Environ Sci Pollut Res Int. 2024 Feb 2. doi: 10.1007/s11356-024-31963-5. Online ahead of print.

ABSTRACT

The breathtaking economic development put a heavy toll on ecology, especially on water pollution. Efficient water resource management has a long-term influence on the sustainable development of the economy and society. Economic development and ecology preservation are tangled together, and the growth of one is not possible without the other. Deep learning (DL) is ubiquitous in autonomous driving, medical imaging, speech recognition, etc. The spectacular success of deep learning comes from its power of richer representation of data. In view of the bright prospects of DL, this review comprehensively focuses on the development of DL applications in water resources management, water environment protection, and water ecology. First, the concept and modeling steps of DL are briefly introduced, including data preparation, algorithm selection, and model evaluation. Finally, the advantages and disadvantages of commonly used algorithms are analyzed according to their structures and mechanisms, and recommendations on the selection of DL algorithms for different studies, as well as prospects for the application and development of DL in water science are proposed. This review provides references for solving a wider range of water-related problems and brings further insights into the intelligent development of water science.

PMID:38305966 | DOI:10.1007/s11356-024-31963-5

Infect Dis (Lond). 2024 Feb 2:1-11. doi: 10.1080/23744235.2024.2311281. Online ahead of print.

ABSTRACT

BACKGROUND: Web search data have proven to bea valuable early indicator of COVID-19 outbreaks. However, the influence of co-morbid conditions with similar symptoms and the effect of media coverage on symptom-related searches are often overlooked, leading to potential inaccuracies in COVID-19 simulations.

METHOD: This study introduces a machine learning-based approach to estimate the magnitude of the impact of media coverage and comorbid conditions with similar symptoms on online symptom searches, based on two scenarios with quantile levels 10-90 and 25-75. An incremental batch learning RNN-LSTM model was then developed for the COVID-19 simulation in Australia and New Zealand, allowing the model to dynamically simulate different infection rates and transmissibility of SARS-CoV-2 variants.

RESULT: The COVID-19 infected person-directed symptom searches were found to account for only a small proportion of the total search volume (on average 33.68% in Australia vs. 36.89% in New Zealand) compared to searches influenced by media coverage and comorbid conditions (on average 44.88% in Australia vs. 50.94% in New Zealand). The proposed method, which incorporates estimated symptom component ratios into the RNN-LSTM embedding model, significantly improved COVID-19 simulation performance.

CONCLUSION: Media coverage and comorbid conditions with similar symptoms dominate the total number of online symptom searches, suggesting that direct use of online symptom search data in COVID-19 simulations may overestimate COVID-19 infections. Our approach provides new insights into the accurate estimation of COVID-19 infections using online symptom searches, thereby assisting governments in developing complementary methods for public health surveillance.

PMID:38305899 | DOI:10.1080/23744235.2024.2311281

Mol Divers. 2024 Feb 2. doi: 10.1007/s11030-023-10799-0. Online ahead of print.

ABSTRACT

Phosphoinositide 3-kinase alpha (PI3Kα) is one of the most frequently dysregulated kinases known for their pivotal role in many oncogenic diseases. While the side effects linked to existing drugs against PI3Kα-induced cancers provide an avenue for further research, the significant structural conservation among PI3Ks makes it extremely difficult to develop new isoform-selective PI3Kα inhibitors. Embracing this challenge, we herein designed a hybrid protocol by integrating machine learning (ML) with in silico drug-designing strategies. A deep learning classification model was developed and trained on the physicochemical descriptors data of known PI3Kα inhibitors and used as a screening filter for a database of small molecules. This approach led us to the prediction of 662 compounds showcasing appropriate features to be considered as PI3Kα inhibitors. Subsequently, a multiphase molecular docking was applied to further characterize the predicted hits in terms of their binding affinities and binding modes in the targeted cavity of the PI3Kα. As a result, a total of 12 compounds were identified whereas the best poses highlighted the efficiency of these ligands in maintaining interactions with the crucial residues of the protein to be targeted for the inhibition of associated activity. Notably, potential activity of compound 12 in counteracting PI3Kα function was found in a previous in vitro study. Following the drug-likeness and pharmacokinetic characterizations, six compounds (compounds 1, 2, 3, 6, 7, and 11) with suitable ADME-T profiles and promising bioavailability were selected. The mechanistic studies in dynamic mode further endorsed the potential of identified hits in blocking the ATP-binding site of the receptor with higher binding affinities than the native inhibitor, alpelisib (BYL-719), particularly the compounds 1, 2, and 11. These outcomes support the reliability of the developed classification model and the devised computational strategy for identifying new isoform-selective drug candidates for PI3Kα inhibition.

PMID:38305819 | DOI:10.1007/s11030-023-10799-0

Phys Chem Chem Phys. 2024 Feb 2. doi: 10.1039/d4cp00039k. Online ahead of print.

ABSTRACT

Poly-drug therapy is now recognized as a crucial treatment, and the analysis of drug-drug interactions (DDIs) offers substantial theoretical support and guidance for its implementation. Predicting potential DDIs using intelligent algorithms is an emerging approach in pharmacological research. However, the existing supervised models and deep learning-based techniques still have several limitations. This paper proposes a novel DDI analysis and prediction framework called the Multi-View Semi-supervised Graph-based (MVSG) framework, which provides a comprehensive judgment by integrating multiple DDI features and functions without any time-consuming training process. Unlike conventional approaches, MVSG can search for the most suitable similarity (or distance) measurement among DDI data and construct graph structures for each feature. By employing a parameter self-tuning strategy, MVSG fuses multiple graphs according to the contributions of features' information. The actual anticancer drug data are extracted from the authoritative public database for evaluating the effectiveness of our framework, including 904 drugs, 7730 DDI records and 19 types of drug interactions. Validation results indicate that the prediction is more accurate when multiple features are adopted by our framework. In comparison to conventional machine learning techniques, MVSG can achieve higher performance even with less labeled data and without a training process. Finally, MVSG is employed to narrow down the search for potential valuable combinations.

PMID:38305788 | DOI:10.1039/d4cp00039k

Med Phys. 2024 Feb 2. doi: 10.1002/mp.16961. Online ahead of print.

ABSTRACT

BACKGROUND: Objective and quantitative evaluation for low-contrast detectability that correlates with human observer performance is lacking for routine CT quality control testing. Channelized Hotelling observer (CHO) is considered a strong candidate to fill the need but has long been deemed impractical to implement due to its requirement of a large number of repeated scans in order to provide accurate and precise estimates of index of detectability (d'). In our previous work, we optimized a CHO model observer on the American College of Radiology (ACR) CT accreditation phantom and achieved accurate measurement of d' with only 1-3 repeat scans.

PURPOSE: In this work, we aim to validate the repeatability of the proposed CHO-based low-contrast evaluation on four scanner models using the ACR CT accreditation phantom.

METHODS: The repeatability test was performed on four different scanners from two major CT manufacturers: Siemens Force and Alpha; Canon Prism and Prime SP. An ACR CT phantom was scanned 10 times, each time after repositioning of the phantom. For each repositioning, 3 repeated scans were acquired at 24, 12, and 6 mGy on all four scanner models. CHO was applied at the measured dose levels for different low-contrast object sizes (4-6 mm). The CHO was also applied to images created using deep learning-based reconstructions on Canon Prism and to four different scan/reconstruction modes on the Siemens Alpha, a photon-counting-detector (PCD)-CT. The repeatability was evaluated by the probability that a measurement would fall within the ±15% tolerance (P<15% ).

RESULTS: With the CHO setting optimized for the ACR phantom and the use of 3 repeated scans and 9 non-overlapping slices per scan, the CHO measurement could provide high repeatability with P<15% of 98.8%-99.9% at 12 mGy with IR reconstruction on all four scanners. On scanner A, P<15% were 91.5%-99.9% at the three dose levels and for all three object sizes while the numbers were 93.6%-99.998% on scanner B. P<15% were 96.5%-97.2% for the two deep learning reconstructions and 97.0%-99.97% for the four scan/reconstruction modes on the PCD-CT.

CONCLUSION: The CHO provided highly repeatable measurements with over 95% probability that a CHO measurement would lie within the ±15% tolerance for most of the dose levels and object sizes on the ACR phantom. The repeatability was maintained when the CHO was applied to images created with a commercial deep learning-based reconstruction and various scan/reconstruction modes on a PCD-CT. This study demonstrates that practical implementation of CHO for routine quality control and performance evaluation is feasible.

PMID:38305692 | DOI:10.1002/mp.16961

Heliyon. 2024 Jan 17;10(2):e24547. doi: 10.1016/j.heliyon.2024.e24547. eCollection 2024 Jan 30.

ABSTRACT

RATIONALE AND OBJECTIVES: This study investigated the effects of implementing an attention-based deep learning model for the detection of aortic dissection (AD) using non-contrast-enhanced chest computed tomography (CT).

MATERIALS AND METHODS: We analysed the records of 1300 patients who underwent contrast-enhanced chest CT at 2 medical centres between January 2015 and February 2023. We considered an internal cohort of 200 patients with AD and 200 patients without AD and an external test cohort of 40 patients with AD and 40 patients without AD. The internal cohort was divided into training and test sets, and a deep learning model was trained using 9600 CT images. A convolutional block attention module (CBAM) and a traditional deep learning architecture (namely, You Only Look Once version 5 [YOLOv5]) were combined into an attention-based model (i.e., YOLOv5-CBAM). Its performance was measured against the unmodified YOLOv5 model, and the accuracy, sensitivity, and specificity of the algorithm were evaluated by two independent radiologists.

RESULTS: The CBAM-based model outperformed the traditional deep learning model. In the external testing set, YOLOv5-CBAM achieved an area under the curve (AUC) of 0.938, accuracy of 91.5 %, sensitivity of 90.0 %, and specificity of 92.9 %, whereas the unmodified model achieved an AUC of 0.844, accuracy of 83.6 %, sensitivity of 71.2 %, and specificity of 96.0 %. The sensitivity results of the unmodified algorithms were not significantly different from those of the radiologists; however, the proposed YOLOv5-CBAM algorithm outperformed the unmodified algorithms in terms of detection.

CONCLUSIONS: Incorporating the CBAM attention mechanism into a deep learning model can significantly improve AD detection in non-contrast-enhanced chest CT. This approach may aid radiologists in the timely and accurate diagnosis of AD, which is important for improving patient outcomes.

PMID:38304839 | PMC:PMC10831773 | DOI:10.1016/j.heliyon.2024.e24547

Heliyon. 2024 Jan 17;10(2):e24620. doi: 10.1016/j.heliyon.2024.e24620. eCollection 2024 Jan 30.

ABSTRACT

BACKGROUND AND OBJECTIVE: Although interest in predicting drug-drug interactions is growing, many predictions are not verified by real-world data. This study aimed to confirm whether predicted polypharmacy side effects using public data also occur in data from actual patients.

METHODS: We utilized a deep learning-based polypharmacy side effects prediction model to identify cefpodoxime-chlorpheniramine-lung edema combination with a high prediction score and a significant patient population. The retrospective study analyzed patients over 18 years old who were admitted to the Asan medical center between January 2000 and December 2020 and took cefpodoxime or chlorpheniramine orally. The three groups, cefpodoxime-treated, chlorpheniramine-treated, and cefpodoxime & chlorpheniramine-treated were compared using inverse probability of treatment weighting (IPTW) to balance them. Differences between the three groups were analyzed using the Kaplan-Meier method and Cox proportional hazards model.

RESULTS: The study population comprised 54,043 patients with a history of taking cefpodoxime, 203,897 patients with a history of taking chlorpheniramine, and 1,628 patients with a history of taking cefpodoxime and chlorpheniramine simultaneously. After adjustment, the 1-year cumulative incidence of lung edema in the patient group that took cefpodoxime and chlorpheniramine simultaneously was significantly higher than in the patient groups that took cefpodoxime or chlorpheniramine only (p=0.001). Patients taking cefpodoxime and chlorpheniramine together had an increased risk of lung edema compared to those taking cefpodoxime alone [hazard ratio (HR) 2.10, 95% CI 1.26-3.52, p<0.005] and those taking chlorpheniramine alone, which also increased the risk of lung edema (HR 1.64, 95% CI 0.99-2.69, p=0.05).

CONCLUSIONS: Validation of polypharmacy side effect predictions with real-world data can aid patient and clinician decision-making before conducting randomized controlled trials. Simultaneous use of cefpodoxime and chlorpheniramine was associated with a higher long-term risk of lung edema compared to the use of cefpodoxime or chlorpheniramine alone.

PMID:38304832 | PMC:PMC10831713 | DOI:10.1016/j.heliyon.2024.e24620

Heliyon. 2024 Jan 17;10(2):e24878. doi: 10.1016/j.heliyon.2024.e24878. eCollection 2024 Jan 30.

ABSTRACT

OBJECTIVE: This study aimed to develop a nomogram combining CT-based handcrafted radiomics and deep learning (DL) features to preoperatively predict muscle invasion in bladder cancer (BCa) with multi-center validation.

METHODS: In this retrospective study, 323 patients underwent radical cystectomy with pathologically confirmed BCa were enrolled and randomly divided into the training cohort (n = 226) and internal validation cohort (n = 97). And fifty-two patients from another independent medical center were enrolled as an independent external validation cohort. Handcrafted radiomics and DL features were constructed from preoperative nephrographic phase CT images. Least absolute shrinkage and selection operator (LASSO) regression was used to identify the most discriminative features in train cohort. Multivariate logistic regression was used to develop the predictive model and a deep learning radiomics nomogram (DLRN) was constructed. The predictive performance of models was evaluated by area under the curves (AUC) in the three cohorts. The calibration and clinical usefulness of DLRN were estimated by calibration curve and decision curve analysis.

RESULTS: The nomogram that incorporated radiomics signature and DL signature demonstrated satisfactory predictive performance for differentiating non-muscle invasive bladder cancer (NMIBC) from muscle invasive bladder cancer (MIBC), with an AUC of 0.884 (95 % CI: 0.813-0.953) in internal validation cohort and 0.862 (95 % CI: 0.756-0.968) in external validation cohort, respectively. Decision curve analysis confirmed the clinical usefulness of the nomogram.

CONCLUSIONS: A CT-based deep learning radiomics nomogram exhibited a promising performance for preoperative prediction of muscle invasion in bladder cancer, and may be helpful in the clinical decision-making process.

PMID:38304824 | PMC:PMC10831750 | DOI:10.1016/j.heliyon.2024.e24878

Heliyon. 2024 Jan 17;10(2):e24892. doi: 10.1016/j.heliyon.2024.e24892. eCollection 2024 Jan 30.

ABSTRACT

Music genre categorization is a fundamental use of sound processing methods in the realm of music retrieval. Typically, people are responsible for categorizing music genres. Machine learning approaches can automate this procedure. Therefore, in recent years, several approaches have been suggested to achieve this objective. Nevertheless, the given findings indicate that there is still a discrepancy between the observed results and an optimal categorization method. Hence, this paper introduces a novel approach for accurately forecasting music genres by using deep learning methodologies. The proposed approach involves preprocessing the input signals and then representing the characteristics of each signal using a combination of Mel Frequency Cepstral Coefficients (MFCC) and Short-Time Fourier Transform (STFT) features. Subsequently, a convolutional neural network (CNN) is applied to process each group of these characteristics. The proposed technique utilizes two CNN models to analyze MFCC and STFT data. Although the structure of these models is identical, the hyper-parameters of each model are individually adjusted using the black hole optimization (BHO) algorithm. Here, the optimization method fine-tunes the hyperparameters of each CNN model to minimize their training error. Ultimately, the results of two Convolutional Neural Network (CNN) models are combined to determine the music genre using a classifier based on SoftMax. The efficacy of the suggested methodology in categorizing music genres has been assessed using the GTZAN and Extended-Ballroom datasets. The experimental findings demonstrated that the suggested approach achieved classification accuracies of 95.2 % and 95.7 % in the two datasets, respectively, indicating its superiority over earlier efforts.

PMID:38304785 | PMC:PMC10830873 | DOI:10.1016/j.heliyon.2024.e24892

Heliyon. 2024 Jan 11;10(2):e24403. doi: 10.1016/j.heliyon.2024.e24403. eCollection 2024 Jan 30.

ABSTRACT

The HT-29 cell line, derived from human colon cancer, is valuable for biological and cancer research applications. Early detection is crucial for improving the chances of survival, and researchers are introducing new techniques for accurate cancer diagnosis. This study introduces an efficient deep learning-based method for detecting and counting colorectal cancer cells (HT-29). The colorectal cancer cell line was procured from a company. Further, the cancer cells were cultured, and a transwell experiment was conducted in the lab to collect the dataset of colorectal cancer cell images via fluorescence microscopy. Of the 566 images, 80 % were allocated to the training set, and the remaining 20 % were assigned to the testing set. The HT-29 cell detection and counting in medical images is performed by integrating YOLOv2, ResNet-50, and ResNet-18 architectures. The accuracy achieved by ResNet-18 is 98.70 % and ResNet-50 is 96.66 %. The study achieves its primary objective by focusing on detecting and quantifying congested and overlapping colorectal cancer cells within the images. This innovative work constitutes a significant development in overlapping cancer cell detection and counting, paving the way for novel advancements and opening new avenues for research and clinical applications. Researchers can extend the study by exploring variations in ResNet and YOLO architectures to optimize object detection performance. Further investigation into real-time deployment strategies will enhance the practical applicability of these models.

PMID:38304780 | PMC:PMC10831604 | DOI:10.1016/j.heliyon.2024.e24403

Eur J Radiol Open. 2024 Jan 19;12:100549. doi: 10.1016/j.ejro.2024.100549. eCollection 2024 Jun.

ABSTRACT

PURPOSE: Programmed cell death protein-1 ligand (PD-L1) is an important prognostic predictor for immunotherapy of non-small cell lung cancer (NSCLC). This study aimed to develop a non-invasive deep learning and radiomics model based on positron emission tomography and computed tomography (PET/CT) to predict PD-L1 expression in NSCLC.

METHODS: A total of 136 patients with NSCLC between January 2021 and September 2022 were enrolled in this study. The patients were randomly divided into the training dataset and the validation dataset in a ratio of 7:3. Radiomics feature and deep learning feature were extracted from their PET/CT images. The Mann-whitney U-test, Least Absolute Shrinkage and Selection Operator algorithm and Spearman correlation analysis were used to select the top significant features. Then we developed a radiomics model, a deep learning model, and a fusion model based on the selected features. The performance of three models were compared by the area under the curve (AUC), sensitivity, specificity, accuracy, positive predictive value, and negative predictive value.

RESULTS: Of the patients, 42 patients were PD-L1 negative and 94 patients were PD-L1 positive. A total of 2446 radiomics features and 4096 deep learning features were extracted per patient. In the training dataset, the fusion model achieved a highest AUC (0.954, 95% confident internal [CI]: 0.890-0.986) compared with the radiomics model (0.829, 95%CI: 0.738-0.898) and the deep learning model (0.935, 95%CI: 0.865-0.975). In the validation dataset, the AUC of the fusion model (0.910, 95% CI: 0.779-0.977) was also higher than that of the radiomics model (0.785, 95% CI: 0.628-0.897) and the deep learning model (0.867, 95% CI: 0.724-0.952).

CONCLUSION: The PET/CT-based deep learning radiomics model can predict the PD-L1 expression accurately in NSCLC patients, and provides a non-invasive tool for clinicians to select positive PD-L1 patients.

PMID:38304572 | PMC:PMC10831499 | DOI:10.1016/j.ejro.2024.100549

Comput Struct Biotechnol J. 2024 Jan 17;23:759-770. doi: 10.1016/j.csbj.2024.01.009. eCollection 2024 Dec.

ABSTRACT

Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.

PMID:38304547 | PMC:PMC10831124 | DOI:10.1016/j.csbj.2024.01.009

Saudi J Biol Sci. 2024 Mar;31(3):103934. doi: 10.1016/j.sjbs.2024.103934. Epub 2024 Jan 14.

ABSTRACT

Pneumonia is declared a global emergency public health crisis in children less than five age and the geriatric population. Recent advancements in deep learning models could be utilized effectively for the timely and early diagnosis of pneumonia in immune-compromised patients to avoid complications. This systematic review and meta-analysis utilized PRISMA guidelines for the selection of ten articles included in this study. The literature search was done through electronic databases including PubMed, Scopus, and Google Scholar from 1st January 2016 till 1 July 2023. Overall studies included a total of 126,610 images and 1706 patients in this meta-analysis. At a 95% confidence interval, for pooled sensitivity was 0.90 (0.85-0.94) and I2 statistics 90.20 (88.56 - 91.92). The pooled specificity for deep learning models' diagnostic accuracy was 0.89 (0.86---0.92) and I2 statistics 92.72 (91.50 - 94.83). I2 statistics showed low heterogeneity across studies highlighting consistent and reliable estimates, and instilling confidence in these findings for researchers and healthcare practitioners. The study highlighted the recent deep learning models single or in combination with high accuracy, sensitivity, and specificity to ensure reliable use for bacterial pneumonia identification and differentiate from other viral, fungal pneumonia in children and adults through chest x-rays and radiographs.

PMID:38304541 | PMC:PMC10831261 | DOI:10.1016/j.sjbs.2024.103934

Front Plant Sci. 2024 Jan 18;14:1335194. doi: 10.3389/fpls.2023.1335194. eCollection 2023.

ABSTRACT

INTRODUCTION: In the actual planting of wheat, there are often shortages of seedlings and broken seedlings on long ridges in the field, thus affecting grain yield and indirectly causing economic losses. Variety identification of wheat seedlings using physical methods timeliness and is unsuitable for universal dissemination. Recognition of wheat seedling varieties using deep learning models has high timeliness and accuracy, but fewer researchers exist. Therefore, in this paper, a lightweight wheat seedling variety recognition model, MssiapNet, is proposed.

METHODS: The model is based on the MobileVit-XS and increases the model's sensitivity to subtle differences between different varieties by introducing the scSE attention mechanism in the MV2 module, so the recognition accuracy is improved. In addition, this paper proposes the IAP module to fuse the identified feature information. Subsequently, training was performed on a self-constructed real dataset, which included 29,020 photographs of wheat seedlings of 29 varieties.

RESULTS: The recognition accuracy of this model is 96.85%, which is higher than the other nine mainstream classification models. Although it is only 0.06 higher than the Resnet34 model, the number of parameters is only 1/3 of that. The number of parameters required for MssiapNet is 29.70MB, and the single image Execution time and the single image Delay time are 0.16s and 0.05s. The MssiapNet was visualized, and the heat map showed that the model was superior for wheat seedling variety identification compared with MobileVit-XS.

DISCUSSION: The proposed model has a good recognition effect on wheat seedling varieties and uses a few parameters with fast inference speed, which makes it easy to be subsequently deployed on mobile terminals for practical performance testing.

PMID:38304454 | PMC:PMC10830677 | DOI:10.3389/fpls.2023.1335194

Data Brief. 2024 Jan 15;52:110069. doi: 10.1016/j.dib.2024.110069. eCollection 2024 Feb.

ABSTRACT

Unmanned aerial vehicles (UAV) rely on a variety of sensors to perceive and navigate their airborne environment with precision. The autopilot software interprets this sensory data, acting as the control mechanism for autonomous flights. As UAVs are exposed to physical environment, they are vulnerable to potential impairments in their sensory mechanism. Their real-time interactions with the actual atmosphere make them susceptible to cyber exploitations as well, where sensory data alterations through counterfeit wireless signals pose a significant threat. In this context, sensor failures can result into unsafe flight conditions, as the fault handling logic may fail to anticipate the context of the issue, allowing autopilot to execute operations without necessary adjustments. Untimely control of sensor failures can result in mid-air collisions or crashes. To address these challenges, we created Biomisa Arducopter Sensory Critique (BASiC) dataset, a state-of-the-art resource for UAV sensor failure analysis. The BASiC dataset comprises 70 autonomous flight data, spanning over 7 hours. It encompasses 3+ hours of (each) pre-failure and post-failure data, along with 1+ hour of no-failure data. We selected the ArduPilot platform as our demonstration aerial vehicle to conduct the experiments. By engineering Software in the Loop (SITL) parameters, we effectively executed sensor failure test simulations. Our dataset incorporates six representative sensors failures which are critical to UAV operations: global positioning system (GPS) for precise aerial positioning, remote control for communication with the ground control station (GCS), accelerometer for measuring linear acceleration, gyroscope for rotational acceleration measurement, compass providing heading information, and barometer for maintaining flight height based on atmospheric pressure data. The availability of the BASiC dataset will benefit the research community, empowering researchers to explore and experiment with state-of-the-art deep learning models by tailoring them for time series signal analysis. It may also contribute in enhancing the safety and reliability of mission-critical autonomous UAV flights.

PMID:38304386 | PMC:PMC10831493 | DOI:10.1016/j.dib.2024.110069

BMC Med Imaging. 2024 Feb 1;24(1):30. doi: 10.1186/s12880-024-01192-w.

ABSTRACT

BACKGROUND: Lung diseases, both infectious and non-infectious, are the most prevalent cause of mortality overall in the world. Medical research has identified pneumonia, lung cancer, and Corona Virus Disease 2019 (COVID-19) as prominent lung diseases prioritized over others. Imaging modalities, including X-rays, computer tomography (CT) scans, magnetic resonance imaging (MRIs), positron emission tomography (PET) scans, and others, are primarily employed in medical assessments because they provide computed data that can be utilized as input datasets for computer-assisted diagnostic systems. Imaging datasets are used to develop and evaluate machine learning (ML) methods to analyze and predict prominent lung diseases.

OBJECTIVE: This review analyzes ML paradigms, imaging modalities' utilization, and recent developments for prominent lung diseases. Furthermore, the research also explores various datasets available publically that are being used for prominent lung diseases.

METHODS: The well-known databases of academic studies that have been subjected to peer review, namely ScienceDirect, arXiv, IEEE Xplore, MDPI, and many more, were used for the search of relevant articles. Applied keywords and combinations used to search procedures with primary considerations for review, such as pneumonia, lung cancer, COVID-19, various imaging modalities, ML, convolutional neural networks (CNNs), transfer learning, and ensemble learning.

RESULTS: This research finding indicates that X-ray datasets are preferred for detecting pneumonia, while CT scan datasets are predominantly favored for detecting lung cancer. Furthermore, in COVID-19 detection, X-ray datasets are prioritized over CT scan datasets. The analysis reveals that X-rays and CT scans have surpassed all other imaging techniques. It has been observed that using CNNs yields a high degree of accuracy and practicability in identifying prominent lung diseases. Transfer learning and ensemble learning are complementary techniques to CNNs to facilitate analysis. Furthermore, accuracy is the most favored metric for assessment.

PMID:38302883 | DOI:10.1186/s12880-024-01192-w

Acad Radiol. 2024 Jan 31:S1076-6332(23)00721-3. doi: 10.1016/j.acra.2023.12.042. Online ahead of print.

ABSTRACT

RATIONALE AND OBJECTIVES: To explore the classification and prediction efficacy of the deep learning model for benign prostate lesions, non-clinically significant prostate cancer (non-csPCa) and clinically significant prostate cancer (csPCa) in Prostate Imaging-Reporting and Data System (PI-RADS) 3 lesions.

MATERIALS AND METHODS: From January 2015 to December 2021, lesions diagnosed with PI-RADS 3 by multi-parametric MRI or bi-parametric MRI were retrospectively included. They were classified as benign prostate lesions, non-csPCa, and csPCa according to the pathological results. T2-weighted images of the lesions were divided into a training set and a test set according to 8:2. ResNet-18 was used for model training. All statistical analyses were performed using Python open-source libraries. The receiver operating characteristic curve (ROC) was used to evaluate the predictive effectiveness of the model. T-SNE was used for image semantic feature visualization. The class activation mapping was used to visualize the area focused by the model.

RESULTS: A total of 428 benign prostate lesion images, 158 non-csPCa images and 273 csPCa images were included. The precision in predicting benign prostate disease, non-csPCa and csPCa were 0.882, 0.681 and 0.851, and the area under the ROC were 0.875, 0.89 and 0.929, respectively. Semantic feature analysis showed strong classification separability between csPCa and benign prostate lesions. The class activation map showed that the deep learning model can focus on the area of the prostate or the location of PI-RADS 3 lesions.

CONCLUSION: Deep learning model with T2-weighted images based on ResNet-18 can realize accurate classification of PI-RADS 3 lesions.

PMID:38302387 | DOI:10.1016/j.acra.2023.12.042

Eur Urol Oncol. 2024 Jan 31:S2588-9311(24)00029-4. doi: 10.1016/j.euo.2024.01.004. Online ahead of print.

ABSTRACT

BACKGROUND: Accurate risk stratification is critical to guide management decisions in localized prostate cancer (PCa). Previously, we had developed and validated a multimodal artificial intelligence (MMAI) model generated from digital histopathology and clinical features. Here, we externally validate this model on men with high-risk or locally advanced PCa treated and followed as part of a phase 3 randomized control trial.

OBJECTIVE: To externally validate the MMAI model on men with high-risk or locally advanced PCa treated and followed as part of a phase 3 randomized control trial.

DESIGN, SETTING, AND PARTICIPANTS: Our validation cohort included 318 localized high-risk PCa patients from NRG/RTOG 9902 with available histopathology (337 [85%] of the 397 patients enrolled into the trial had available slides, of which 19 [5.6%] failed due to poor image quality).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Two previously locked prognostic MMAI models were validated for their intended endpoint: distant metastasis (DM) and PCa-specific mortality (PCSM). Individual clinical factors and the number of National Comprehensive Cancer Network (NCCN) high-risk features served as comparators. Subdistribution hazard ratio (sHR) was reported per standard deviation increase of the score with corresponding 95% confidence interval (CI) using Fine-Gray or Cox proportional hazards models.

RESULTS AND LIMITATIONS: The DM and PCSM MMAI algorithms were significantly and independently associated with the risk of DM (sHR [95% CI] = 2.33 [1.60-3.38], p < 0.001) and PCSM, respectively (sHR [95% CI] = 3.54 [2.38-5.28], p < 0.001) when compared against other prognostic clinical factors and NCCN high-risk features. The lower 75% of patients by DM MMAI had estimated 5- and 10-yr DM rates of 4% and 7%, and the highest quartile had average 5- and 10-yr DM rates of 19% and 32%, respectively (p < 0.001). Similar results were observed for the PCSM MMAI algorithm.

CONCLUSIONS: We externally validated the prognostic ability of MMAI models previously developed among men with localized high-risk disease. MMAI prognostic models further risk stratify beyond the clinical and pathological variables for DM and PCSM in a population of men already at a high risk for disease progression. This study provides evidence for consistent validation of our deep learning MMAI models to improve prognostication and enable more informed decision-making for patient care.

PATIENT SUMMARY: This paper presents a novel approach using images from pathology slides along with clinical variables to validate artificial intelligence (computer-generated) prognostic models. When implemented, clinicians can offer a more personalized and tailored prognostic discussion for men with localized prostate cancer.

PMID:38302323 | DOI:10.1016/j.euo.2024.01.004

Eur Radiol Exp. 2024 Feb 2;8(1):20. doi: 10.1186/s41747-023-00416-y.

ABSTRACT

BACKGROUND: Artificial intelligence (AI) seems promising in diagnosing pneumonia on chest x-rays (CXR), but deep learning (DL) algorithms have primarily been compared with radiologists, whose diagnosis can be not completely accurate. Therefore, we evaluated the accuracy of DL in diagnosing pneumonia on CXR using a more robust reference diagnosis.

METHODS: We trained a DL convolutional neural network model to diagnose pneumonia and evaluated its accuracy in two prospective pneumonia cohorts including 430 patients, for whom the reference diagnosis was determined a posteriori by a multidisciplinary expert panel using multimodal data. The performance of the DL model was compared with that of senior radiologists and emergency physicians reviewing CXRs and that of radiologists reviewing computed tomography (CT) performed concomitantly.

RESULTS: Radiologists and DL showed a similar accuracy on CXR for both cohorts (p ≥ 0.269): cohort 1, radiologist 1 75.5% (95% confidence interval 69.1-80.9), radiologist 2 71.0% (64.4-76.8), DL 71.0% (64.4-76.8); cohort 2, radiologist 70.9% (64.7-76.4), DL 72.6% (66.5-78.0). The accuracy of radiologists and DL was significantly higher (p ≤ 0.022) than that of emergency physicians (cohort 1 64.0% [57.1-70.3], cohort 2 63.0% [55.6-69.0]). Accuracy was significantly higher for CT (cohort 1 79.0% [72.8-84.1], cohort 2 89.6% [84.9-92.9]) than for CXR readers including radiologists, clinicians, and DL (all p-values < 0.001).

CONCLUSIONS: When compared with a robust reference diagnosis, the performance of AI models to identify pneumonia on CXRs was inferior than previously reported but similar to that of radiologists and better than that of emergency physicians.

RELEVANCE STATEMENT: The clinical relevance of AI models for pneumonia diagnosis may have been overestimated. AI models should be benchmarked against robust reference multimodal diagnosis to avoid overestimating its performance.

TRIAL REGISTRATION: NCT02467192 , and NCT01574066 .

KEY POINT: • We evaluated an openly-access convolutional neural network (CNN) model to diagnose pneumonia on CXRs. • CNN was validated against a strong multimodal reference diagnosis. • In our study, the CNN performance (area under the receiver operating characteristics curve 0.74) was lower than that previously reported when validated against radiologists' diagnosis (0.99 in a recent meta-analysis). • The CNN performance was significantly higher than emergency physicians' (p ≤ 0.022) and comparable to that of board-certified radiologists (p ≥ 0.269).

PMID:38302850 | DOI:10.1186/s41747-023-00416-y

J Cancer Res Clin Oncol. 2024 Feb 1;150(2):67. doi: 10.1007/s00432-023-05602-4.

ABSTRACT

BACKGROUND: There are potential uncertainties and overtreatment existing in radical prostatectomy (RP) for prostate cancer (PCa) patients, thus identifying optimal candidates is quite important.

PURPOSE: This study aims to establish a novel causal inference deep learning (DL) model to discern whether a patient can benefit more from RP and to identify heterogeneity in treatment responses among PCa patients.

METHODS: We introduce the Self-Normalizing Balanced individual treatment effect for survival data (SNB). Six models were trained to make individualized treatment recommendations for PCa patients. Inverse probability treatment weighting (IPTW) was used to avoid treatment selection bias.

RESULTS: 35,236 patients were included. Patients whose actual treatment was consistent with SNB recommendations had better survival outcomes than those who were inconsistent (multivariate hazard ratio (HR): 0.76, 95% confidence interval (CI), 0.64-0.92; IPTW-adjusted HR: 0.77, 95% CI, 0.61-0.95; risk difference (RD): 3.80, 95% CI, 2.48-5.11; IPTW-adjusted RD: 2.17, 95% CI, 0.92-3.35; the difference in restricted mean survival time (dRMST): 3.81, 95% CI, 2.66-4.85; IPTW-adjusted dRMST: 3.23, 95% CI, 2.06-4.45). Keeping other covariates unchanged, patients with 1 ng/mL increase in PSA levels received RP caused 1.77 months increase in the time to 90% mortality, and the similar results could be found in age, Gleason score, tumor size, TNM stages, and metastasis status.

CONCLUSIONS: Our highly interpretable and reliable DL model (SNB) may identify patients with PCa who could benefit from RP, outperforming other models and clinical guidelines. Additionally, the DL-based treatment guidelines obtained can provide priori evidence for subsequent studies.

PMID:38302801 | DOI:10.1007/s00432-023-05602-4