Cell Syst. 2024 May 15;15(5):475-482.e6. doi: 10.1016/j.cels.2024.04.006.

ABSTRACT

Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep-learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from multiplexed error-robust FISH (MERFISH), sequential fluorescence in situ hybridization (seqFISH), or in situ RNA sequencing (ISS) experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.

PMID:38754367 | DOI:10.1016/j.cels.2024.04.006

Cell Syst. 2024 May 15;15(5):411-424.e9. doi: 10.1016/j.cels.2024.04.004.

ABSTRACT

The snapshot nature of single-cell transcriptomics presents a challenge for studying the dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal information at single-cell level, but current methods have limitations. Here, we present a framework that overcomes these limitations: experimentally, we developed sci-FATE2, an optimized method for metabolic labeling with increased data quality, which we used to profile 45,000 embryonic stem (ES) cells differentiating into neural tube identities. Computationally, we developed a two-stage framework for dynamical modeling: VelvetVAE, a variational autoencoder (VAE) for velocity inference that outperforms all other tools tested, and VelvetSDE, a neural stochastic differential equation (nSDE) framework for simulating trajectory distributions. These recapitulate underlying dataset distributions and capture features such as decision boundaries between alternative fates and fate-specific gene expression. These methods recast single-cell analyses from descriptions of observed data to models of the dynamics that generated them, providing a framework for investigating developmental fate decisions.

PMID:38754365 | DOI:10.1016/j.cels.2024.04.004

Comput Biol Chem. 2024 May 10;110:108092. doi: 10.1016/j.compbiolchem.2024.108092. Online ahead of print.

ABSTRACT

The number of mitotic cells is an important indicator of grading invasive breast cancer. It is very challenging for pathologists to identify and count mitotic cells in pathological sections with naked eyes under the microscope. Therefore, many computational models for the automatic identification of mitotic cells based on machine learning, especially deep learning, have been proposed. However, converging to the local optimal solution is one of the main problems in model training. In this paper, we proposed a novel multilevel iterative training strategy to address the problem. To evaluate the proposed training strategy, we constructed the mitotic cell classification model with ResNet50 and trained the model with different training strategies. The results showed that the models trained with the proposed training strategy performed better than those trained with the conventional strategy in the independent test set, illustrating the effectiveness of the new training strategy. Furthermore, after training with our proposed strategy, the ResNet50 model with Adam optimizer has achieved 89.26% F1 score on the public MITOSI14 dataset, which is higher than that of the state-of-the-art methods reported in the literature.

PMID:38754259 | DOI:10.1016/j.compbiolchem.2024.108092

Environ Int. 2024 May 11;188:108739. doi: 10.1016/j.envint.2024.108739. Online ahead of print.

ABSTRACT

INTRODUCTION: Protective associations of greenspace with Parkinson's disease (PD) have been observed in some studies. Visual exposure to greenspace seems to be important for some of the proposed pathways underlying these associations. However, most studies use overhead-view measures (e.g., satellite imagery, land-classification data) that do not capture street-view greenspace and cannot distinguish between specific greenspace types. We aimed to evaluate associations of street-view greenspace measures with hospitalizations with a PD diagnosis code (PD-involved hospitalization).

METHODS: We created an open cohort of about 45.6 million Medicare fee-for-service beneficiaries aged 65 + years living in core based statistical areas (i.e. non-rural areas) in the contiguous US (2007-2016). We obtained 350 million Google Street View images across the US and applied deep learning algorithms to identify percentages of specific greenspace features in each image, including trees, grass, and other green features (i.e., plants, flowers, fields). We assessed yearly average street-view greenspace features for each ZIP code. A Cox-equivalent re-parameterized Poisson model adjusted for potential confounders (i.e. age, race/ethnicity, socioeconomic status) was used to evaluate associations with first PD-involved hospitalization.

RESULTS: There were 506,899 first PD-involved hospitalizations over 254,917,192 person-years of follow-up. We found a hazard ratio (95% confidence interval) of 0.96 (0.95, 0.96) per interquartile range (IQR) increase for trees and a HR of 0.97 (0.96, 0.97) per IQR increase for other green features. In contrast, we found a HR of 1.06 (1.04, 1.07) per IQR increase for grass. Associations of trees were generally stronger for low-income (i.e. Medicaid eligible) individuals, Black individuals, and in areas with a lower median household income and a higher population density.

CONCLUSION: Increasing exposure to trees and other green features may reduce PD-involved hospitalizations, while increasing exposure to grass may increase hospitalizations. The protective associations may be stronger for marginalized individuals and individuals living in densely populated areas.

PMID:38754245 | DOI:10.1016/j.envint.2024.108739

Comput Biol Med. 2024 May 8;176:108560. doi: 10.1016/j.compbiomed.2024.108560. Online ahead of print.

ABSTRACT

Mutagenicity assessment plays a pivotal role in the safety evaluation of chemicals, pharmaceuticals, and environmental compounds. In recent years, the development of robust computational models for predicting chemical mutagenicity has gained significant attention, driven by the need for efficient and cost-effective toxicity assessments. In this paper, we proposed AMPred-CNN, an innovative Ames mutagenicity prediction model based on Convolutional Neural Networks (CNNs), uniquely employing molecular structures as images to leverage CNNs' powerful feature extraction capabilities. The study employs the widely used benchmark mutagenicity dataset from Hansen et al. for model development and evaluation. Comparative analyses with traditional ML models on different molecular features reveal substantial performance enhancements. AMPred-CNN outshines these models, demonstrating superior accuracy, AUC, F1 score, MCC, sensitivity, and specificity on the test set. Notably, AMPred-CNN is further benchmarked against seven recent ML and DL models, consistently showcasing superior performance with an impressive AUC of 0.954. Our study highlights the effectiveness of CNNs in advancing mutagenicity prediction, paving the way for broader applications in toxicology and drug development.

PMID:38754218 | DOI:10.1016/j.compbiomed.2024.108560

JMIR Dermatol. 2024 May 16;7:e55898. doi: 10.2196/55898.

ABSTRACT

BACKGROUND: Dermatologic patient education materials (PEMs) are often written above the national average seventh- to eighth-grade reading level. ChatGPT-3.5, GPT-4, DermGPT, and DocsGPT are large language models (LLMs) that are responsive to user prompts. Our project assesses their use in generating dermatologic PEMs at specified reading levels.

OBJECTIVE: This study aims to assess the ability of select LLMs to generate PEMs for common and rare dermatologic conditions at unspecified and specified reading levels. Further, the study aims to assess the preservation of meaning across such LLM-generated PEMs, as assessed by dermatology resident trainees.

METHODS: The Flesch-Kincaid reading level (FKRL) of current American Academy of Dermatology PEMs was evaluated for 4 common (atopic dermatitis, acne vulgaris, psoriasis, and herpes zoster) and 4 rare (epidermolysis bullosa, bullous pemphigoid, lamellar ichthyosis, and lichen planus) dermatologic conditions. We prompted ChatGPT-3.5, GPT-4, DermGPT, and DocsGPT to "Create a patient education handout about [condition] at a [FKRL]" to iteratively generate 10 PEMs per condition at unspecified fifth- and seventh-grade FKRLs, evaluated with Microsoft Word readability statistics. The preservation of meaning across LLMs was assessed by 2 dermatology resident trainees.

RESULTS: The current American Academy of Dermatology PEMs had an average (SD) FKRL of 9.35 (1.26) and 9.50 (2.3) for common and rare diseases, respectively. For common diseases, the FKRLs of LLM-produced PEMs ranged between 9.8 and 11.21 (unspecified prompt), between 4.22 and 7.43 (fifth-grade prompt), and between 5.98 and 7.28 (seventh-grade prompt). For rare diseases, the FKRLs of LLM-produced PEMs ranged between 9.85 and 11.45 (unspecified prompt), between 4.22 and 7.43 (fifth-grade prompt), and between 5.98 and 7.28 (seventh-grade prompt). At the fifth-grade reading level, GPT-4 was better at producing PEMs for both common and rare conditions than ChatGPT-3.5 (P=.001 and P=.01, respectively), DermGPT (P<.001 and P=.03, respectively), and DocsGPT (P<.001 and P=.02, respectively). At the seventh-grade reading level, no significant difference was found between ChatGPT-3.5, GPT-4, DocsGPT, or DermGPT in producing PEMs for common conditions (all P>.05); however, for rare conditions, ChatGPT-3.5 and DocsGPT outperformed GPT-4 (P=.003 and P<.001, respectively). The preservation of meaning analysis revealed that for common conditions, DermGPT ranked the highest for overall ease of reading, patient understandability, and accuracy (14.75/15, 98%); for rare conditions, handouts generated by GPT-4 ranked the highest (14.5/15, 97%).

CONCLUSIONS: GPT-4 appeared to outperform ChatGPT-3.5, DocsGPT, and DermGPT at the fifth-grade FKRL for both common and rare conditions, although both ChatGPT-3.5 and DocsGPT performed better than GPT-4 at the seventh-grade FKRL for rare conditions. LLM-produced PEMs may reliably meet seventh-grade FKRLs for select common and rare dermatologic conditions and are easy to read, understandable for patients, and mostly accurate. LLMs may play a role in enhancing health literacy and disseminating accessible, understandable PEMs in dermatology.

PMID:38754096 | DOI:10.2196/55898

J Endourol. 2024 May 16. doi: 10.1089/end.2023.0751. Online ahead of print.

ABSTRACT

BACKGROUND: Endoscopy image enhancement technology provides doctors with clearer and more detailed images for observation and diagnosis, allowing doctors to assess lesions more accurately. Unlike most other endoscopy images, cystoscopy images face more complex and diverse image degradation due to their underwater imaging characteristics. Among the various causes of image degradation, the blood haze resulting from bladder mucosal bleeding make the background blurry and unclear, severely affecting diagnostic efficiency, even leading to misjudgment.

MATERIALS AND METHODS: We propose a deep learning-based approach to mitigate the impact of blood haze on cystoscopy images. The approach consists of two parts: a blood haze removal network and a contrast enhancement algorithm. Firstly, we adopt Feature Fusion Attention Network (FFA-Net) and transfer learning in the field of deep learning to remove blood haze from cystoscopy images, and introduce perceptual loss to constrain the network for better visual results. Secondly, we enhance the image contrast by remapping the gray scale of the blood haze-free image and performing weighted fusion of the processed image and the original image.

RESULTS: In the blood haze removal stage, the algorithm proposed in this paper achieves an average peak signal-to-noise ratio of 29.44 decibels, which is 15% higher than state-of-the-art traditional methods. The average structural similarity and perceptual image patch similarity reach 0.9269 and 0.1146, respectively, both superior to state-of-the-art traditional methods. Besides, our method is the best in keeping color balance after removing the blood haze. In the image enhancement stage, our algorithm enhances the contrast of vessels and tissues while preserving the original colors, expanding the dynamic range of the image.

CONCLUSION: The deep learning-based cystoscopy images enhancement method is significantly better than other traditional methods in both qualitative and quantitative evaluation. The application of artificial intelligence will provide clearer, higher contrast cystoscopy images for medical diagnosis.

PMID:38753720 | DOI:10.1089/end.2023.0751

PLoS One. 2024 May 16;19(5):e0302641. doi: 10.1371/journal.pone.0302641. eCollection 2024.

ABSTRACT

The development of automated tools using advanced technologies like deep learning holds great promise for improving the accuracy of lung nodule classification in computed tomography (CT) imaging, ultimately reducing lung cancer mortality rates. However, lung nodules can be difficult to detect and classify, from CT images since different imaging modalities may provide varying levels of detail and clarity. Besides, the existing convolutional neural network may struggle to detect nodules that are small or located in difficult-to-detect regions of the lung. Therefore, the attention pyramid pooling network (APPN) is proposed to identify and classify lung nodules. First, a strong feature extractor, named vgg16, is used to obtain features from CT images. Then, the attention primary pyramid module is proposed by combining the attention mechanism and pyramid pooling module, which allows for the fusion of features at different scales and focuses on the most important features for nodule classification. Finally, we use the gated spatial memory technique to decode the general features, which is able to extract more accurate features for classifying lung nodules. The experimental results on the LIDC-IDRI dataset show that the APPN can achieve highly accurate and effective for classifying lung nodules, with sensitivity of 87.59%, specificity of 90.46%, accuracy of 88.47%, positive predictive value of 95.41%, negative predictive value of 76.29% and area under receiver operating characteristic curve of 0.914.

PMID:38753596 | DOI:10.1371/journal.pone.0302641

Med Phys. 2024 May 16. doi: 10.1002/mp.17130. Online ahead of print.

ABSTRACT

BACKGROUND: Liver fibrosis poses a significant public health challenge given its elevated incidence and associated mortality rates. Diffusion-Weighted Imaging (DWI) serves as a non-invasive diagnostic tool for supporting the identification of liver fibrosis. Deep learning, as a computer-aided diagnostic technology, can assist in recognizing the stage of liver fibrosis by extracting abstract features from DWI images. However, gathering samples is often challenging, posing a common dilemma in previous research. Moreover, previous studies frequently overlooked the cross-comparison information and latent connections among different DWI parameters. Thus, it is becoming a challenge to identify effective DWI parameters and dig potential features from multiple categories in a dataset with limited samples.

PURPOSE: A self-defined Multi-view Contrastive Learning Network is developed to automatically classify multi-parameter DWI images and explore synergies between different DWI parameters.

METHODS: A Dense-fusion Attention Contrastive Learning Network (DACLN) is designed and used to recognize DWI images. Concretely, a multi-view contrastive learning framework is constructed to train and extract features from raw multi-parameter DWI. Besides, a Dense-fusion module is designed to integrate feature and output predicted labels.

RESULTS: We evaluated the performance of the proposed model on a set of real clinical data and analyzed the interpretability by Grad-CAM and annotation analysis, achieving average scores of 0.8825, 0.8702, 0.8933, 0.8727, and 0.8779 for accuracy, precision, recall, specificity and F-1 score. Of note, the experimental results revealed that IVIM-f, CTRW-β, and MONO-ADC exhibited significant recognition ability and complementarity.

CONCLUSION: Our method achieves competitive accuracy in liver fibrosis diagnosis using the limited multi-parameter DWI dataset and finds three types of DWI parameters with high sensitivity for diagnosing liver fibrosis, which suggests potential directions for future research.

PMID:38753547 | DOI:10.1002/mp.17130

Proc Natl Acad Sci U S A. 2024 May 21;121(21):e2309905121. doi: 10.1073/pnas.2309905121. Epub 2024 May 16.

ABSTRACT

Interest in logics with some notion of real-valued truths has existed since at least Boole and has been increasing in AI due to the emergence of neuro-symbolic approaches, though often their logical inference capabilities are characterized only qualitatively. We provide foundations for establishing the correctness and power of such systems. We introduce a rich class of multidimensional sentences, with a sound and complete axiomatization that can be parameterized to cover many real-valued logics, including all the common fuzzy logics, and extend these to weighted versions, and to the case where the truth values are probabilities. Our multidimensional sentences form a very rich class. Each of our multidimensional sentences describes a set of possible truth values for a collection of formulas of the real-valued logic, including which combinations of truth values are possible. Our completeness result is strong, in the sense that it allows us to derive exactly what information can be inferred about the combinations of truth values of a collection of formulas given information about the combinations of truth values of a finite number of other collections of formulas. We give a decision procedure based on linear programming for deciding, for certain real-valued logics and under certain natural assumptions, whether a set of our sentences logically implies another of our sentences. The generality of this work, compared to many previous works on special cases, may provide insights for both existing and new real-valued logics whose inference properties have never been characterized. This work may also provide insights into the reasoning capabilities of deep learning models.

PMID:38753505 | DOI:10.1073/pnas.2309905121

Curr Cardiol Rep. 2024 May 16. doi: 10.1007/s11886-024-02062-1. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: Artificial intelligence (AI) is transforming electrocardiography (ECG) interpretation. AI diagnostics can reach beyond human capabilities, facilitate automated access to nuanced ECG interpretation, and expand the scope of cardiovascular screening in the population. AI can be applied to the standard 12-lead resting ECG and single-lead ECGs in external monitors, implantable devices, and direct-to-consumer smart devices. We summarize the current state of the literature on AI-ECG.

RECENT FINDINGS: Rhythm classification was the first application of AI-ECG. Subsequently, AI-ECG models have been developed for screening structural heart disease including hypertrophic cardiomyopathy, cardiac amyloidosis, aortic stenosis, pulmonary hypertension, and left ventricular systolic dysfunction. Further, AI models can predict future events like development of systolic heart failure and atrial fibrillation. AI-ECG exhibits potential in acute cardiac events and non-cardiac applications, including acute pulmonary embolism, electrolyte abnormalities, monitoring drugs therapy, sleep apnea, and predicting all-cause mortality. Many AI models in the domain of cardiac monitors and smart watches have received Food and Drug Administration (FDA) clearance for rhythm classification, while others for identification of cardiac amyloidosis, pulmonary hypertension and left ventricular dysfunction have received breakthrough device designation. As AI-ECG models continue to be developed, in addition to regulatory oversight and monetization challenges, thoughtful clinical implementation to streamline workflows, avoiding information overload and overwhelming of healthcare systems with false positive results is necessary. Research to demonstrate and validate improvement in healthcare efficiency and improved patient outcomes would be required before widespread adoption of any AI-ECG model.

PMID:38753291 | DOI:10.1007/s11886-024-02062-1

Eur Radiol. 2024 May 16. doi: 10.1007/s00330-024-10793-6. Online ahead of print.

ABSTRACT

OBJECTIVES: To investigate the feasibility of low-radiation dose and low iodinated contrast medium (ICM) dose protocol combining low-tube voltage and deep-learning reconstruction (DLR) algorithm in thin-slice abdominal CT.

METHODS: This prospective study included 148 patients who underwent contrast-enhanced abdominal CT with either 120-kVp (600 mgL/kg, n = 74) or 80-kVp protocol (360 mgL/kg, n = 74). The 120-kVp images were reconstructed using hybrid iterative reconstruction (HIR) (120-kVp-HIR), while 80-kVp images were reconstructed using HIR (80-kVp-HIR) and DLR (80-kVp-DLR) with 0.5 mm thickness. Size-specific dose estimate (SSDE) and iodine dose were compared between protocols. Image noise, CT attenuation, and contrast-to-noise ratio (CNR) were quantified. Noise power spectrum (NPS) and edge rise slope (ERS) were used to evaluate noise texture and edge sharpness, respectively. The subjective image quality was rated on a 4-point scale.

RESULTS: SSDE and iodine doses of 80-kVp were 40.4% (8.1 ± 0.9 vs. 13.6 ± 2.7 mGy) and 36.3% (21.2 ± 3.9 vs. 33.3 ± 4.3 gL) lower, respectively, than those of 120-kVp (both, p < 0.001). CT attenuation of vessels and solid organs was higher in 80-kVp than in 120-kVp images (all, p < 0.001). Image noise of 80-kVp-HIR and 80-kVp-DLR was higher and lower, respectively than that of 120-kVp-HIR (both p < 0.001). The highest CNR and subjective scores were attained in 80-kVp-DLR (all, p < 0.001). There were no significant differences in average NPS frequency and ERS between 120-kVp-HIR and 80-kVp-DLR (p ≥ 0.38).

CONCLUSION: Compared with the 120-kVp-HIR protocol, the combined use of 80-kVp and DLR techniques yielded superior subjective and objective image quality with reduced radiation and ICM doses at thin-section abdominal CT.

CLINICAL RELEVANCE STATEMENT: Scanning at low-tube voltage (80-kVp) combined with the deep-learning reconstruction algorithm may enhance diagnostic efficiency and patient safety by improving image quality and reducing radiation and contrast doses of thin-slice abdominal CT.

KEY POINTS: Reducing radiation and iodine doses is desirable; however, contrast and noise degradation can be detrimental. The 80-kVp scan with the deep-learning reconstruction technique provided better images with lower radiation and contrast doses. This technique may be efficient for improving diagnostic confidence and patient safety in thin-slice abdominal CT.

PMID:38753193 | DOI:10.1007/s00330-024-10793-6

Network. 2024 May 16:1-32. doi: 10.1080/0954898X.2024.2350579. Online ahead of print.

ABSTRACT

One of the most used diagnostic imaging techniques for identifying a variety of lung and bone-related conditions is the chest X-ray. Recent developments in deep learning have demonstrated several successful cases of illness diagnosis from chest X-rays. However, issues of stability and class imbalance still need to be resolved. Hence in this manuscript, multi-class lung disease classification in chest x-ray images using a hybrid manta-ray foraging volcano eruption algorithm boosted multilayer perceptron neural network approach is proposed (MPNN-Hyb-MRF-VEA). Initially, the input chest X-ray images are taken from the Covid-Chest X-ray dataset. Anisotropic diffusion Kuwahara filtering (ADKF) is used to enhance the quality of these images and lower noise. To capture significant discriminative features, the Term frequency-inverse document frequency (TF-IDF) based feature extraction method is utilized in this case. The Multilayer Perceptron Neural Network (MPNN) serves as the classification model for multi-class lung disorders classification as COVID-19, pneumonia, tuberculosis (TB), and normal. A Hybrid Manta-Ray Foraging and Volcano Eruption Algorithm (Hyb-MRF-VEA) is introduced to further optimize and fine-tune the MPNN's parameters. The Python platform is used to accurately evaluate the proposed methodology. The performance of the proposed method provides 23.21%, 12.09%, and 5.66% higher accuracy compared with existing methods like NFM, SVM, and CNN respectively.

PMID:38753162 | DOI:10.1080/0954898X.2024.2350579

Int J Clin Pharm. 2024 May 16. doi: 10.1007/s11096-024-01724-y. Online ahead of print.

ABSTRACT

BACKGROUND: Venlafaxine is frequently prescribed for patients with depression. To control the concentration of venlafaxine within the therapeutic window for the best treatment effect, a model to predict venlafaxine concentration is necessary.

AIM: Our objective was to develop a prediction model for venlafaxine concentration using real-world evidence based on machine learning and deep learning techniques.

METHOD: Patients who underwent venlafaxine treatment between November 2019 and August 2022 were included in the study. Important variables affecting venlafaxine concentration were identified using a combination of univariate analysis, sequential forward selection, and machine learning techniques. Predictive performance of nine machine learning and deep learning algorithms were assessed, and the one with the optimal performance was selected for modeling. The final model was interpreted using SHapley Additive exPlanations.

RESULTS: A total of 330 eligible patients were included. Five influential variables that affect venlafaxine concentration were venlafaxine daily dose, sex, age, hyperlipidemia, and adenosine deaminase. The venlafaxine concentration prediction model was developed using the eXtreme Gradient Boosting algorithm (R2 = 0.65, mean absolute error = 77.92, root mean square error = 93.58). In the testing cohort, the accuracy of the predicted concentration within ± 30% of the actual concentration was 73.49%. In the subgroup analysis, the prediction accuracy was 69.39% within the recommended therapeutic range of venlafaxine concentration within ± 30% of the actual value.

CONCLUSION: The XGBoost model for predicting blood concentration of venlafaxine using real-world evidence was developed, guiding the adjustment of regimen in clinical practice.

PMID:38753076 | DOI:10.1007/s11096-024-01724-y

Chemphyschem. 2024 May 16:e202400176. doi: 10.1002/cphc.202400176. Online ahead of print.

ABSTRACT

We report a deep learning-based approach to accurately predict the emission spectra of phosphorescent heteroleptic [Ir(C^N)2(NN)]+ complexes, enabling the rapid discovery of novel Ir(III) chromophores for diverse applications including organic light-emitting diodes and solar fuel cells. The deep learning models utilize graph neural networks and other chemical features in architectures that reflect the inherent structure of the heteroleptic complexes, composed of C^N and N^N ligands, and are thus geared towards efficient training over the dataset. By leveraging experimental emission data, our models reliably predict the full emission spectra of these complexes across various emission profiles, surpassing the accuracy of conventional DFT and correlated wavefunction methods, while simultaneously achieving robustness to the presence of imperfect (noisy, low-quality) training spectra. We showcase the potential applications for these and related models for \insilico\ prediction of complexes with tailored emission properties, as well as in "design of experiment'' contexts to reduce the synthetic burden of high-throughput screening. In the latter case, we demonstrate that the models allow to exploit a limited amount of experimental data to explore a wide range of chemical space, thus leveraging a modest synthetic effort.

PMID:38752882 | DOI:10.1002/cphc.202400176

Brief Bioinform. 2024 Mar 27;25(3):bbae224. doi: 10.1093/bib/bbae224.

ABSTRACT

Avian reoviruses continue to cause disease in turkeys with varied pathogenicity and tissue tropism. Turkey enteric reovirus has been identified as a causative agent of enteritis or inapparent infections in turkeys. The new emerging variants of turkey reovirus, tentatively named turkey arthritis reovirus (TARV) and turkey hepatitis reovirus (THRV), are linked to tenosynovitis/arthritis and hepatitis, respectively. Turkey arthritis and hepatitis reoviruses are causing significant economic losses to the turkey industry. These infections can lead to poor weight gain, uneven growth, poor feed conversion, increased morbidity and mortality and reduced marketability of commercial turkeys. To combat these issues, detecting and classifying the types of reoviruses in turkey populations is essential. This research aims to employ clustering methods, specifically K-means and Hierarchical clustering, to differentiate three types of turkey reoviruses and identify novel emerging variants. Additionally, it focuses on classifying variants of turkey reoviruses by leveraging various machine learning algorithms such as Support Vector Machines, Naive Bayes, Random Forest, Decision Tree, and deep learning algorithms, including convolutional neural networks (CNNs). The experiments use real turkey reovirus sequence data, allowing for robust analysis and evaluation of the proposed methods. The results indicate that machine learning methods achieve an average accuracy of 92%, F1-Macro of 93% and F1-Weighted of 92% scores in classifying reovirus types. In contrast, the CNN model demonstrates an average accuracy of 85%, F1-Macro of 71% and F1-Weighted of 84% scores in the same classification task. The superior performance of the machine learning classifiers provides valuable insights into reovirus evolution and mutation, aiding in detecting emerging variants of pathogenic TARVs and THRVs.

PMID:38752857 | DOI:10.1093/bib/bbae224

Crit Care Med. 2024 Jun 1;52(6):e330-e331. doi: 10.1097/CCM.0000000000006291. Epub 2024 May 16.

NO ABSTRACT

PMID:38752829 | DOI:10.1097/CCM.0000000000006291

Technol Cancer Res Treat. 2024 Jan-Dec;23:15330338241254060. doi: 10.1177/15330338241254060.

ABSTRACT

Objectives: This study aimed to build a comprehensive deep-learning model for the prediction of radiation pneumonitis using chest computed tomography (CT), clinical, dosimetric, and laboratory data. Introduction: Radiation therapy is an effective tool for treating patients with lung cancer. Despite its effectiveness, the risk of radiation pneumonitis limits its application. Although several studies have demonstrated models to predict radiation pneumonitis, no reliable model has been developed yet. Herein, we developed prediction models using pretreatment chest CT and various clinical data to assess the likelihood of radiation pneumonitis in lung cancer patients. Methods: This retrospective study analyzed 3-dimensional (3D) lung volume data from chest CT scans and 27 features including dosimetric, clinical, and laboratory data from 548 patients who were treated at our institution between 2010 and 2021. We developed a neural network, named MergeNet, which processes lung 3D CT, clinical, dosimetric, and laboratory data. The MergeNet integrates a convolutional neural network with subsequent fully connected layers. A support vector machine (SVM) and light gradient boosting machine (LGBM) model were also implemented for comparison. For comparison, the convolution-only neural network was implemented as well. Three-dimensional Resnet-10 network and 4-fold cross-validation were used. Results: Classification performance was quantified by using the area under the receiver operative characteristic curve (AUC) metrics. MergeNet showed the AUC of 0.689. SVM, LGBM, and convolution-only networks showed AUCs of 0.525, 0.541, and 0.550, respectively. Application of DeLong test to pairs of receiver operating characteristic curves respectively yielded P values of .001 for the MergeNet-SVM pair and 0.001 for the MergeNet-LGBM pair. Conclusion: The MergeNet model, which incorporates chest CT, clinical, dosimetric, and laboratory data, demonstrated superior performance compared to other models. However, since its prediction performance has not yet reached an efficient level for clinical application, further research is required. Contribution: This study showed that MergeNet may be an effective means to predict radiation pneumonitis. Various predictive factors can be used together for the radiation pneumonitis prediction task via the MergeNet.

PMID:38752262 | DOI:10.1177/15330338241254060

Proc SPIE Int Soc Opt Eng. 2024 Feb;12933:129330T. doi: 10.1117/12.3006796. Epub 2024 Apr 3.

ABSTRACT

Tumor budding refers to a cluster of one to four tumor cells located at the tumor-invasive front. While tumor budding is a prognostic factor for colorectal cancer, counting and grading tumor budding are time consuming and not highly reproducible. There could be high inter- and intra-reader disagreement on H&E evaluation. This leads to the noisy training (imperfect ground truth) of deep learning algorithms, resulting in high variability and losing their ability to generalize on unseen datasets. Pan-cytokeratin staining is one of the potential solutions to enhance the agreement, but it is not routinely used to identify tumor buds and can lead to false positives. Therefore, we aim to develop a weakly-supervised deep learning method for tumor bud detection from routine H&E-stained images that does not require strict tissue-level annotations. We also propose Bayesian Multiple Instance Learning (BMIL) that combines multiple annotated regions during the training process to further enhance the generalizability and stability in tumor bud detection. Our dataset consists of 29 colorectal cancer H&E-stained images that contain 115 tumor buds per slide on average. In six-fold cross-validation, our method demonstrated an average precision and recall of 0.94, and 0.86 respectively. These results provide preliminary evidence of the feasibility of our approach in improving the generalizability in tumor budding detection using H&E images while avoiding the need for non-routine immunohistochemical staining methods.

PMID:38752165 | PMC:PMC11095418 | DOI:10.1117/12.3006796

Med Image Comput Comput Assist Interv. 2023 Oct;14220:651-662. doi: 10.1007/978-3-031-43907-0_62. Epub 2023 Oct 1.

ABSTRACT

Deep learning nowadays offers expert-level and sometimes even super-expert-level performance, but achieving such performance demands massive annotated data for training (e.g., Google's proprietary CXR Foundation Model (CXR-FM) was trained on 821,544 labeled and mostly private chest X-rays (CXRs)). Numerous datasets are publicly available in medical imaging but individually small and heterogeneous in expert labels. We envision a powerful and robust foundation model that can be trained by aggregating numerous small public datasets. To realize this vision, we have developed Ark, a framework that accrues and reuses knowledge from heterogeneous expert annotations in various datasets. As a proof of concept, we have trained two Ark models on 335,484 and 704,363 CXRs, respectively, by merging several datasets including ChestX-ray14, CheXpert, MIMIC-II, and VinDr-CXR, evaluated them on a wide range of imaging tasks covering both classification and segmentation via fine-tuning, linear-probing, and gender-bias analysis, and demonstrated our Ark's superior and robust performance over the state-of-the-art (SOTA) fully/self-supervised baselines and Google's proprietary CXR-FM. This enhanced performance is attributed to our simple yet powerful observation that aggregating numerous public datasets diversifies patient populations and accrues knowledge from diverse experts, yielding unprecedented performance yet saving annotation cost. With all codes and pretrained models released at GitHub.com/JLiangLab/Ark, we hope that Ark exerts an important impact on open science, as accruing and reusing knowledge from expert annotations in public datasets can potentially surpass the performance of proprietary models trained on unusually large data, inspiring many more researchers worldwide to share codes and datasets to build open foundation models, accelerate open science, and democratize deep learning for medical imaging.

PMID:38751905 | PMC:PMC11095392 | DOI:10.1007/978-3-031-43907-0_62