PLoS One. 2025 Mar 18;20(3):e0317863. doi: 10.1371/journal.pone.0317863. eCollection 2025.

ABSTRACT

Efficient image retrieval from a variety of datasets is crucial in today's digital world. Visual properties are represented using primitive image signatures in Content Based Image Retrieval (CBIR). Feature vectors are employed to classify images into predefined categories. This research presents a unique feature identification technique based on suppression to locate interest points by computing productive sum of pixel derivatives by computing the differentials for corner scores. Scale space interpolation is applied to define interest points by combining color features from spatially ordered L2 normalized coefficients with shape and object information. Object based feature vectors are formed using high variance coefficients to reduce the complexity and are converted into bag-of-visual-words (BoVW) for effective retrieval and ranking. The presented method encompass feature vectors for information synthesis and improves the discriminating strength of the retrieval system by extracting deep image features including primitive, spatial, and overlayed using multilayer fusion of Convolutional Neural Networks(CNNs). Extensive experimentation is performed on standard image datasets benchmarks, including ALOT, Cifar-10, Corel-10k, Tropical Fruits, and Zubud. These datasets cover wide range of categories including shape, color, texture, spatial, and complicated objects. Experimental results demonstrate considerable improvements in precision and recall rates, average retrieval precision and recall, and mean average precision and recall rates across various image semantic groups within versatile datasets. The integration of traditional feature extraction methods fusion with multilevel CNN advances image sensing and retrieval systems, promising more accurate and efficient image retrieval solutions.

PMID:40100801 | DOI:10.1371/journal.pone.0317863

PLoS One. 2025 Mar 18;20(3):e0320337. doi: 10.1371/journal.pone.0320337. eCollection 2025.

NO ABSTRACT

PMID:40100785 | DOI:10.1371/journal.pone.0320337

IEEE Trans Neural Syst Rehabil Eng. 2025 Mar 18;PP. doi: 10.1109/TNSRE.2025.3552530. Online ahead of print.

ABSTRACT

Current surface electromyography (sEMG) methods for locomotion mode prediction face limitations in anticipatory capability due to computation delays and constrained window lengths typically below 500ms-a practice historically tied to stationarity requirements of handcrafted feature extraction. This study investigates whether end-to-end convolutional neural networks (CNNs) processing raw sEMG signals can overcome these constraints through extended window lengths (250ms to 1500 ms). We systematically evaluate six window lengths paired with three prediction horizons (model forecasts 50ms to 150ms ahead) in a continuous locomotion task involving eight modes and 16 transitions. The optimal configuration (1000ms window with 150ms horizon) achieved subject-average accuracies of 96.93% (steady states) and 97.50% (transient states), maintaining 95.03% and 85.53% respectively in real-time simulations. With a net averaged anticipation time of 147.9ms after 2.1ms computation latency, this approach demonstrates that windows covering 74% of the gait cycle can synergize with deep learning to balance the inherent trade-off between extracting richer information and maintaining system responsiveness to changes in activity.

PMID:40100693 | DOI:10.1109/TNSRE.2025.3552530

IEEE J Biomed Health Inform. 2025 Mar 18;PP. doi: 10.1109/JBHI.2025.3551720. Online ahead of print.

ABSTRACT

The intelligent analysis of Whole Slide Images (WSI) in digital pathology is critical for advancing precision medicine, particularly in oncology. However, the availability of WSI datasets is often limited by privacy regulations, which constrains the performance and generalizability of deep learning models. To address this challenge, this paper proposes an improved data augmentation method based on Deep Convolutional Generative Adversarial Network (DCGAN). Our approach leverages self-supervised pretraining with the CTransPath model to extract diverse and representationally rich WSI features, which guide the generation of high-quality synthetic images. We further enhance the model by introducing a least-squares adversarial loss and a frequency domain loss to improve pixel-level accuracy and structural fidelity, while incorporating residual blocks and skip connections to increase network depth, mitigate gradient vanishing, and improve training stability. Experimental results on the PatchCamelyon dataset demonstrate that our improved DCGAN achieves superior SSIM and FID scores compared to traditional models. The augmented datasets significantly enhance the performance of downstream classification tasks, improving accuracy, AUC, and F1 scores.

PMID:40100674 | DOI:10.1109/JBHI.2025.3551720

IEEE Trans Biomed Eng. 2025 Mar 18;PP. doi: 10.1109/TBME.2025.3550842. Online ahead of print.

ABSTRACT

OBJECTIVE: Predicting normative pediatric growth is crucial to identify developmental anomalies. While traditional statistical and computational methods have shown promising results predicting personalized development, they either rely on statistical assumptions that limit generalizability or require longitudinal datasets, which are scarce in children. Recent deep learning methods trained with cross-sectional dataset have shown potential to predict temporal changes but have only succeeded at predicting local intensity changes and can hardly model major anatomical changes that occur during childhood. We present a novel deep learning method for image synthesis that can be trained using only cross-sectional data to make personalized predictions of pediatric development.

METHODS: We designed a new generative adversarial network (GAN) with a novel Siamese cyclic encoder-decoder generator architecture and an identity preservation mechanism. Our design allows the encoder to learn age- and sex-independent identity-preserving representations of patient phenotypes from single images by leveraging the statistical distributions in the cross-sectional dataset. The decoder learns to synthesize personalized images from the encoded representations at any age.

RESULTS: Trained using only cross-sectional head CT images from 2,014 subjects (age 0-10 years), our model demonstrated state-of-the-art performance evaluated on an independent longitudinal dataset with images from 51 subjects.

CONCLUSION: Our method can predict pediatric development and synthesize temporal image sequences with state-of-the-art accuracy without requiring longitudinal images for training.

SIGNIFICANCE: Our method enables the personalized prediction of pediatric growth and longitudinal synthesis of clinical images, hence providing a patient-specific reference of normative development.

PMID:40100672 | DOI:10.1109/TBME.2025.3550842

IEEE Trans Neural Netw Learn Syst. 2025 Mar 18;PP. doi: 10.1109/TNNLS.2025.3540291. Online ahead of print.

ABSTRACT

Protein complex structural data are growing at an unprecedented pace, but its complexity and diversity pose significant challenges for protein function research. Although deep learning models have been widely used to capture the syntactic structure, word semantics, or semantic meanings of polypeptide and protein sequences, these models often overlook the complex contextual information of sequences. Here, we propose interpretable interaction deep learning (IIDL)-peptide-protein interaction (PepPI), a deep learning model designed to tackle these challenges using data-driven and interpretable pragmatic analysis to profile PepPIs. IIDL-PepPI constructs bidirectional attention modules to represent the contextual information of peptides and proteins, enabling pragmatic analysis. It then adopts a progressive transfer learning framework to simultaneously predict PepPIs and identify binding residues for specific interactions, providing a solution for multilevel in-depth profiling. We validate the performance and robustness of IIDL-PepPI in accurately predicting peptide-protein binary interactions and identifying binding residues compared with the state-of-the-art methods. We further demonstrate the capability of IIDL-PepPI in peptide virtual drug screening and binding affinity assessment, which is expected to advance artificial intelligence-based peptide drug discovery and protein function elucidation.

PMID:40100664 | DOI:10.1109/TNNLS.2025.3540291

IEEE Trans Pattern Anal Mach Intell. 2025 Mar 18;PP. doi: 10.1109/TPAMI.2025.3552484. Online ahead of print.

ABSTRACT

The divergence between labeled training data and unlabeled testing data is a significant challenge for recent deep learning models. Unsupervised domain adaptation (UDA) attempts to solve such problem. Recent works show that self-training is a powerful approach to UDA. However, existing methods have difficulty in balancing the scalability and performance. In this paper, we propose a hard-aware instance adaptive self-training framework for UDA on the task of semantic segmentation. To effectively improve the quality and diversity of pseudo-labels, we develop a novel pseudo-label generation strategy with an instance adaptive selector. We further enrich the hard class pseudo-labels with inter-image information through a skillfully designed hard-aware pseudo-label augmentation. Besides, we propose the region-adaptive regularization to smooth the pseudo-label region and sharpen the non-pseudo-label region. For the non-pseudo-label region, consistency constraint is also constructed to introduce stronger supervision signals during model optimization. Our method is so concise and efficient that it is easy to be generalized to other UDA methods. Experiments on GTA5 Cityscapes, SYNTHIA Cityscapes, and Cityscapes Oxford RobotCar demonstrate the superior performance of our approach compared with the state-of-the-art methods. Our codes are available at https://github.com/bupt-ai-cz/HIAST.

PMID:40100655 | DOI:10.1109/TPAMI.2025.3552484

J Med Internet Res. 2025 Mar 18;27:e57358. doi: 10.2196/57358.

ABSTRACT

BACKGROUND: The use of structured electronic health records in health care systems has grown rapidly. These systems collect huge amounts of patient information, including diagnosis codes representing temporal medical history. Sequential diagnostic information has proven valuable for predicting patient outcomes. However, the extent to which these types of data have been incorporated into deep learning (DL) models has not been examined.

OBJECTIVE: This systematic review aims to describe the use of sequential diagnostic data in DL models, specifically to understand how these data are integrated, whether sample size improves performance, and whether the identified models are generalizable.

METHODS: Relevant studies published up to May 15, 2023, were identified using 4 databases: PubMed, Embase, IEEE Xplore, and Web of Science. We included all studies using DL algorithms trained on sequential diagnosis codes to predict patient outcomes. We excluded review articles and non-peer-reviewed papers. We evaluated the following aspects in the included papers: DL techniques, characteristics of the dataset, prediction tasks, performance evaluation, generalizability, and explainability. We also assessed the risk of bias and applicability of the studies using the Prediction Model Study Risk of Bias Assessment Tool (PROBAST). We used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) checklist to report our findings.

RESULTS: Of the 740 identified papers, 84 (11.4%) met the eligibility criteria. Publications in this area increased yearly. Recurrent neural networks (and their derivatives; 47/84, 56%) and transformers (22/84, 26%) were the most commonly used architectures in DL-based models. Most studies (45/84, 54%) presented their input features as sequences of visit embeddings. Medications (38/84, 45%) were the most common additional feature. Of the 128 predictive outcome tasks, the most frequent was next-visit diagnosis (n=30, 23%), followed by heart failure (n=18, 14%) and mortality (n=17, 13%). Only 7 (8%) of the 84 studies evaluated their models in terms of generalizability. A positive correlation was observed between training sample size and model performance (area under the receiver operating characteristic curve; P=.02). However, 59 (70%) of the 84 studies had a high risk of bias.

CONCLUSIONS: The application of DL for advanced modeling of sequential medical codes has demonstrated remarkable promise in predicting patient outcomes. The main limitation of this study was the heterogeneity of methods and outcomes. However, our analysis found that using multiple types of features, integrating time intervals, and including larger sample sizes were generally related to an improved predictive performance. This review also highlights that very few studies (7/84, 8%) reported on challenges related to generalizability and less than half (38/84, 45%) of the studies reported on challenges related to explainability. Addressing these shortcomings will be instrumental in unlocking the full potential of DL for enhancing health care outcomes and patient care.

TRIAL REGISTRATION: PROSPERO CRD42018112161; https://tinyurl.com/yc6h9rwu.

PMID:40100249 | DOI:10.2196/57358

Protein Sci. 2025 Apr;34(4):e70083. doi: 10.1002/pro.70083.

ABSTRACT

The ever-growing global health threat of antibiotic resistance is compelling researchers to explore alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging as a promising solution to fill this need. Naturally occurring AMPs are produced by all forms of life as part of the innate immune system. High-throughput bioinformatics tools have enabled fast and large-scale discovery of AMPs from genomic, transcriptomic, and proteomic resources of selected organisms. Public protein sequence databases, comprising over 200 million records and growing, serve as comprehensive compendia of sequences from a broad range of source organisms. Yet, large-scale in silico probing of those databases for novel AMP discovery using modern deep learning techniques has rarely been reported. In the present study, we propose an AMP mining workflow to predict novel AMPs from the UniProtKB/Swiss-Prot database using the AMP prediction tool, AMPlify, as its discovery engine. Using this workflow, we identified 8008 novel putative AMPs from all eukaryotic sequences in the database. Focusing on the practical use of AMPs as suitable antimicrobial agents with applications in the poultry industry, we prioritized 40 of those AMPs based on their similarities to known chicken AMPs in predicted structures. In our tests, 13 out of the 38 successfully synthesized peptides showed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus. AMPlify and the companion scripts supporting the AMP mining workflow presented herein are publicly available at https://github.com/bcgsc/AMPlify.

PMID:40100125 | DOI:10.1002/pro.70083

Sarcoidosis Vasc Diffuse Lung Dis. 2025 Mar 18;42(1):15378. doi: 10.36141/svdld.v42i1.15378.

NO ABSTRACT

PMID:40100114 | DOI:10.36141/svdld.v42i1.15378

Biomol Biomed. 2025 Mar 17. doi: 10.17305/bb.2025.12010. Online ahead of print.

ABSTRACT

Differentiating early-stage breast cancer from benign breast masses is crucial for radiologists. Additionally, accurately assessing axillary lymph node metastasis (ALNM) plays a significant role in clinical management and prognosis for breast cancer patients. Chest computed tomography (CT) is a commonly used imaging modality in physical and preoperative evaluations. This study aims to develop a deep learning model based on chest CT imaging to improve the preliminary assessment of breast lesions, potentially reducing the need for costly follow-up procedures such as magnetic resonance imaging (MRI) or positron emission tomography-CT and alleviating the financial and emotional burden on patients. We retrospectively collected chest CT images from 482 patients with breast masses, classifying them as benign (n = 224) or malignant (n = 258) based on pathological findings. The malignant group was further categorized into ALNM-positive (n = 91) and ALNM-negative (n = 167) subgroups. Patients were randomly divided into training, validation, and test sets in an 8:1:1 ratio, with the test set excluded from model development. All patients underwent non-contrast chest CT before surgery. After preprocessing the images through cropping, scaling, and standardization, we applied ResNet-34, ResNet-50, and ResNet-101 architectures to differentiate between benign and malignant masses and to assess ALNM. Model performance was evaluated using sensitivity, specificity, accuracy, receiver operating characteristic (ROC) curves, and the area under the curve (AUC). The ResNet models effectively distinguished benign from malignant masses, with ResNet-101 achieving the highest performance (AUC: 0.964; 95% CI: 0.948-0.981). It also demonstrated excellent predictive capability for ALNM (AUC: 0.951; 95% CI: 0.926-0.975). In conclusion, these deep learning models show strong diagnostic potential for both breast mass classification and ALNM prediction, offering a valuable tool for improving clinical decision-making.

PMID:40100034 | DOI:10.17305/bb.2025.12010

Anal Chem. 2025 Mar 18. doi: 10.1021/acs.analchem.4c07061. Online ahead of print.

ABSTRACT

Tetracyclines are widely used in bacteria infection treatment, while the subtle chemical differences between tetracyclines make it a challenge to accurate discrimination via biosensors. A 3D fluorescence spectrum can provide fingerprint structure information for many analytes, but a single probe-based method is prone to information overlap. Here, aptamers are first reported to obtain abundant information in a ratiometric, 3D fluorescence spectrum for deep learning to accurately discriminate tetracyclines. So, each tetracycline can be related to a distinct, ratiometric, 3D fluorescence spectrum via the strategy of dual biomolecules recognition. One artificial neural network model can efficiently treat this fingerprint information, and the qualitative/quantitative analysis of tetracyclines is successfully realized. The proposed dual biomolecule recognition strategy has been demonstrated to show a higher accuracy than a conventional single probe method. So, the ratiometric 3D fluorescence spectrum can enrich the fingerprint information for deep learning, providing a new strategy for 3D fluorescence-based analytes discrimination.

PMID:40099919 | DOI:10.1021/acs.analchem.4c07061

Mol Inform. 2025 Mar;44(3):e202400159. doi: 10.1002/minf.202400159.

ABSTRACT

The challenges of drug discovery from hit identification to clinical development sometimes involves addressing scaffold hopping issues, in order to optimise molecular biological activity or ADME properties, or mitigate toxicology concerns of a drug candidate. Docking is usually viewed as the method of choice for identification of isofunctional molecules, i. e. highly dissimilar molecules that share common binding modes with a protein target. However, the structure of the protein may not be suitable for docking because of a low resolution, or may even be unknown. This problem is frequently encountered in the case of membrane proteins, although they constitute an important category of the druggable proteome. In such cases, ligand-based approaches offer promise but are often inadequate to handle large-step scaffold hopping, because they usually rely on molecular structure. Therefore, we propose the Interaction Fingerprints Profile (IFPP), a molecular representation that captures molecules binding modes based on docking experiments against a panel of diverse high-quality proteins structures. Evaluation on the LH benchmark demonstrates the interest of IFPP for identification of isofunctional molecules. Nevertheless, computation of IFPPs is expensive, which limits its scalability for screening very large molecular libraries. We propose to overcome this limitation by leveraging Metric Learning approaches, allowing fast estimation of molecules IFPP similarities, thus providing an efficient pre-screening strategy that in applicable to very large molecular libraries. Overall, our results suggest that IFPP provides an interesting and complementary tool alongside existing methods, in order to address challenging scaffold hopping problems effectively in drug discovery.

PMID:40099892 | DOI:10.1002/minf.202400159

J Comput Chem. 2025 Mar 30;46(8):e70081. doi: 10.1002/jcc.70081.

ABSTRACT

With the development of artificial neural networks (ANNs), its applications in chemistry have become increasingly widespread, especially in the prediction of various molecular properties. This work introduces the X2-PEC method, that is, the second generalization of the X1 series of ANN methods developed in our group, utilizing pair energy correction (PEC). The essence of the X2 model lies in its feature vector construction, using overlap integrals and core Hamiltonian integrals to incorporate physical and chemical information into the feature vectors to describe atomic interactions. It aims to enhance the accuracy of low-rung density functional theory (DFT) calculations, such as those from the widely used BLYP/6-31G(d) or B3LYP/6-31G(2df,p) methods, to the level of top-rung DFT calculations, such as those from the highly accurate doubly hybrid XYGJ-OS/GTLarge method. Trained on the QM9 dataset, X2-PEC excels in predicting the atomization energies of isomers such as C6H8 and C4H4N2O with varying bonding structures. The performance of the X2-PEC model on standard enthalpies of formation for datasets such as G2-HCNOF, PSH36, ALKANE28, BIGMOL20, and HEDM45, as well as a HCNOF subset of BH9 for reaction barriers, is equally commendable, demonstrating its good generalization ability and predictive accuracy, as well as its potential for further development to achieve greater accuracy. These outcomes highlight the practical significance of the X2-PEC model in elevating the results from lower-rung DFT calculations to the level of higher-rung DFT calculations through deep learning.

PMID:40099806 | DOI:10.1002/jcc.70081

J Am Geriatr Soc. 2025 Mar 18. doi: 10.1111/jgs.19440. Online ahead of print.

ABSTRACT

BACKGROUND: Recent evidence underscores the significant impact of social determinants of health (SDoH) on cardiovascular disease (CVD). However, available CVD risk assessment tools often neglect SDoH. This study aimed to integrate SDoH with traditional risk factors to predict CVD risk.

METHODS: The data was sourced from the ASPirin in Reducing Events in the Elderly (ASPREE) longitudinal study, and its sub-study, the ASPREE Longitudinal Study of Older Persons (ALSOP). The study included 12,896 people (5884 men and 7012 women) aged 70 or older who were initially free of CVD, dementia, and independence-limiting physical disability. The participants were followed for a median of eight years. CVD risk was predicted using state-of-the-art machine learning (ML) and deep learning (DL) models: Random Survival Forest (RSF), Deepsurv, and Neural Multi-Task Logistic Regression (NMTLR), incorporating both SDoH and traditional CVD risk factors as candidate predictors. The permutation-based feature importance method was further utilized to assess the predictive potential of the candidate predictors.

RESULTS: Among men, the RSF model achieved relatively good performance (C-index = 0.732, integrated brier score (IBS) = 0.071, 5-year and 10-year AUC = 0.657 and 0.676 respectively). For women, DeepSurv was the best-performing model (C-index = 0.670, IBS = 0.042, 5-year and 10-year AUC = 0.676 and 0.677 respectively). Regarding the contribution of the candidate predictors, for men, age, urine albumin-to-creatinine ratio, and smoking, along with SDoH variables, were identified as the most significant predictors of CVD. For women, SDoH variables, such as social network, living arrangement, and education, predicted CVD risk better than the traditional risk factors, with age being the exception.

CONCLUSION: SDoH can improve the accuracy of CVD risk prediction and emerge among the main predictors for CVD. The influence of SDoH was greater for women than for men, reflecting gender-specific impacts of SDoH.

PMID:40099367 | DOI:10.1111/jgs.19440

Front Endocrinol (Lausanne). 2025 Mar 3;16:1495306. doi: 10.3389/fendo.2025.1495306. eCollection 2025.

ABSTRACT

BACKGROUND: Machine learning (ML) models are being increasingly employed to predict the risk of developing and progressing diabetic kidney disease (DKD) in patients with type 2 diabetes mellitus (T2DM). However, the performance of these models still varies, which limits their widespread adoption and practical application. Therefore, we conducted a systematic review and meta-analysis to summarize and evaluate the performance and clinical applicability of these risk predictive models and to identify key research gaps.

METHODS: We conducted a systematic review and meta-analysis to compare the performance of ML predictive models. We searched PubMed, Embase, the Cochrane Library, and Web of Science for English-language studies using ML algorithms to predict the risk of DKD in patients with T2DM, covering the period from database inception to April 18, 2024. The primary performance metric for the models was the area under the receiver operating characteristic curve (AUC) with a 95% confidence interval (CI). The risk of bias was assessed using the Prediction Model Risk of Bias Assessment Tool (PROBAST) checklist.

RESULTS: 26 studies that met the eligibility criteria were included into the meta-analysis. 25 studies performed internal validation, but only 8 studies conducted external validation. A total of 94 ML models were developed, with 81 models evaluated in the internal validation sets and 13 in the external validation sets. The pooled AUC was 0.839 (95% CI 0.787-0.890) in the internal validation and 0.830 (95% CI 0.784-0.877) in the external validation sets. Subgroup analysis based on the type of ML showed that the pooled AUC for traditional regression ML was 0.797 (95% CI 0.777-0.816), for ML was 0.811 (95% CI 0.785-0.836), and for deep learning was 0.863 (95% CI 0.825-0.900). A total of 26 ML models were included, and the AUCs of models that were used three or more times were pooled. Among them, the random forest (RF) models demonstrated the best performance with a pooled AUC of 0.848 (95% CI 0.785-0.911).

CONCLUSION: This meta-analysis demonstrates that ML exhibit high performance in predicting DKD risk in T2DM patients. However, challenges related to data bias during model development and validation still need to be addressed. Future research should focus on enhancing data transparency and standardization, as well as validating these models' generalizability through multicenter studies.

SYSTEMATIC REVIEW REGISTRATION: https://inplasy.com/inplasy-2024-9-0038/, identifier INPLASY202490038.

PMID:40099258 | PMC:PMC11911190 | DOI:10.3389/fendo.2025.1495306

Clin Ophthalmol. 2025 Mar 13;19:907-914. doi: 10.2147/OPTH.S506519. eCollection 2025.

ABSTRACT

PURPOSE: This study introduces a fully automated approach using deep learning-based segmentation to select the conjunctiva as the region of interest (ROI) for large-scale, multi-site clinical trials. By integrating a precise, objective grading system, we aim to minimize inter- and intra-grader variability due to perceptual biases. We evaluate the impact of adding a "horizontality" parameter to the grading system and assess this method's potential to enhance grading precision, reduce sample size, and improve clinical trial efficiency.

METHODS: We analyzed 29,640 images from 450 subjects in a multi-visit, multi-site clinical trial to assess the performance of an automated grading model compared to expert graders. Images were graded on a 0-4 scale, in 0.5 increments. The model utilizes the DeepLabV3 architecture for image segmentation, extracting two key features-horizontality and redness. The algorithm then uses these features to predict eye redness, validated by comparison with expert grader scores.

RESULTS: The bivariate model using both redness and horizontality performed best, with a Mean Absolute Error (MAE) of 0.450 points (SD=0.334) on the redness scale relative to expert scores. Expert graded scores were within one unit of the mean grade in over 85% cases, ensuring consistency and optimal training set for the predictive model. Models incorporating both features outperformed those using only redness, reducing MAE by 5-6%. The optimal generalized model improved predictive accuracy with horizontality such that 93.0% of images were predicted with an absolute error less than one unit difference in grading.

CONCLUSION: This study demonstrates that fully automating image analysis allows thousands of images to be graded efficiently. The addition of the horizontality parameter enhances model performance, reduces error, and supports its relevance to specific Dry Eye manifestations. This automated method provides a continuous scale and greater sensitivity to treatment effects than standard clinical scales.

PMID:40099234 | PMC:PMC11912931 | DOI:10.2147/OPTH.S506519

J Pharm Anal. 2025 Mar;15(3):101144. doi: 10.1016/j.jpha.2024.101144. Epub 2024 Nov 14.

ABSTRACT

Drug development remains a critical issue in the field of biomedicine. With the rapid advancement of information technologies such as artificial intelligence (AI) and the advent of the big data era, AI-assisted drug development has become a new trend, particularly in predicting drug-target associations. To address the challenge of drug-target prediction, AI-driven models have emerged as powerful tools, offering innovative solutions by effectively extracting features from complex biological data, accurately modeling molecular interactions, and precisely predicting potential drug-target outcomes. Traditional machine learning (ML), network-based, and advanced deep learning architectures such as convolutional neural networks (CNNs), graph convolutional networks (GCNs), and transformers play a pivotal role. This review systematically compiles and evaluates AI algorithms for drug- and drug combination-target predictions, highlighting their theoretical frameworks, strengths, and limitations. CNNs effectively identify spatial patterns and molecular features critical for drug-target interactions. GCNs provide deep insights into molecular interactions via relational data, whereas transformers increase prediction accuracy by capturing complex dependencies within biological sequences. Network-based models offer a systematic perspective by integrating diverse data sources, and traditional ML efficiently handles large datasets to improve overall predictive accuracy. Collectively, these AI-driven methods are transforming drug-target predictions and advancing the development of personalized therapy. This review summarizes the application of AI in drug development, particularly in drug-target prediction, and offers recommendations on models and algorithms for researchers engaged in biomedical research. It also provides typical cases to better illustrate how AI can further accelerate development in the fields of biomedicine and drug discovery.

PMID:40099205 | PMC:PMC11910364 | DOI:10.1016/j.jpha.2024.101144

Front Psychiatry. 2025 Feb 20;16:1485286. doi: 10.3389/fpsyt.2025.1485286. eCollection 2025.

ABSTRACT

INTRODUCTION: Autism Spectrum Disorder (ASD) identification poses significant challenges due to its multifaceted and diverse nature, necessitating early discovery for operative involvement. In a recent study, there has been a lot of talk about how deep learning algorithms might improve the diagnosis of ASD by analyzing neuroimaging data.

METHOD: To overrule the negatives of current techniques, this research proposed a revolutionary strategic model called the Unified Transformer Block for Multi-View Graph Attention Networks (MVUT_GAT). For the purpose of extracting delicate outlines from physical and efficient functional MRI data, MVUT_GAT combines the advantages of multi-view learning with attention processes.

RESULT: With the use of the ABIDE dataset, a thorough analysis shows that MVUT_GAT performs better than Mutli-view Site Graph Convolution Network (MVS_GCN), outperforming it in accuracy by +3.40%. This enhancement reinforces our suggested model's effectiveness in identifying ASD. The result has implications over higher accuracy metrics. Through improving the accuracy and consistency of ASD diagnosis, MVUT_GAT will help with early interference and assistance for ASD patients.

DISCUSSION: Moreover, the proposed MVUT_GAT's which patches the distance between the models of deep learning and medical visions by helping to identify biomarkers linked to ASD. In the end, this effort advances the knowledge of recognizing autism spectrum disorder along with the powerful ability to enhance results and the value of people who are undergone.

PMID:40099145 | PMC:PMC11913004 | DOI:10.3389/fpsyt.2025.1485286

Front Genet. 2025 Mar 3;16:1471037. doi: 10.3389/fgene.2025.1471037. eCollection 2025.

ABSTRACT

INTRODUCTION: Melanoma, a highly aggressive malignancy characterized by rapid metastasis and elevated mortality rates, predominantly originates in cutaneous tissues. While surgical interventions, immunotherapy, and targeted therapies have advanced, the prognosis for advanced-stage melanoma remains dismal. Globally, melanoma incidence continues to rise, with the United States alone reporting over 100,000 new cases and 7,000 deaths annually. Despite the exponential growth of tumor data facilitated by next-generation sequencing (NGS), current analytical approaches predominantly emphasize single-gene analyses, neglecting critical insights into complex gene interaction networks. This study aims to address this gap by systematically exploring immune gene regulatory dynamics in melanoma progression.

METHODS: We developed a bidirectional, weighted, signed, and directed topological immune gene regulatory network to compare transcriptional landscapes between benign melanocytic nevi and cutaneous melanoma. Advanced network analysis tools were employed to identify structural disparities and functional module shifts. Key driver genes were validated through topological centrality metrics. Additionally, deep learning models were implemented to predict drug-target interactions, leveraging molecular features derived from network analyses.

RESULTS: Significant topological divergences emerged between nevi and melanoma networks, with dominant functional modules transitioning from cell cycle regulation in benign lesions to DNA repair and cell migration pathways in malignant tumors. A group of genes, including AURKA, CCNE1, APEX2, and EXOC8, were identified as potential orchestrators of immune microenvironment remodeling during malignant transformation. The deep learning framework successfully predicted 23 clinically actionable drug candidates targeting these molecular drivers.

DISCUSSION: The observed module shift from cell cycle to invasion-related pathways provides mechanistic insights into melanoma progression, suggesting early therapeutic targeting of DNA repair machinery might mitigate metastatic potential. The identified hub genes, particularly AURKA and DDX19B, represent novel candidates for immunomodulatory interventions. Our computational drug prediction strategy bridges molecular network analysis with clinical translation, offering a paradigm for precision oncology in melanoma. Future studies should validate these targets in preclinical models and explore network-based biomarkers for early detection.

PMID:40098976 | PMC:PMC11911340 | DOI:10.3389/fgene.2025.1471037