J Med Internet Res. 2024 Aug 5;26:e56750. doi: 10.2196/56750.

ABSTRACT

BACKGROUND: Fall detection is of great significance in safeguarding human health. By monitoring the motion data, a fall detection system (FDS) can detect a fall accident. Recently, wearable sensors-based FDSs have become the mainstream of research, which can be categorized into threshold-based FDSs using experience, machine learning-based FDSs using manual feature extraction, and deep learning (DL)-based FDSs using automatic feature extraction. However, most FDSs focus on the global information of sensor data, neglecting the fact that different segments of the data contribute variably to fall detection. This shortcoming makes it challenging for FDSs to accurately distinguish between similar human motion patterns of actual falls and fall-like actions, leading to a decrease in detection accuracy.

OBJECTIVE: This study aims to develop and validate a DL framework to accurately detect falls using acceleration and gyroscope data from wearable sensors. We aim to explore the essential contributing features extracted from sensor data to distinguish falls from activities of daily life. The significance of this study lies in reforming the FDS by designing a weighted feature representation using DL methods to effectively differentiate between fall events and fall-like activities.

METHODS: Based on the 3-axis acceleration and gyroscope data, we proposed a new DL architecture, the dual-stream convolutional neural network self-attention (DSCS) model. Unlike previous studies, the used architecture can extract global feature information from acceleration and gyroscope data. Additionally, we incorporated a self-attention module to assign different weights to the original feature vector, enabling the model to learn the contribution effect of the sensor data and enhance classification accuracy. The proposed model was trained and tested on 2 public data sets: SisFall and MobiFall. In addition, 10 participants were recruited to carry out practical validation of the DSCS model. A total of 1700 trials were performed to test the generalization ability of the model.

RESULTS: The fall detection accuracy of the DSCS model was 99.32% (recall=99.15%; precision=98.58%) and 99.65% (recall=100%; precision=98.39%) on the test sets of SisFall and MobiFall, respectively. In the ablation experiment, we compared the DSCS model with state-of-the-art machine learning and DL models. On the SisFall data set, the DSCS model achieved the second-best accuracy; on the MobiFall data set, the DSCS model achieved the best accuracy, recall, and precision. In practical validation, the accuracy of the DSCS model was 96.41% (recall=95.12%; specificity=97.55%).

CONCLUSIONS: This study demonstrates that the DSCS model can significantly improve the accuracy of fall detection on 2 publicly available data sets and performs robustly in practical validation.

PMID:39102676 | DOI:10.2196/56750

PLoS Comput Biol. 2024 Aug 5;20(8):e1012337. doi: 10.1371/journal.pcbi.1012337. Online ahead of print.

ABSTRACT

A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree, which include extant taxa (external nodes) and their last common ancestors (internal nodes). During phylogenetic tree inference, the branch lengths are typically co-estimated along with other phylogenetic parameters during tree topology space exploration. There are well-known regions of the branch length parameter space where accurate estimation of phylogenetic trees is especially difficult. Several novel studies have recently demonstrated that machine learning approaches have the potential to help solve phylogenetic problems with greater accuracy and computational efficiency. In this study, as a proof of concept, we sought to explore the possibility of machine learning models to predict branch lengths. To that end, we designed several deep learning frameworks to estimate branch lengths on fixed tree topologies from multiple sequence alignments or its representations. Our results show that deep learning methods can exhibit superior performance in some difficult regions of branch length parameter space. For example, in contrast to maximum likelihood inference, which is typically used for estimating branch lengths, deep learning methods are more efficient and accurate. In general, we find that our neural networks achieve similar accuracy to a Bayesian approach and are the best-performing methods when inferring long branches that are associated with distantly related taxa. Together, our findings represent a next step toward accurate, fast, and reliable phylogenetic inference with machine learning approaches.

PMID:39102450 | DOI:10.1371/journal.pcbi.1012337

PLoS Comput Biol. 2024 Aug 5;20(8):e1012327. doi: 10.1371/journal.pcbi.1012327. Online ahead of print.

ABSTRACT

Plasmodium parasites cause Malaria disease, which remains a significant threat to global health, affecting 200 million people and causing 400,000 deaths yearly. Plasmodium falciparum and Plasmodium vivax remain the two main malaria species affecting humans. Identifying the malaria disease in blood smears requires years of expertise, even for highly trained specialists. Literature studies have been coping with the automatic identification and classification of malaria. However, several points must be addressed and investigated so these automatic methods can be used clinically in a Computer-aided Diagnosis (CAD) scenario. In this work, we assess the transfer learning approach by using well-known pre-trained deep learning architectures. We considered a database with 6222 Region of Interest (ROI), of which 6002 are from the Broad Bioimage Benchmark Collection (BBBC), and 220 were acquired locally by us at Fundação Oswaldo Cruz (FIOCRUZ) in Porto Velho Velho, Rondônia-Brazil, which is part of the legal Amazon. We exhaustively cross-validated the dataset using 100 distinct partitions with 80% train and 20% test for each considering circular ROIs (rough segmentation). Our experimental results show that DenseNet201 has a potential to identify Plasmodium parasites in ROIs (infected or uninfected) of microscopic images, achieving 99.41% AUC with a fast processing time. We further validated our results, showing that DenseNet201 was significantly better (99% confidence interval) than the other networks considered in the experiment. Our results support claiming that transfer learning with texture features potentially differentiates subjects with malaria, spotting those with Plasmodium even in Leukocytes images, which is a challenge. In Future work, we intend scale our approach by adding more data and developing a friendly user interface for CAD use. We aim at aiding the worldwide population and our local natives living nearby the legal Amazon's rivers.

PMID:39102445 | DOI:10.1371/journal.pcbi.1012327

PLoS One. 2024 Aug 5;19(8):e0302862. doi: 10.1371/journal.pone.0302862. eCollection 2024.

ABSTRACT

Lumpy skin disease (LSD) is a critical problem for cattle populations, affecting both individual cows and the entire herd. Given cattle's critical role in meeting human needs, effective management of this disease is essential to prevent significant losses. The study proposes a deep learning approach using the MobileNetV2 model and the RMSprop optimizer to address this challenge. Tests on a dataset of healthy and lumpy cattle images show an impressive accuracy of 95%, outperforming existing benchmarks by 4-10%. These results underline the potential of the proposed methodology to revolutionize the diagnosis and management of skin diseases in cattle farming. Researchers and graduate students are the audience for our paper.

PMID:39102387 | DOI:10.1371/journal.pone.0302862

Postgrad Med J. 2024 Aug 5:qgae061. doi: 10.1093/postmj/qgae061. Online ahead of print.

ABSTRACT

BACKGROUND: With the rapid advancement of deep learning network technology, the application of facial recognition technology in the medical field has received increasing attention.

OBJECTIVE: This study aims to systematically review the literature of the past decade on facial recognition technology based on deep learning networks in the diagnosis of rare dysmorphic diseases and facial paralysis, among other conditions, to determine the effectiveness and applicability of this technology in disease identification.

METHODS: This study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for literature search and retrieved relevant literature from multiple databases, including PubMed, on 31 December 2023. The search keywords included deep learning convolutional neural networks, facial recognition, and disease recognition. A total of 208 articles on facial recognition technology based on deep learning networks in disease diagnosis over the past 10 years were screened, and 22 articles were selected for analysis. The meta-analysis was conducted using Stata 14.0 software.

RESULTS: The study collected 22 articles with a total sample size of 57 539 cases, of which 43 301 were samples with various diseases. The meta-analysis results indicated that the accuracy of deep learning in facial recognition for disease diagnosis was 91.0% [95% CI (87.0%, 95.0%)].

CONCLUSION: The study results suggested that facial recognition technology based on deep learning networks has high accuracy in disease diagnosis, providing a reference for further development and application of this technology.

PMID:39102373 | DOI:10.1093/postmj/qgae061

IEEE J Biomed Health Inform. 2024 Aug 5;PP. doi: 10.1109/JBHI.2024.3438439. Online ahead of print.

ABSTRACT

Extensive research indicates that microRNAs (miRNAs) play a crucial role in the analysis of complex human diseases. Recently, numerous methods utilizing graph neural networks have been developed to investigate the complex relationships between miRNAs and diseases. However, these methods often face challenges in terms of overall effectiveness and are sensitive to node positioning. To address these issues, the researchers introduce DARSFormer, an advanced deep learning model that integrates dynamic attention mechanisms with a spectral graph Transformer effectively. In the DARSFormer model, a miRNA-disease heterogeneous network is constructed initially. This network undergoes spectral decomposition into eigenvalues and eigenvectors, with the eigenvalue scalars being mapped into a vector space subsequently. An orthogonal graph neural network is employed to refine the parameter matrix. The enhanced features are then input into a graph Transformer, which utilizes a dynamic attention mechanism to amalgamate features by aggregating the enhanced neighbor features of miRNA and disease nodes. A projection layer is subsequently utilized to derive the association scores between miRNAs and diseases. The performance of DARSFormer in predicting miRNA-disease associations is exemplary. It achieves an AUC of 94.18% in a five-fold cross-validation on the HMDD v2.0 database. Similarly, on HMDD v3.2, it records an AUC of 95.27%. Case studies involving colorectal, esophageal, and prostate tumors confirm 27, 28, and 26 of the top 30 associated miRNAs against the dbDEMC and miR2Disease databases, respectively. The code and data for DARSFormer are accessible at https://github.com/baibaibaialone/DARSFormer.

PMID:39102330 | DOI:10.1109/JBHI.2024.3438439

IEEE J Biomed Health Inform. 2024 Aug 5;PP. doi: 10.1109/JBHI.2024.3438167. Online ahead of print.

ABSTRACT

This paper presents a novel motor imagery classification algorithm that uses an overlapping multiscale multiband convolutional Riemannian network with band-wise Riemannian triplet loss to improve classification performance. Despite the superior performance of the Riemannian approach over the common spatial pattern filter approach, deep learning methods that generalize the Riemannian approach have received less attention. The proposed algorithm develops a state-of-the-art multiband Riemannian network that reduces the potential overfitting problem of Riemannian networks, a drawback of Riemannian networks due to their inherent large feature dimension from covariance matrix, by using fewer subbands with discriminative frequency diversity, by inserting convolutional layers before computing the subband covariance matrix, and by regularizing subband networks with Riemannian triplet loss. The proposed method is evaluated using the publicly available datasets, the BCI Competition IV dataset 2a and the OpenBMI dataset. The experimental results confirm that the proposed method improves performance, in particular achieving state-of-the-art classification accuracy among the currently studied Riemannian networks.

PMID:39102329 | DOI:10.1109/JBHI.2024.3438167

IEEE Trans Neural Syst Rehabil Eng. 2024 Aug 5;PP. doi: 10.1109/TNSRE.2024.3438610. Online ahead of print.

ABSTRACT

Accurate sleep stage classification is significant for sleep health assessment. In recent years, several machine-learning based sleep staging algorithms have been developed, and in particular, deep-learning based algorithms have achieved performance on par with human annotation. Despite improved performance, a limitation of most deep-learning based algorithms is their black-box behavior, which have limited their use in clinical settings. Here, we propose a cross-modal transformer, which is a transformer-based method for sleep stage classification. The proposed cross-modal transformer consists of a cross-modal transformer encoder architecture along with a multi-scale one-dimensional convolutional neural network for automatic representation learning. The performance of our method is on-par with the state-of-the-art methods and eliminates the black-box behavior of deep-learning models by utilizing the interpretability aspect of the attention modules. Furthermore, our method provides considerable reductions in the number of parameters and training time compared to the state-of-the-art methods. Our code is available at https://github.com/Jathurshan0330/Cross-Modal-Transformer. A demo of our work can be found at https://bit.ly/Cross_modal_transformer_demo.

PMID:39102323 | DOI:10.1109/TNSRE.2024.3438610

Invest Ophthalmol Vis Sci. 2024 Aug 1;65(10):7. doi: 10.1167/iovs.65.10.7.

ABSTRACT

PURPOSE: To examine the influence of subfoveal choroidal thickness (SFCT) and choroidal vascularity index (CVI) on axial length (AL) elongation over a 2-year period in highly myopic children.

METHODS: In this is prospective, longitudinal, observational study, 163 participants (74%), who were 8 to 18 years of age with bilateral high myopia (sphere ≤ -6.0 D) and without pathologic myopia, completed follow-up visits over 2 years. All participants underwent baseline and follow-up ocular examinations, including swept-source optical coherence tomography (SS-OCT) and AL measurements. SFCT and CVI were derived from SS-OCT scans using a deep-learning-based program for choroidal structure assessment.

RESULTS: The mean age of the participants at baseline was 15.0 years (±2.3), with males constituting 47% of the cohort. An inverse relationship was observed between AL elongation and increases in baseline age, baseline SFCT, and CVI, as well as a decrease in baseline AL. Adjusting for other factors, every 10-µm increase in SFCT and each 1% increase in CVI were associated with decreases in AL elongation of 0.007 mm (95% confidence interval [CI], -0.013 to -0.002; P = 0.011) and 0.010 mm (95% CI, -0.019 to 0.000; P = 0.050), respectively. The incorporation of SFCT or CVI into predictive models improved discrimination over models using only age, gender, and baseline AL (both P < 0.05, likelihood ratio test).

CONCLUSIONS: Our findings suggest a possible association between a thinner choroid and increased AL elongation over 2 years in children with high myopia, after adjusting for potential baseline risk factors such as age, gender, and initial AL.

PMID:39102263 | DOI:10.1167/iovs.65.10.7

Transl Vis Sci Technol. 2024 Aug 1;13(8):6. doi: 10.1167/tvst.13.8.6.

ABSTRACT

PURPOSE: To explore the contributions of fundus autofluorescence (FAF) topographic imaging features to the performance of convolutional neural network-based deep learning (DL) algorithms in predicting geographic atrophy (GA) growth rate.

METHODS: Retrospective study with data from study eyes from three clinical trials (NCT02247479, NCT02247531, NCT02479386) in GA. The algorithm was initially trained with full FAF images, and its performance was considered benchmark. Ablation experiments investigated the contribution of imaging features to the performance of the algorithms. Three FAF image regions were defined relative to GA: Lesion, Rim, and Background. For No Lesion, No Rim, and No Background datasets, a single region of interest was removed at a time. For Lesion, Rim, and Background Shuffled datasets, individual region pixels were randomly shuffled. For Lesion, Rim, and Background Mask datasets, masks of the regions were used. A Convex Hull dataset was generated to evaluate the importance of lesion size. Squared Pearson correlation (r2) was used to compare the predictive performance of ablated datasets relative to the benchmark.

RESULTS: The Rim region influenced r2 more than the other two regions in all experiments, indicating the most relevant contribution of this region to the performance of the algorithms. In addition, similar performance was observed for all regions when pixels were shuffled or only a mask was used, indicating intensity information was not independently informative without textural context.

CONCLUSIONS: These ablation experiments enabled topographic clinical insights on FAF images from a DL-based GA progression prediction algorithm.

TRANSLATIONAL RELEVANCE: Results from this study may lead to new insights on GA progression prediction.

PMID:39102242 | DOI:10.1167/tvst.13.8.6

Plant Cell Rep. 2024 Aug 5;43(8):208. doi: 10.1007/s00299-024-03294-9.

ABSTRACT

The application of deep learning methods, specifically the utilization of Large Language Models (LLMs), in the field of plant biology holds significant promise for generating novel knowledge on plant cell systems. The LLM framework exhibits exceptional potential, particularly with the development of Protein Language Models (PLMs), allowing for in-depth analyses of nucleic acid and protein sequences. This analytical capacity facilitates the discernment of intricate patterns and relationships within biological data, encompassing multi-scale information within DNA or protein sequences. The contribution of PLMs extends beyond mere sequence patterns and structure--function recognition; it also supports advancements in genetic improvements for agriculture. The integration of deep learning approaches into the domain of plant sciences offers opportunities for major breakthroughs in basic research across multi-scale plant traits. Consequently, the strategic application of deep learning methodologies, particularly leveraging the potential of LLMs, will undoubtedly play a pivotal role in advancing plant sciences, plant production, plant uses and propelling the trajectory toward sustainable agroecological and agro-food transitions.

PMID:39102077 | DOI:10.1007/s00299-024-03294-9

Phys Eng Sci Med. 2024 Aug 5. doi: 10.1007/s13246-024-01462-5. Online ahead of print.

ABSTRACT

Intensity-modulated radiation therapy (IMRT) has been widely used in treating head and neck tumors. However, due to the complex anatomical structures in the head and neck region, it is challenging for the plan optimizer to rapidly generate clinically acceptable IMRT treatment plans. A novel deep learning multi-scale Transformer (MST) model was developed in the current study aiming to accelerate the IMRT planning for head and neck tumors while generating more precise prediction of the voxel-level dose distribution. The proposed end-to-end MST model employs the shunted Transformer to capture multi-scale features and learn a global dependency, and utilizes 3D deformable convolution bottleneck blocks to extract shape-aware feature and compensate the loss of spatial information in the patch merging layers. Moreover, data augmentation and self-knowledge distillation are used to further improve the prediction performance of the model. The MST model was trained and evaluated on the OpenKBP Challenge dataset. Its prediction accuracy was compared with three previous dose prediction models: C3D, TrDosePred, and TSNet. The predicted dose distributions of our proposed MST model in the tumor region are closest to the original clinical dose distribution. The MST model achieves the dose score of 2.23 Gy and the DVH score of 1.34 Gy on the test dataset, outperforming the other three models by 8%-17%. For clinical-related DVH dosimetric metrics, the prediction accuracy in terms of mean absolute error (MAE) is 2.04% for D 99 , 1.54% for D 95 , 1.87% for D 1 , 1.87% for D mean , 1.89% for D 0.1 c c , respectively, superior to the other three models. The quantitative results demonstrated that the proposed MST model achieved more accurate voxel-level dose prediction than the previous models for head and neck tumors. The MST model has a great potential to be applied to other disease sites to further improve the quality and efficiency of radiotherapy planning.

PMID:39101991 | DOI:10.1007/s13246-024-01462-5

Vis Comput Ind Biomed Art. 2024 Aug 5;7(1):20. doi: 10.1186/s42492-024-00171-w.

ABSTRACT

Large language models (LLMs), such as ChatGPT, have demonstrated impressive capabilities in various tasks and attracted increasing interest as a natural language interface across many domains. Recently, large vision-language models (VLMs) that learn rich vision-language correlation from image-text pairs, like BLIP-2 and GPT-4, have been intensively investigated. However, despite these developments, the application of LLMs and VLMs in image quality assessment (IQA), particularly in medical imaging, remains unexplored. This is valuable for objective performance evaluation and potential supplement or even replacement of radiologists' opinions. To this end, this study introduces IQAGPT, an innovative computed tomography (CT) IQA system that integrates image-quality captioning VLM with ChatGPT to generate quality scores and textual reports. First, a CT-IQA dataset comprising 1,000 CT slices with diverse quality levels is professionally annotated and compiled for training and evaluation. To better leverage the capabilities of LLMs, the annotated quality scores are converted into semantically rich text descriptions using a prompt template. Second, the image-quality captioning VLM is fine-tuned on the CT-IQA dataset to generate quality descriptions. The captioning model fuses image and text features through cross-modal attention. Third, based on the quality descriptions, users verbally request ChatGPT to rate image-quality scores or produce radiological quality reports. Results demonstrate the feasibility of assessing image quality using LLMs. The proposed IQAGPT outperformed GPT-4 and CLIP-IQA, as well as multitask classification and regression models that solely rely on images.

PMID:39101954 | DOI:10.1186/s42492-024-00171-w

J Chem Inf Model. 2024 Aug 5. doi: 10.1021/acs.jcim.4c00616. Online ahead of print.

ABSTRACT

Single-cell omics techniques have made it possible to analyze individual cells in biological samples, providing us with a more detailed understanding of cellular heterogeneity and biological systems. Accurate identification of cell types is critical for single-cell RNA sequencing (scRNA-seq) analysis. However, scRNA-seq data are usually high dimensional and sparse, posing a great challenge to analyze scRNA-seq data. Existing cell-type annotation methods are either constrained in modeling scRNA-seq data or lack consideration of long-term dependencies of characterized genes. In this work, we developed a Transformer-based deep learning method, scSwinFormer, for the cell-type annotation of large-scale scRNA-seq data. Sequence modeling of scRNA-seq data is performed using the smooth gene embedding module, and then, the potential dependencies of genes are captured by the self-attention module. Subsequently, the global information inherent in scRNA-seq data is synthesized using the Cell Token, thereby facilitating accurate cell-type annotation. We evaluated the performance of our model against current state-of-the-art scRNA-seq cell-type annotation methods on multiple real data sets. ScSwinFormer outperforms the current state-of-the-art scRNA-seq cell-type annotation methods in both external and benchmark data set experiments.

PMID:39101690 | DOI:10.1021/acs.jcim.4c00616

Clin Oral Implants Res. 2024 Aug 5. doi: 10.1111/clr.14338. Online ahead of print.

ABSTRACT

OBJECTIVES: The objective of this study is to assess accuracy, time-efficiency and consistency of a novel artificial intelligence (AI)-driven automated tool for cone-beam computed tomography (CBCT) and intraoral scan (IOS) registration compared with manual and semi-automated approaches.

MATERIALS AND METHODS: A dataset of 31 intraoral scans (IOSs) and CBCT scans was used to validate automated IOS-CBCT registration (AR) when compared with manual (MR) and semi-automated registration (SR). CBCT scans were conducted by placing cotton rolls between the cheeks and teeth to facilitate gingival delineation. The time taken to perform multimodal registration was recorded in seconds. A qualitative analysis was carried out to assess the correspondence between hard and soft tissue anatomy on IOS and CBCT. In addition, a quantitative analysis was conducted by measuring median surface deviation (MSD) and root mean square (RMS) differences between registered IOSs.

RESULTS: AR was the most time-efficient, taking 51.4 ± 17.2 s, compared with MR (840 ± 168.9 s) and SR approaches (274.7 ± 100.7 s). Both AR and SR resulted in significantly higher qualitative scores, favoring perfect IOS-CBCT registration, compared with MR (p = .001). Additionally, AR demonstrated significantly superior quantitative performance compared with SR, as indicated by low MSD (0.04 ± 0.07 mm) and RMS (0.19 ± 0.31 mm). In contrast, MR exhibited a significantly higher discrepancy compared with both AR (MSD = 0.13 ± 0.20 mm; RMS = 0.32 ± 0.14 mm) and SR (MSD = 0.11 ± 0.15 mm; RMS = 0.40 ± 0.30 mm).

CONCLUSIONS: The novel AI-driven method provided an accurate, time-efficient, and consistent multimodal IOS-CBCT registration, encompassing both soft and hard tissues. This approach stands as a valuable alternative to manual and semi-automated registration approaches in the presurgical implant planning workflow.

PMID:39101603 | DOI:10.1111/clr.14338

J Neuropathol Exp Neurol. 2024 Aug 5:nlae083. doi: 10.1093/jnen/nlae083. Online ahead of print.

ABSTRACT

Neuropathologic changes of Alzheimer disease (AD) including Aβ accumulation and neuroinflammation are frequently observed in the cerebral cortex of patients with idiopathic normal pressure hydrocephalus (iNPH). We created an automated analysis platform to quantify Aβ load and reactive microglia in the vicinity of Aβ plaques and to evaluate their association with cognitive outcome in cortical biopsies of patients with iNPH obtained at the time of shunting. Aiforia Create deep learning software was used on whole slide images of Iba1/4G8 double immunostained frontal cortical biopsies of 120 shunted iNPH patients to identify Iba1-positive microglia somas and Aβ areas, respectively. Dementia, AD clinical syndrome (ACS), and Clinical Dementia Rating Global score (CDR-GS) were evaluated retrospectively after a median follow-up of 4.4 years. Deep learning artificial intelligence yielded excellent (>95%) precision for tissue, Aβ, and microglia somas. Using an age-adjusted model, higher Aβ coverage predicted the development of dementia, the diagnosis of ACS, and more severe memory impairment by CDR-GS whereas measured microglial densities and Aβ-related microglia did not correlate with cognitive outcome in these patients. Therefore, cognitive outcome seems to be hampered by higher Aβ coverage in cortical biopsies in shunted iNPH patients but is not correlated with densities of surrounding microglia.

PMID:39101555 | DOI:10.1093/jnen/nlae083

Cytometry A. 2024 Aug 5. doi: 10.1002/cyto.a.24890. Online ahead of print.

ABSTRACT

Imaging flow cytometry, which combines the advantages of flow cytometry and microscopy, has emerged as a powerful tool for cell analysis in various biomedical fields such as cancer detection. In this study, we develop multiplex imaging flow cytometry (mIFC) by employing a spatial wavelength division multiplexing technique. Our mIFC can simultaneously obtain brightfield and multi-color fluorescence images of individual cells in flow, which are excited by a metal halide lamp and measured by a single detector. Statistical analysis results of multiplex imaging experiments with resolution test lens, magnification test lens, and fluorescent microspheres validate the operation of the mIFC with good imaging channel consistency and micron-scale differentiation capabilities. A deep learning method is designed for multiplex image processing that consists of three deep learning networks (U-net, very deep super resolution, and visual geometry group 19). It is demonstrated that the cluster of differentiation 24 (CD24) imaging channel is more sensitive than the brightfield, nucleus, or cancer antigen 125 (CA125) imaging channel in classifying the three types of ovarian cell lines (IOSE80 normal cell, A2780, and OVCAR3 cancer cells). An average accuracy rate of 97.1% is achieved for the classification of these three types of cells by deep learning analysis when all four imaging channels are considered. Our single-detector mIFC is promising for the development of future imaging flow cytometers and for the automatic single-cell analysis with deep learning in various biomedical fields.

PMID:39101554 | DOI:10.1002/cyto.a.24890

Brief Bioinform. 2024 Jul 25;25(5):bbae358. doi: 10.1093/bib/bbae358.

ABSTRACT

PROteolysis TArgeting Chimeras (PROTACs) has recently emerged as a promising technology. However, the design of rational PROTACs, especially the linker component, remains challenging due to the absence of structure-activity relationships and experimental data. Leveraging the structural characteristics of PROTACs, fragment-based drug design (FBDD) provides a feasible approach for PROTAC research. Concurrently, artificial intelligence-generated content has attracted considerable attention, with diffusion models and Transformers emerging as indispensable tools in this field. In response, we present a new diffusion model, DiffPROTACs, harnessing the power of Transformers to learn and generate new PROTAC linkers based on given ligands. To introduce the essential inductive biases required for molecular generation, we propose the O(3) equivariant graph Transformer module, which augments Transformers with graph neural networks (GNNs), using Transformers to update nodes and GNNs to update the coordinates of PROTAC atoms. DiffPROTACs effectively competes with existing models and achieves comparable performance on two traditional FBDD datasets, ZINC and GEOM. To differentiate the molecular characteristics between PROTACs and traditional small molecules, we fine-tuned the model on our self-built PROTACs dataset, achieving a 93.86% validity rate for generated PROTACs. Additionally, we provide a generated PROTAC database for further research, which can be accessed at https://bailab.siais.shanghaitech.edu.cn/service/DiffPROTACs-generated.tgz. The corresponding code is available at https://github.com/Fenglei104/DiffPROTACs and the server is at https://bailab.siais.shanghaitech.edu.cn/services/diffprotacs.

PMID:39101502 | DOI:10.1093/bib/bbae358

Adv Sci (Weinh). 2024 Aug 5:e2304305. doi: 10.1002/advs.202304305. Online ahead of print.

ABSTRACT

Self-supervised neural language models have recently achieved unprecedented success from natural language processing to learning the languages of biological sequences and organic molecules. These models have demonstrated superior performance in the generation, structure classification, and functional predictions for proteins and molecules with learned representations. However, most of the masking-based pre-trained language models are not designed for generative design, and their black-box nature makes it difficult to interpret their design logic. Here a Blank-filling Language Model for Materials (BLMM) Crystal Transformer is proposed, a neural network-based probabilistic generative model for generative and tinkering design of inorganic materials. The model is built on the blank-filling language model for text generation and has demonstrated unique advantages in learning the "materials grammars" together with high-quality generation, interpretability, and data efficiency. It can generate chemically valid materials compositions with as high as 89.7% charge neutrality and 84.8% balanced electronegativity, which are more than four and eight times higher compared to a pseudo-random sampling baseline. The probabilistic generation process of BLMM allows it to recommend materials tinkering operations based on learned materials chemistry, which makes it useful for materials doping. The model is applied to discover a set of new materials as validated using the Density Functional Theory (DFT) calculations. This work thus brings the unsupervised transformer language models based generative artificial intelligence to inorganic materials. A user-friendly web app for tinkering materials design has been developed and can be accessed freely at www.materialsatlas.org/blmtinker.

PMID:39101275 | DOI:10.1002/advs.202304305

MethodsX. 2024 Jul 3;13:102843. doi: 10.1016/j.mex.2024.102843. eCollection 2024 Dec.

ABSTRACT

Event of the disastrous scenarios are actively discussed on microblogging platforms like Twitter which can lead to chaotic situations. In the era of machine learning and deep learning, these chaotic situations can be effectively controlled by developing efficient methods and models that can assist in classifying real and fake tweets. In this research article, an efficient method named BERT Embedding based CNN model with RMSProp Optimizer is proposed to effectively classify the tweets related disastrous scenario. Tweet classification is carried out via some of the popular the machine learning algorithms such as logistic regression and decision tree classifiers. Noting the low accuracy of machine learning models, Convolutional Neural Network (CNN) based deep learning model is selected as the primary classification method. CNNs performance is improved via optimization of the parameters with gradient based optimizers. To further elevate accuracy and to capture contextual semantics from the text data, BERT embeddings are included in the proposed model. The performance of proposed method - BERT Embedding based CNN model with RMSProp Optimizer achieved an F1 score of 0.80 and an Accuracy of 0.83. The methodology presented in this research article is comprised of the following key contributions:•Identification of suitable text classification model that can effectively capture complex patterns when dealing with large vocabularies or nuanced language structures in disaster management scenarios.•The method explores the gradient based optimization techniques such as Adam Optimizer, Stochastic Gradient Descent (SGD) Optimizer, AdaGrad, and RMSprop Optimizer to identify the most appropriate optimizer that meets the characteristics of the dataset and the CNN model architecture.•"BERT Embedding based CNN model with RMSProp Optimizer" - a method to classify the disaster tweets and capture semantic representations by leveraging BERT embeddings with appropriate feature selection is presented and models are validated with appropriate comparative analysis.

PMID:39101121 | PMC:PMC11296064 | DOI:10.1016/j.mex.2024.102843