from modest training sets. This work establishes a generalizable framework for programmable control of mammalian gene expression in vivo, opening new avenues in functional genomics, synthetic biology and gene therapy.

Animals↗
PubMed2026

Quantitative assessment of the fingerprint evidential value using machine learning.

Fingerprints as physical evidence have long supported criminal investigation and adjudication. In practice, however, fingerprint identification relies mainly on examiners' experience. Furthermore, expert opinions tend to be categorical, even though the opinions with the same conclusion could differ substantially in evidential strength. To quantitatively assess fingerprint evidential value, this study proposes a machine learning-based framework as an interpretable decision-support tool. A lightweight residual one-dimensional convolutional neural network was constructed, incorporating channel recalibration and a similarity-driven attention mechanism to learn adaptive contribution weights for different matched minutiae (minutiae for short). Controlled experiments revealed that the predicted evidential value increased with the number of minutiae and was significantly influenced by the quality of minutiae. With 10 minutiae, the mean predicted scores were 4.49, 7.00, and 9.09 for blurred, moderately blurred, and clear minutiae, respectively. Multiple regression analysis indicated that replacing a pair of blurred minutiae with a pair of clear minutiae increased the score by 0.492, whereas replacing it with a pair of moderately blurred minutiae increased the score by only 0.216. By mapping predicted scores to graded levels of evidential strength, the framework contributes to a paradigm shift from categorical expert opinions to graded ones, helping courts evaluate fingerprint evidence more scientifically.

Humans↗