Effects of annotation granularity in deep learning models for histopathological images

Disease prediction based on modeling the correlations between compounded indicator factors is a widely used technique in high incidence chronic disease prevention diagnosis. Predictive models based on personal health information have been developed historically by using simple regression fitting over relatively few factors. Regression approaches have been favored in previous prediction modeling approaches because they are simplest and do not assume any non-linearity in the model for contributions of the chosen factors. In practice, many factors are correlated and have underlying non-linear relationships to the predicted outcome. Deep learning offers a means to construct a more complex modeling approach, along with automation and adaptation. The aim of this paper is to assess the ability of a deep learning model to predict the heart disease incidence using a common benchmark dataset (University of California, Irvine (UCI) dataset). The performance of deep learning model has been compared with four popular machine learning models (two linear and two nonlinear) in predicting the incidence of heart disease using data from 567 participants from two cohorts taken from UCI database. The deep learning model was able to achieve the best accuracy of 94% and an AUC score of 0.964 when compared to other models. The performance of deep learning and nonlinear machine learning models was significantly better compared to the linear machine learning models with increase in the dataset size.

The remarkable growth of deep learning (DL) algorithms in hyperspectral images (HSIs) in recent years has garnered a lot of research space. This study examines and analyses over 250 newly proposed breakthroughs, the majority from 2019 onwards, that focussed on DL methods for HSI classification. Initially, a meta-analysis was performed to analyse the state-of-the-art literature, followed by an in-depth investigation of the performance of DL models on benchmark hyperspectral datasets. It provides an adequate grasp of how DL models are employed with the suggested improvisations and evaluates the performance of these state-of-the-art models. It investigates the accuracy of benchmark hyperspectral datasets by applying the newly proposed DL models. This study discusses the challenges that researchers have faced and the solutions that have been proposed. In particular, the scarcity of non-traditional hyperspectral data sets with labels impedes the performance of novel DL algorithms. As a result, this article clarifies the supervised, semi-supervised, and unsupervised training modes employed by the models and analyses the performance of the DL models while utilizing them.

Emotion recognition (ER) is crucial for understanding human behaviours, social interactions, and psychological well-being. Electroencephalography (EEG) has emerged as a promising tool for capturing the neural correlates of emotions. This work is a systematic review of articles in ER using EEG signals. A total of 120 articles from 1041 articles were selected based on PRISMA guidelines using defined inclusion and exclusion criteria, published between 2018 and 2024. This article aims to provide an in-depth understanding of the current landscape of ER from EEG signals utilizing deep learning (DL). This review offers valuable guidance for researchers and practitioners seeking more refined and reliable emotion classification systems. To explore the effectiveness of DL models in EEG-based ER, several potential DL models, such as convolutional neural network, long short-term memory (LSTM), gated recurrent unit (GRU), hybrid bidirectional LSTM (BiLSTM), bidirectional GRU, and advanced DL models such as convolutional recurrent neural network and EEG-Conformer models are applied to two popular datasets, SEED and GAMEEMO, respectively, to depict the full process of ER. Additionally, the performance of DL models is also compared with the performance of basic machine learning (ML) models such as SVM, k-nearest neighbors, logistic regression, and boosting algorithms such as AdaBoost, XGBoost and LightGBM. Through extensive experiments and performance evaluations, the performance of different models when applied to the datasets mentioned above is compared. The accuracy, precision, recall, and F1-scores are analysed to determine the most effective model for EEG-based ER. The findings of this study demonstrate that the performance of hybrid DL models is more efficacious than that of ML models. The best-performing model (BiLSTM) classified the emotions, with an accuracy of 90.54% when applied to the GAMEEMO dataset. This research contributes to the growing body of literature on ER and provides insights into the feasibility of using EEG signals to understand emotional states, and presents a structured roadmap for future exploration. The findings can aid in the development of more accurate and reliable ER systems, which can have wide-ranging applications in psychology, social sciences, and human-computer interactions.

COVID-19 is highly infectious and causes acute respiratory disease. Machine learning (ML) and deep learning (DL) models are vital in detecting disease from computerized chest tomography (CT) scans. The DL models outperformed the ML models. For COVID-19 detection from CT scan images, DL models are used as end-to-end models. Thus, the performance of the model is evaluated for the quality of the extracted feature and classification accuracy. There are four contributions included in this work. First, this research is motivated by studying the quality of the extracted feature from the DL by feeding these extracted to an ML model. In other words, we proposed comparing the end-to-end DL model performance against the approach of using DL for feature extraction and ML for the classification of COVID-19 CT scan images. Second, we proposed studying the effect of fusing extracted features from image descriptors, e.g., Scale-Invariant Feature Transform (SIFT), with extracted features from DL models. Third, we proposed a new Convolutional Neural Network (CNN) to be trained from scratch and then compared to the deep transfer learning on the same classification problem. Finally, we studied the performance gap between classic ML models against ensemble learning models. The proposed framework is evaluated using a CT dataset, where the obtained results are evaluated using five different metrics The obtained results revealed that using the proposed CNN model is better than using the well-known DL model for the purpose of feature extraction. Moreover, using a DL model for feature extraction and an ML model for the classification task achieved better results in comparison to using an end-to-end DL model for detecting COVID-19 CT scan images. Of note, the accuracy rate of the former method improved by using ensemble learning models instead of the classic ML models. The proposed method achieved the best accuracy rate of 99.39%.

This dissertation explores the critical role of loss functions in enhancing the predictive performance of deep machine learning models. Loss functions are an integral element of all the ongoing advances we witness daily in this domain. I design custom loss functions and their impacts on various machine learning tasks, particularly in computer vision. In the first stage of my research, I aim to improve the prediction performance of deep learning models by providing them with more precise feedback associated with task requirements. This led me to create the concept of assistive loss functions. My first proposed loss function, inspired by the Active Shape Model (ASM), is ASM Loss, designed to improve the detection of facial landmarks and head pose accuracy in facial images. Additionally, influenced by Knowledge Distillation (KD), I introduce KD-Loss, a loss designed specifically for regression tasks, focusing on detecting facial landmarks. Proceeding to the second phase of my research, I focus on regression problems. Building upon my prior work, I introduce Adaptive Coordinate-based Regression (ACR)-Loss, a context-aware loss function with face alignment implication. I provide a mechanism to dynamically measure how hard the localization of each landmark point is, and accordingly, ACR-Loss provides unique feedback to the model. Furthermore, I introduce Intensity-aware Categorical (IC)-Loss for detecting sagittal cervical spine landmark points in medical images. It effectively deploys characteristics from classification problems to enhance regression optimization. Both ACR-Loss and IC-Loss comprise contextual information, leading to a significant enhancement in localization precision. In the third phase, I turned my attention toward classification problems within the domain of deep machine learning. I introduce Adaptive Correlation-based (Ad-corre) Loss, designed to enhance the discriminative capabilities of deep learning models, with a specific focus on improving classification accuracy in automatic facial expression recognition. Furthermore, I introduce Informative (Info) Loss, a specialized loss function developed for medical applications, specifically aimed at distinguishing between Mild Cognitive Impairment and Normal Cognition groups based on transcriptions of interviews conducted as part of the I-CONECT study. Overall, I have proposed custom loss functions to improve the predictive performance in both regression and classification problems. Furthermore, I have introduced assistive loss functions, designed to enhance the performance of the main loss functions. The collective outcomes of this extensive exploration highlight the critical role of loss functions, adapting and optimizing them for various domains in deep machine learning. This research suggests and proposes a variety of methodologies for designing adaptive and context-aware loss functions within deep machine learning.

Area under the curve may hide poor generalisation to external datasets

Soil temperature (ST) plays an important role in agriculture and other fields, and has a close relationship with plant growth and development. Therefore, accurate ST prediction methods are widely needed. Deep learning (DL) models have been widely applied for ST prediction. However, the traditional DL models may fail to capture the spatiotemporal relationship due to its complex dependency under different related hydrologic variables. Hence, the DL models with Ensemble Empirical Mode Decomposition (EEMD) are proposed in this study. The proposed models can capture more complex spatiotemporal relationship after decomposing the ST into different intrinsic mode functions. Therefore, the performance of models is further improved. The results show that the performance of DL models with EEMD are better than that of corresponding DL models without EEMD. Moreover, EEMD-Conv3d has the best performance among all the experimental models. It has the highest R2 ranging from 0.9826 to 0.9893, the lowest RMSE ranging from 1.3096 to 1.6497 and the lowest MAE ranging from 0.9656 to 1.2056 in predicting ST at the lead time from one to five days. In addition, the lines between predicted ST and observed ST are closer to the ideal line (y = x) than other DL models. The results show that our EEMD-Conv3D can better capture spatiotemporal correlation and is an applicable method for predicting spatiotemporal ST.

This paper presents a supervised learning scheme that employs key-frame extraction to enhance the performance of pre-trained deep learning models for object detection in surveillance videos. Developing supervised deep learning models requires a significant amount of annotated video frames as training data, which demands substantial human effort for preparation. Key frames, which encompass frames containing false negative or false positive objects, can introduce diversity into the training data and contribute to model improvements. Our proposed approach focuses on detecting false negatives by leveraging the motion information within video frames that contain the detected object region. Key-frame extraction significantly reduces the human effort involved in video frame extraction. We employ interactive labeling to annotate false negative video frames with accurate bounding boxes and labels. These annotated frames are then integrated with the existing training data to create a comprehensive training dataset for subsequent training cycles. Repeating the training cycles gradually improves the object detection performance of deep learning models to monitor a new environment. Experiment results demonstrate that the proposed learning approach improves the performance of the object detection model in a new operating environment, increasing the mean average precision (mAP@0.5) from 54% to 98%. Manual annotation of key frames is reduced by 81% through the proposed key-frame extraction method.

Deep learning (DL) is appearing as a powerful tool for spectral data modelling. In many cases, the DL models have been shown to outperform the classical chemometric spectral data modelling approaches. However, a main challenge with the DL models is the limited model interpretability as there are no scores and loadings generated in DL models. Scores and loadings are key parts of chemometric modelling as they facilitate the interpretation of the models. Furthermore, most of the time in the reported literature, the performance of DL models is compared with basic chemometric approaches with less attention being paid to optimizing these chemometric models. This study aims to test the hypothesis that proper chemometric modelling of spectral data can lead to performance equivalent to that of DL models while having all the useful information such as scores, loadings, and regression coefficients to support model interpretation. To test this, a case study is presented for the prediction of nitrogen content in rapeseed (Brassica napus L.) by Vis-NIR spectroscopy. On the classical chemometric side, two recently developed pre-processing fusion approaches, i.e. sequential pre-processing through orthogonalization (SPORT) and parallel pre-processing through orthogonalization (PORTO) were used. On the DL side, the previously published with DL modelling results for the same data set were used as the benchmark. Such a comparison was valid as the chemometric analysis was performed on the same calibration and test sets as used previously for the DL modelling. Results showed that the sequential and parallel learning approaches attained the same accuracy as that of the previously reported DL procedure on the same data set. The information related to scores, loading and regression coefficients could be used for model interpretation.

The International Classification of Diseases (ICD) serves as a widely employed framework for assigning diagnosis codes to electronic health records of patients. These codes facilitate the encapsulation of diagnoses and procedures conducted during a patient’s hospitalisation. This study aims to devise a predictive model for ICD codes based on the MIMIC-III clinical text dataset. Leveraging natural language processing techniques and deep learning architectures, we constructed a pipeline to distill pertinent information from the MIMIC-III dataset: the Medical Information Mart for Intensive Care III (MIMIC-III), a sizable, de-identified, and publicly accessible repository of medical records. Our method entails predicting diagnosis codes from unstructured data, such as discharge summaries and notes encompassing symptoms. We used state-of-the-art deep learning algorithms, such as recurrent neural networks (RNNs), long short-term memory (LSTM) networks, bidirectional LSTM (BiLSTM) and BERT models after tokenizing the clinical test with Bio-ClinicalBERT, a pre-trained model from Hugging Face. To evaluate the efficacy of our approach, we conducted experiments utilizing the discharge dataset within MIMIC-III. Employing the BERT model, our methodology exhibited commendable accuracy in predicting the top 10 and top 50 diagnosis codes within the MIMIC-III dataset, achieving average accuracies of 88% and 80%, respectively. In comparison to recent studies by Biseda and Kerang, as well as Gangavarapu, which reported F1 scores of 0.72 in predicting the top 10 ICD-10 codes, our model demonstrated better performance, with an F1 score of 0.87. Similarly, in predicting the top 50 ICD-10 codes, previous research achieved an F1 score of 0.75, whereas our method attained an F1 score of 0.81. These results underscore the better performance of deep learning models over conventional machine learning approaches in this domain, thus validating our findings. The ability to predict diagnoses early from clinical notes holds promise in assisting doctors or physicians in determining effective treatments, thereby reshaping the conventional paradigm of diagnosis-then-treatment care. Our code is available online.

ObjectiveThis study aims to tackle the critical challenge of adapting deep learning (DL) models for deployment in real-world healthcare settings, specifically focusing on catastrophic forgetting due to distribution shifts between hospital and non-hospital environments. Metabolic syndrome (MetS) is susceptible to misdiagnosis by DL models due to distribution shifts. This work demonstrates the potential of continual learning (CL) to enhance model performance in MetS identification across diverse settings.Materials and MethodsWe utilized 3 healthcare datasets from 2 distinct settings: Medical Information Mart for Intensive Care (MIMIC; from a hospital setting), National Health and Nutrition Examination Survey (NHANES), and a proprietary dataset (both from non-hospital settings). We proposed a robust MetS identification pipeline with CL strategies and evaluated its effectiveness in mitigating catastrophic forgetting while maintaining high predictive performance under distribution shift.ResultsThe CL method outperformed the control (sequential training without any strategies) method. The CL method reached a cumulative area under the ROC curve (AUROC) of 0.85 and area under the precision-recall curve of 0.65 on the combined test set. Moreover, training order proved critical: models trained from hospital to non-hospital settings achieved a 7.6% improvement in AUROC, increasing from 0.79 to 0.85, compared to the reverse order.DiscussionOur results demonstrate the potential of CL for applications across healthcare settings, particularly between hospital and non-hospital settings. We also discuss the impact of training order on the results.ConclusionThe proposed CL model effectively mitigates catastrophic forgetting, enhancing the overall performance of DL models. Our results underscore the prospect of CL methods in developing medical DL models and maintaining scalability across diverse healthcare settings.

Deep learning techniques for DDoS attack detection: Concepts, analyses, challenges, and future directions

The World Health Organization glioma classification highlights genetic profiles, such as isocitrate dehydrogenase (IDH) mutation. This study developed an uncertainty-aware deep learning model to predict IDH mutations in glioma patients, employing conformal prediction (CP) for uncertainty quantification (UQ). The UCSF dataset split into training (70%) and validation (30%) sets, and the UPENN dataset divided into calibration (30%) and external test (70%) sets. We developed various 3D convolutional neural network models and selected the best based on the validation set area under the precision-recall curve (AUPRC). Also, we trained a logistic regression (LR) ensemble classifier on the training set and selected the best ensemble model based on the validation set AUPRC. Finally, we employed CP, with nonconformity thresholds set at the error rate of 0.01. The conformal model was calibrated on the calibration set and was evaluated on the external test set using the AUPRC and the area under the receiver operating characteristic (AUROC). 3D convolutional models achieved a mean AUROC and AUPRC of 0.9004 and 0.8102 on the validation set, and a mean AUROC and AUPRC of 0.7340 and 0.2139 on the external test set, respectively. Using the LR ensemble model, the model achieved an AUROC and AUPRC of 0.79820 and 0.2583 on the external test set, respectively. CP with a 0.01 nonconformity threshold with 0.9917 coverage reached an AUROC and AUPRC of 0.8592 and 0.5217, respectively. Integrating CP for UQ improves the performance of deep learning models for predicting IDH mutation in glioma patients.

Deep learning has proven to be a powerful approach to solving challenging problems, ranging from natural language processing, speech recognition, to computer vision. The proposed model has capable of matching the expanding amount of facts as well as complexity of the algorithms is demands of deep researching methodologies. These demands cannot be met with traditional computing environments. This is why cloud computing technologies have developed, offering a scalable and affordable alternative for executing deep learning algorithms. Cloud computing platforms provide the resources necessary to run deep learning workloads including compute, storage, and networking. This means you no longer have to spend lots of money on expensive hardware and makes it easier for teams and researchers to deploy and train deep learning models faster. Cloud computing has ushered in a new era of deep learning developments by mobilizing the power of specialized hardware, notably GPUs, to accelerate the training and performance of deep learning models.

Deep learning is employed in many applications, such as computer vision, natural language processing, robotics, and recommender systems. Large and complex neural networks lead to high accuracy; however, they adversely affect many aspects of deep learning performance, such as training time, latency, throughput, energy consumption, and memory usage in the training and inference stages. To solve these challenges, various optimization techniques and frameworks have been developed for the efficient performance of deep learning models in the training and inference stages. Although optimization techniques such as quantization have been studied thoroughly in the past, less work has been done to study the performance of frameworks that provide quantization techniques. In this paper, we have used different performance metrics to study the performance of various quantization frameworks, including TensorFlow automatic mixed precision and TensorRT. These performance metrics include training time and memory utilization in the training stage along with latency and throughput for graphics processing units (GPUs) in the inference stage. We have applied the automatic mixed precision (AMP) technique during the training stage using the TensorFlow framework, while for inference we have utilized the TensorRT framework for the post-training quantization technique using the TensorFlow TensorRT (TF-TRT) application programming interface (API).We performed model profiling for different deep learning models, datasets, image sizes, and batch sizes for both the training and inference stages, the results of which can help developers and researchers to devise and deploy efficient deep learning models for GPUs.