ESC Heart Fail. 2024 Jul 9. doi: 10.1002/ehf2.14918. Online ahead of print.

ABSTRACT

AIMS: Assessing the risk for HF rehospitalization is important for managing and treating patients with HF. To address this need, various risk prediction models have been developed. However, none of them used deep learning methods with real-world data. This study aimed to develop a deep learning-based prediction model for HF rehospitalization within 30, 90, and 365 days after acute HF (AHF) discharge.

METHODS AND RESULTS: We analysed the data of patients admitted due to AHF between January 2014 and January 2019 in a tertiary hospital. In performing deep learning-based predictive algorithms for HF rehospitalization, we use hyperbolic tangent activation layers followed by recurrent layers with gated recurrent units. To assess the readmission prediction, we used the AUC, precision, recall, specificity, and F1 measure. We applied the Shapley value to identify which features contributed to HF readmission. Twenty-two prognostic features exhibiting statistically significant associations with HF rehospitalization were identified, consisting of 6 time-independent and 16 time-dependent features. The AUC value shows moderate discrimination for predicting readmission within 30, 90, and 365 days of follow-up (FU) (AUC:0.63, 0.74, and 0.76, respectively). The features during the FU have a relatively higher contribution to HF rehospitalization than features from other time points.

CONCLUSIONS: Our deep learning-based model using real-world data could provide valid predictions of HF rehospitalization in 1 year follow-up. It can be easily utilized to guide appropriate interventions or care strategies for patients with HF. The closed monitoring and blood test in daily clinics are important for assessing the risk of HF rehospitalization.

PMID:38981003 | DOI:10.1002/ehf2.14918

ACS Appl Mater Interfaces. 2024 Jul 9. doi: 10.1021/acsami.4c04223. Online ahead of print.

ABSTRACT

Intelligent colorimetric freshness indicator is a low-cost way to intuitively monitor the freshness of fresh food. A colorimetric strip sensor array was prepared by p-dimethylaminocinnamaldehyde (PDL)-doped poly(vinyl alcohol) (PVA) and chitosan (Chit) for the quantitative analysis of indole, which is an indicator of shrimp freshness. As a result of indole simulation, the array strip turned from faint yellow to pink or mulberry color with the increasing indole concentration, like a progress bar. The indicator film exhibited excellent permeability, mechanical and thermal stability, and color responsiveness to indole, which was attributed to the interactions between PDL and Chit/PVA. Furthermore, the colorimetric strip sensor array provided a good relationship between the indole concentration and the color intensity within a range of 50-350 ppb. The pathogens and spoilage bacteria of shrimp possessed the ability to produce indole, which caused the color changes of the strip sensor array. In the shrimp freshness monitoring experiment, the color-changing progress of the strip sensor array was in agreement with the simulation and could distinguish the shrimp freshness levels. The image classification system based on deep learning were developed, the accuracies of four DCNN algorithms are above 90%, with VGG16 achieving the highest accuracy at 97.89%. Consequently, a "progress bar" strip sensor array has the potential to realize nondestructive, more precise, and commercially available food freshness monitoring using simple visual inspection and intelligent equipment identification.

PMID:38980942 | DOI:10.1021/acsami.4c04223

PLoS One. 2024 Jul 9;19(7):e0293777. doi: 10.1371/journal.pone.0293777. eCollection 2024.

ABSTRACT

An improved algorithm based on Yolov8s is proposed to address the slower speed, higher number of parameters, and larger computational cost of deep learning in coal gangue target detection. A lightweight network, Fasternet, is used as the backbone to increase the speed of object detection and reduce the model complexity. By replacing Slimneck with the C2F part in the HEAD module, the aim is to reduce model complexity and improve detection accuracy. The detection accuracy is effectively improved by replacing the Detect layer with Detect-DyHead. The introduction of DIoU loss function instead of CIoU loss function and the combination of BAM block attention mechanism makes the model pay more attention to critical features, which further improves the detection performance. The results show that the improved model compresses the storage size of the model by 28%, reduces the number of parameters by 28.8%, reduces the computational effort by 34.8%, and improves the detection accuracy by 2.5% compared to the original model. The Yolov8s-change model provides a fast, real-time and efficient detection solution for gangue sorting. This provides a strong support for the intelligent sorting of coal gangue.

PMID:38980881 | DOI:10.1371/journal.pone.0293777

IEEE Trans Neural Netw Learn Syst. 2024 Jul 9;PP. doi: 10.1109/TNNLS.2024.3419250. Online ahead of print.

ABSTRACT

Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific functional category containing multiple child ontologies, and the relationships of parent and child ontologies create a directed acyclic graph. Protein functions are categorized using GO, which divides them into three main groups: cellular component ontology, molecular function ontology, and biological process ontology. Therefore, the GO annotation of protein is a hierarchical multilabel classification problem. This hierarchical relationship introduces complexities such as mixed ontology problem, leading to performance bottlenecks in existing computational methods due to label dependency and data sparsity. To overcome bottleneck issues brought by mixed ontology problem, we propose ProFun-SOM, an innovative multilabel classifier that utilizes multiple sequence alignments (MSAs) to accurately annotate gene ontologies. ProFun-SOM enhances the initial MSAs through a reconstruction process and integrates them into a deep learning architecture. It then predicts annotations within the cellular component, molecular function, biological process, and mixed ontologies. Our evaluation results on three datasets (CAFA3, SwissProt, and NetGO2) demonstrate that ProFun-SOM surpasses state-of-the-art methods. This study confirmed that utilizing MSAs of proteins can effectively overcome the two main bottlenecks issues, label dependency and data sparsity, thereby alleviating the root problem, mixed ontology. A freely accessible web server is available at http://bliulab.net/ ProFun-SOM/.

PMID:38980781 | DOI:10.1109/TNNLS.2024.3419250

IEEE J Biomed Health Inform. 2024 Jul 9;PP. doi: 10.1109/JBHI.2024.3425434. Online ahead of print.

ABSTRACT

Image analysis can play an important role in supporting histopathological diagnoses of lung cancer, with deep learning methods already achieving remarkable results. However, due to the large scale of whole-slide images (WSIs), creating manual pixel-wise annotations from expert pathologists is expensive and time-consuming. In addition, the heterogeneity of tumors and similarities in the morphological phenotype of tumor subtypes have caused inter-observer variability in annotations, which limits optimal performance. Effective use of weak labels could potentially alleviate these issues. In this paper, we propose a two-stage transformer-based weakly supervised learning framework called Simple Shuffle-Remix Vision Transformer (SSRViT). Firstly, we introduce a Shuffle-Remix Vision Transformer (SRViT) to retrieve discriminative local tokens and extract effective representative features. Then, the token features are selected and aggregated to generate sparse representations of WSIs, which are fed into a simple transformer-based classifier (SViT) for slide-level prediction. Experimental results demonstrate that the performance of our proposed SSRViT is significantly improved compared with other state-of-the-art methods in discriminating between adenocarcinoma, pulmonary sclerosing pneumocytoma and normal lung tissue (accuracy of 96.9% and AUC of 99.6%).

PMID:38980777 | DOI:10.1109/JBHI.2024.3425434

IEEE J Biomed Health Inform. 2024 Jul 9;PP. doi: 10.1109/JBHI.2024.3424869. Online ahead of print.

ABSTRACT

Marker-based motion capture (mocap) is a conventional method used in biomechanics research to precisely analyze human movement. However, the time-consuming marker placement process and extensive post-processing limit its wider adoption. Therefore, markerless mocap systems that use deep learning to estimate 2D keypoint from images have emerged as a promising alternative, but annotation errors in training datasets used by deep learning models can affect estimation accuracy. To improve the precision of 2D keypoint annotation, we present a method that uses anatomical landmarks based on marker-based mocap. Specifically, we use multiple RGB cameras synchronized and calibrated with a marker-based mocap system to create a high-quality dataset (RRIS40) of images annotated with surface anatomical landmarks. A deep neural network is then trained to estimate these 2D anatomical landmarks and a ray-distance-based triangulation is used to calculate the 3D marker positions. We conducted extensive evaluations on our RRIS40 test set, which consists of 10 subjects performing various movements. Compared against a marker-based system, our method achieves a mean Euclidean error of 13.23 mm in 3D marker position, which is comparable to the precision of marker placement itself. By learning directly to predict anatomical keypoints from images, our method outperforms OpenCap's augmentation of 3D anatomical landmarks from triangulated wild keypoints. This highlights the potential of facilitating wider integration of markerless mocap into biomechanics research. The RRIS40 test set is made publicly available for research purposes at koonyook.github.io/rris40.

PMID:38980775 | DOI:10.1109/JBHI.2024.3424869

J Imaging Inform Med. 2024 Jul 9. doi: 10.1007/s10278-024-01128-4. Online ahead of print.

ABSTRACT

Accurate image classification and retrieval are of importance for clinical diagnosis and treatment decision-making. The recent contrastive language-image pre-training (CLIP) model has shown remarkable proficiency in understanding natural images. Drawing inspiration from CLIP, pathology-dedicated CLIP (PathCLIP) has been developed, utilizing over 200,000 image and text pairs in training. While the performance the PathCLIP is impressive, its robustness under a wide range of image corruptions remains unknown. Therefore, we conduct an extensive evaluation to analyze the performance of PathCLIP on various corrupted images from the datasets of osteosarcoma and WSSS4LUAD. In our experiments, we introduce eleven corruption types including brightness, contrast, defocus, resolution, saturation, hue, markup, deformation, incompleteness, rotation, and flipping at various settings. Through experiments, we find that PathCLIP surpasses OpenAI-CLIP and the pathology language-image pre-training (PLIP) model in zero-shot classification. It is relatively robust to image corruptions including contrast, saturation, incompleteness, and orientation factors. Among the eleven corruptions, hue, markup, deformation, defocus, and resolution can cause relatively severe performance fluctuation of the PathCLIP. This indicates that ensuring the quality of images is crucial before conducting a clinical test. Additionally, we assess the robustness of PathCLIP in the task of image-to-image retrieval, revealing that PathCLIP performs less effectively than PLIP on osteosarcoma but performs better on WSSS4LUAD under diverse corruptions. Overall, PathCLIP presents impressive zero-shot classification and retrieval performance for pathology images, but appropriate care needs to be taken when using it.

PMID:38980627 | DOI:10.1007/s10278-024-01128-4

J Imaging Inform Med. 2024 Jul 9. doi: 10.1007/s10278-024-01181-z. Online ahead of print.

ABSTRACT

Malposition of a nasogastric tube (NGT) can lead to severe complications. We aimed to develop a computer-aided detection (CAD) system to localize NGTs and detect NGT malposition on portable chest X-rays (CXRs). A total of 7378 portable CXRs were retrospectively retrieved from two hospitals between 2015 and 2020. All CXRs were annotated with pixel-level labels for NGT localization and image-level labels for NGT presence and malposition. In the CAD system, DeepLabv3 + with backbone ResNeSt50 and DenseNet121 served as the model architecture for segmentation and classification models, respectively. The CAD system was tested on images from chronologically different datasets (National Taiwan University Hospital (National Taiwan University Hospital)-20), geographically different datasets (National Taiwan University Hospital-Yunlin Branch (YB)), and the public CLiP dataset. For the segmentation model, the Dice coefficients indicated accurate delineation of the NGT course (National Taiwan University Hospital-20: 0.665, 95% confidence interval (CI) 0.630-0.696; National Taiwan University Hospital-Yunlin Branch: 0.646, 95% CI 0.614-0.678). The distance between the predicted and ground-truth NGT tips suggested accurate tip localization (National Taiwan University Hospital-20: 1.64 cm, 95% CI 0.99-2.41; National Taiwan University Hospital-Yunlin Branch: 2.83 cm, 95% CI 1.94-3.76). For the classification model, NGT presence was detected with high accuracy (area under the receiver operating characteristic curve (AUC): National Taiwan University Hospital-20: 0.998, 95% CI 0.995-1.000; National Taiwan University Hospital-Yunlin Branch: 0.998, 95% CI 0.995-1.000; CLiP dataset: 0.991, 95% CI 0.990-0.992). The CAD system also detected NGT malposition with high accuracy (AUC: National Taiwan University Hospital-20: 0.964, 95% CI 0.917-1.000; National Taiwan University Hospital-Yunlin Branch: 0.991, 95% CI 0.970-1.000) and detected abnormal nasoenteric tube positions with favorable performance (AUC: 0.839, 95% CI 0.807-0.869). The CAD system accurately localized NGTs and detected NGT malposition, demonstrating excellent potential for external generalizability.

PMID:38980623 | DOI:10.1007/s10278-024-01181-z

Brief Bioinform. 2024 May 23;25(4):bbae336. doi: 10.1093/bib/bbae336.

ABSTRACT

Structural variation (SV) is an important form of genomic variation that influences gene function and expression by altering the structure of the genome. Although long-read data have been proven to better characterize SVs, SVs detected from noisy long-read data still include a considerable portion of false-positive calls. To accurately detect SVs in long-read data, we present SVDF, a method that employs a learning-based noise filtering strategy and an SV signature-adaptive clustering algorithm, for effectively reducing the likelihood of false-positive events. Benchmarking results from multiple orthogonal experiments demonstrate that, across different sequencing platforms and depths, SVDF achieves higher calling accuracy for each sample compared to several existing general SV calling tools. We believe that, with its meticulous and sensitive SV detection capability, SVDF can bring new opportunities and advancements to cutting-edge genomic research.

PMID:38980375 | DOI:10.1093/bib/bbae336

Brief Bioinform. 2024 May 23;25(4):bbae334. doi: 10.1093/bib/bbae334.

ABSTRACT

Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.

PMID:38980373 | DOI:10.1093/bib/bbae334

Brief Bioinform. 2024 May 23;25(4):bbae332. doi: 10.1093/bib/bbae332.

ABSTRACT

Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and artificial intelligence (AI), we focus on an elusive and intriguing mechanism of gene function regulation, RNA editing, in which a single nucleotide from an RNA molecule is changed, with a remarkable impact in the increase of the complexity of the transcriptome and proteome. We present a new generation approach to assess the functional conservation of the RNA-editing targeting mechanism using two AI learning algorithms, random forest (RF) and bidirectional long short-term memory (biLSTM) neural networks with an attention layer. These algorithms, combined with RNA-editing data coming from databases and variant calling from same-individual RNA and DNA-seq experiments from different species, allowed us to predict RNA-editing events using both primary sequence and secondary structure. Then, we devised a method for assessing conservation or divergence in the molecular mechanisms of editing completely in silico: the cross-testing analysis. This novel method not only helps to understand the conservation of the editing mechanism through evolution but could set the basis for achieving a better understanding of the adenosine-targeting mechanism in other fields.

PMID:38980372 | DOI:10.1093/bib/bbae332

Brief Bioinform. 2024 May 23;25(4):bbae325. doi: 10.1093/bib/bbae325.

ABSTRACT

Recent studies have extensively used deep learning algorithms to analyze gene expression to predict disease diagnosis, treatment effectiveness, and survival outcomes. Survival analysis studies on diseases with high mortality rates, such as cancer, are indispensable. However, deep learning models are plagued by overfitting owing to the limited sample size relative to the large number of genes. Consequently, the latest style-transfer deep generative models have been implemented to generate gene expression data. However, these models are limited in their applicability for clinical purposes because they generate only transcriptomic data. Therefore, this study proposes ctGAN, which enables the combined transformation of gene expression and survival data using a generative adversarial network (GAN). ctGAN improves survival analysis by augmenting data through style transformations between breast cancer and 11 other cancer types. We evaluated the concordance index (C-index) enhancements compared with previous models to demonstrate its superiority. Performance improvements were observed in nine of the 11 cancer types. Moreover, ctGAN outperformed previous models in seven out of the 11 cancer types, with colon adenocarcinoma (COAD) exhibiting the most significant improvement (median C-index increase of ~15.70%). Furthermore, integrating the generated COAD enhanced the log-rank p-value (0.041) compared with using only the real COAD (p-value = 0.797). Based on the data distribution, we demonstrated that the model generated highly plausible data. In clustering evaluation, ctGAN exhibited the highest performance in most cases (89.62%). These findings suggest that ctGAN can be meaningfully utilized to predict disease progression and select personalized treatments in the medical field.

PMID:38980369 | DOI:10.1093/bib/bbae325

Ophthalmic Physiol Opt. 2024 Jul 9. doi: 10.1111/opo.13360. Online ahead of print.

ABSTRACT

PURPOSE: To optimise the precision and efficacy of orthokeratology, this investigation evaluated a deep neural network (DNN) model for lens fitting. The objective was to refine the standardisation of fitting procedures and curtail subjective evaluations, thereby augmenting patient safety in the context of increasing global myopia.

METHODS: A retrospective study of successful orthokeratology treatment was conducted on 266 patients, with 449 eyes being analysed. A DNN model with an 80%-20% training-validation split predicted lens parameters (curvature, power and diameter) using corneal topography and refractive indices. The model featured two hidden layers for precision.

RESULTS: The DNN model achieved mean absolute errors of 0.21 D for alignment curvature (AC), 0.19 D for target power (TP) and 0.02 mm for lens diameter (LD), with R2 values of 0.97, 0.95 and 0.91, respectively. Accuracy decreased for myopia of less than 1.00 D, astigmatism exceeding 2.00 D and corneal curvatures >45.00 D. Approximately, 2% of cases with unique physiological characteristics showed notable prediction variances.

CONCLUSION: While exhibiting high accuracy, the DNN model's limitations in specifying myopia, cylinder power and corneal curvature cases highlight the need for algorithmic refinement and clinical validation in orthokeratology practice.

PMID:38980216 | DOI:10.1111/opo.13360

Rev Sci Instrum. 2024 Jul 1;95(7):073509. doi: 10.1063/5.0190354.

ABSTRACT

Active feedback control in magnetic confinement fusion devices is desirable to mitigate plasma instabilities and enable robust operation. Optical high-speed cameras provide a powerful, non-invasive diagnostic and can be suitable for these applications. In this study, we process high-speed camera data, at rates exceeding 100 kfps, on in situ field-programmable gate array (FPGA) hardware to track magnetohydrodynamic (MHD) mode evolution and generate control signals in real time. Our system utilizes a convolutional neural network (CNN) model, which predicts the n = 1 MHD mode amplitude and phase using camera images with better accuracy than other tested non-deep-learning-based methods. By implementing this model directly within the standard FPGA readout hardware of the high-speed camera diagnostic, our mode tracking system achieves a total trigger-to-output latency of 17.6 μs and a throughput of up to 120 kfps. This study at the High Beta Tokamak-Extended Pulse (HBT-EP) experiment demonstrates an FPGA-based high-speed camera data acquisition and processing system, enabling application in real-time machine-learning-based tokamak diagnostic and control as well as potential applications in other scientific domains.

PMID:38980128 | DOI:10.1063/5.0190354

Med Phys. 2024 Jul 9. doi: 10.1002/mp.17294. Online ahead of print.

ABSTRACT

BACKGROUND: Protoacoustic (PA) imaging has the potential to provide real-time 3D dose verification of proton therapy. However, PA images are susceptible to severe distortion due to limited angle acquisition. Our previous studies showed the potential of using deep learning to enhance PA images. As the model was trained using a limited number of patients' data, its efficacy was limited when applied to individual patients.

PURPOSE: In this study, we developed a patient-specific deep learning method for protoacoustic imaging to improve the reconstruction quality of protoacoustic imaging and the accuracy of dose verification for individual patients.

METHODS: Our method consists of two stages: in the first stage, a group model is trained from a diverse training set containing all patients, where a novel deep learning network is employed to directly reconstruct the initial pressure maps from the radiofrequency (RF) signals; in the second stage, we apply transfer learning on the pre-trained group model using patient-specific dataset derived from a novel data augmentation method to tune it into a patient-specific model. Raw PA signals were simulated based on computed tomography (CT) images and the pressure map derived from the planned dose. The reconstructed PA images were evaluated against the ground truth by using the root mean squared errors (RMSE), structural similarity index measure (SSIM) and gamma index on 10 specific prostate cancer patients. The significance level was evaluated by t-test with the p-value threshold of 0.05 compared with the results from the group model.

RESULTS: The patient-specific model achieved an average RMSE of 0.014 ( p < 0.05 ${{{p}}}&lt;{0.05}$ ), and an average SSIM of 0.981 ( p < 0.05 ${{{p}}}&lt;{0.05}$ ), out-performing the group model. Qualitative results also demonstrated that our patient-specific approach acquired better imaging quality with more details reconstructed when comparing with the group model. Dose verification achieved an average RMSE of 0.011 ( p < 0.05 ${{{p}}}&lt;{0.05}$ ), and an average SSIM of 0.995 ( p < 0.05 ${{{p}}}&lt;{0.05}$ ). Gamma index evaluation demonstrated a high agreement (97.4% [ p < 0.05 ${{{p}}}&lt;{0.05}$ ] and 97.9% [ p < 0.05 ${{{p}}}&lt;{0.05}$ ] for 1%/3 and 1%/5 mm) between the predicted and the ground truth dose maps. Our approach approximately took 6 s to reconstruct PA images for each patient, demonstrating its feasibility for online 3D dose verification for prostate proton therapy.

CONCLUSIONS: Our method demonstrated the feasibility of achieving 3D high-precision PA-based dose verification using patient-specific deep-learning approaches, which can potentially be used to guide the treatment to mitigate the impact of range uncertainty and improve the precision. Further studies are needed to validate the clinical impact of the technique.

PMID:38980065 | DOI:10.1002/mp.17294

Microbiol Spectr. 2024 Jul 9:e0003224. doi: 10.1128/spectrum.00032-24. Online ahead of print.

ABSTRACT

Time-lapse microscopy offers a powerful approach for analyzing cellular activity. In particular, this technique is valuable for assessing the behavior of bacterial populations, which can exhibit growth and intercellular interactions in a monolayer. Such time-lapse imaging typically generates large quantities of data, limiting the options for manual investigation. Several image-processing software packages have been developed to facilitate analysis. It can thus be a challenge to identify the software package best suited to a particular research goal. Here, we compare four software packages that support the analysis of 2D time-lapse images of cellular populations: CellProfiler, SuperSegger-Omnipose, DeLTA, and FAST. We compare their performance against benchmarked results on time-lapse observations of Escherichia coli populations. Performance varies across the packages, with each of the four outperforming the others in at least one aspect of the analysis. Not surprisingly, the packages that have been in development for longer showed the strongest performance. We found that deep learning-based approaches to object segmentation outperformed traditional approaches, but the opposite was true for frame-to-frame object tracking. We offer these comparisons, together with insight into usability, computational efficiency, and feature availability, as a guide to researchers seeking image-processing solutions.

IMPORTANCE: Time-lapse microscopy provides a detailed window into the world of bacterial behavior. However, the vast amount of data produced by these techniques is difficult to analyze manually. We have analyzed four software tools designed to process such data and compared their performance, using populations of commonly studied bacterial species as our test subjects. Our findings offer a roadmap to scientists, helping them choose the right tool for their research. This comparison bridges a gap between microbiology and computational analysis, streamlining research efforts.

PMID:38980028 | DOI:10.1128/spectrum.00032-24

J Comput Biol. 2024 Jul 9. doi: 10.1089/cmb.2023.0102. Online ahead of print.

ABSTRACT

Proteins are essential to life, and understanding their intrinsic roles requires determining their structure. The field of proteomics has opened up new opportunities by applying deep learning algorithms to large databases of solved protein structures. With the availability of large data sets and advanced machine learning methods, the prediction of protein residue interactions has greatly improved. Protein contact maps provide empirical evidence of the interacting residue pairs within a protein sequence. Template-free protein structure prediction systems rely heavily on this information. This article proposes UNet-CON, an attention-integrated UNet architecture, trained to predict residue-residue contacts in protein sequences. With the predicted contacts being more accurate than state-of-the-art methods on the PDB25 test set, the model paves the way for the development of more powerful deep learning algorithms for predicting protein residue interactions. The source codes are available in the GitHub link: (https://github.com/jisnava/UNet CON).

PMID:38979621 | DOI:10.1089/cmb.2023.0102

Bioanalysis. 2024 Jul 9:1-3. doi: 10.1080/17576180.2024.2365528. Online ahead of print.

NO ABSTRACT

PMID:38979574 | DOI:10.1080/17576180.2024.2365528

bioRxiv [Preprint]. 2024 Jun 27:2024.06.27.600937. doi: 10.1101/2024.06.27.600937.

ABSTRACT

Approaches studying the dynamics of resting-state functional magnetic resonance imaging (rs-fMRI) activity often focus on time-resolved functional connectivity (tr-FC). While many approaches have been proposed, these typically focus on linear approaches like computing the linear correlation at a timestep or within a window. In this work, we propose to use a generative non-linear deep learning model, a disentangled variational autoencoder (DSVAE), that factorizes out window-specific (context) information from timestep-specific (local) information. This has the advantage of allowing our model to capture differences at multiple temporal scales. For the timestep-specific scale, which has higher temporal precision, we find significant differences between schizophrenia patients and control subjects in their temporal step distance through our model's latent space. We also find that window-specific embeddings, or as we refer to them, context embeddings, more accurately separate windows from schizophrenia patients and control subjects than the standard tr-FC approach. Moreover, we find that for individuals with schizophrenia, our model's context embedding space is significantly correlated with both age and symptom severity. Interestingly, patients appear to spend more time in three clusters, one closer to controls which shows increased visual-sensorimotor, cerebellar-subcortical, and reduced cerebellar-sensorimotor functional network connectivity (FNC), an intermediate station showing increased subcortical-sensorimotor FNC, and one that shows decreased visual-sensorimotor, decreased subcortical-sensorimotor, and increased visual-subcortical domains. We verify that our model captures features that are complementary to - but not the same as - standard tr-FC features. Our model can thus help broaden the neuroimaging toolset in analyzing fMRI dynamics and shows potential as an approach for finding psychiatric links that are more sensitive to individual and group characteristics.

PMID:38979316 | PMC:PMC11230350 | DOI:10.1101/2024.06.27.600937

bioRxiv [Preprint]. 2024 Jun 28:2024.03.15.585121. doi: 10.1101/2024.03.15.585121.

ABSTRACT

The ability to accurately predict antibody-antigen complex structures from their sequences could greatly advance our understanding of the immune system and would aid in the development of novel antibody therapeutics. There have been considerable recent advancements in predicting protein-protein interactions (PPIs) fueled by progress in machine learning (ML). To understand the current state of the field, we compare six representative methods for predicting antibody-antigen complexes from sequence, including two deep learning approaches trained to predict PPIs in general (AlphaFold-Multimer, RoseTTAFold), two composite methods that initially predict antibody and antigen structures separately and dock them (using antibody-mode ClusPro), local refinement in Rosetta (SnugDock) of globally docked poses from ClusPro, and a pipeline combining homology modeling with rigid-body docking informed by ML-based epitope and paratope prediction (AbAdapt). We find that AlphaFold-Multimer outperformed other methods, although the absolute performance leaves considerable room for improvement. AlphaFold-Multimer models of lower-quality display significant structural biases at the level of tertiary motifs (TERMs) towards having fewer structural matches in non-antibody containing structures from the Protein Data Bank (PDB). Specifically, better models exhibit more common PDB-like TERMs at the antibody-antigen interface than worse ones. Importantly, the clear relationship between performance and the commonness of interfacial TERMs suggests that scarcity of interfacial geometry data in the structural database may currently limit application of machine learning to the prediction of antibody-antigen interactions.

PMID:38979267 | PMC:PMC11230293 | DOI:10.1101/2024.03.15.585121