Application Of Deep Learning Research Articles

Systematic Review of Deep Learning Techniques in Skin Cancer Detection

Skin cancer is a serious health condition, as it can locally evolve into disfiguring states or metastasize to different tissues. Early detection of this disease is critical because it increases the effectiveness of treatment, which contributes to improved patient prognosis and reduced healthcare costs. Visual assessment and histopathological examination are the gold standards for diagnosing these types of lesions. Nevertheless, these processes are strongly dependent on dermatologists’ experience, with excision advised only when cancer is suspected by a physician. Multiple approaches have surfed over the last few years, particularly those based on deep learning (DL) strategies, with the goal of assisting medical professionals in the diagnosis process and ultimately diminishing diagnostic uncertainty. This systematic review focused on the analysis of relevant studies based on DL applications for skin cancer diagnosis. The qualitative assessment included 164 records relevant to the topic. The AlexNet, ResNet-50, VGG-16, and GoogLeNet architectures are considered the top choices for obtaining the best classification results, and multiclassification approaches are the current trend. Public databases are considered key elements in this area and should be maintained and improved to facilitate scientific research.

Dengue Prediction using Short-Term Memory

Dengue is a severe infectious disease on the rise in Malaysia, and there is a demand for artificial intelligence to support the health system. However, the application of deep learning, specifically Long Short-Term Memory (LSTM) time series forecasting, has not been explored by many in dengue prediction studies. However, considering the availability of daily weather data being collected, the ability of LSTM to capture long term dependencies can be leveraged in forecasting dengue cases. Therefore, this study investigates the performance and viability of LSTM time series forecasting on predicting dengue cases. An LSTM model is developed and evaluated to be compared to a Support Vector Regression (SVR) model by utilising the availability of a dengue dataset consisting of weather and climate data. The results indicated LSTM time series forecasting performed better than SVR, with R2 and MAE scoring 0.75 and 8.76. In short, LSTM has shown better performance and, in addition, capturing trends in the rise and fall of dengue cases. Altogether, this research could contribute to the fight against the increase of dengue cases without relying on forecasted weather data but instead, history.

Predictive Health Monitoring of Palm Trees: Techniques and Applications for Enhanced Processing

This paper presents new framework for predictive health monitoring in palm trees using advanced deep learning methods. The system then selects the YOLOv8 method for the detection of the health of palm trees and further divides them into their real-time classification. Here, the model will, after training on its dataset, classify the palm tree as healthy, diseased, and stressed trees, keeping all the influential factors of the growth of the palm tree in consideration. It makes provision for the profiling of health status by way of early intervention, reducing risks and preventing diseases with a view to optimizing crop yields within palm plantations. The proposed model leverages state-of-the-art methodologies in object detection to process images of the palm tree with identification of key indicators of health issues. This approach has great implications for agricultural productivity in view of the maintenance of plant health through early detection. Further, the paper discusses challenges presented during the training and validation of the model, their strategies for overcoming such obstacles, and goes further into relating details to the technical architecture of the model. Further details on the works related to plant disease detection, image-based classification, and further applications of deep learning in agriculture have inspired the research work. Based on the obtained results, it can be observed that the proposed system provides a scalable and efficient solution for continuous monitoring and assessment of the health conditions of palm trees, hence enabling sustainable agricultural practices.

A Study to Investigate the Role and Challenges Associated with the Use of Deep Learning in Autonomous Vehicles

The application of deep learning in autonomous vehicles has surged over the years with advancements in technology. This research explores the integration of deep learning algorithms into autonomous vehicles (AVs), focusing on their role in perception, decision-making, localization, mapping, and navigation. It shows how deep learning, as a part of machine learning, mimics the human brain’s neural networks, enabling advancements in perception, decision-making, localization, mapping, and overall navigation. Techniques like convolutional neural networks are used for image detection and steering control, while deep learning is crucial for path planning, automated parking, and traffic maneuvering. Localization and mapping are essential for AVs’ navigation, with deep learning-based object detection mechanisms like Faster R-CNN and YOLO proving effective in real-time obstacle detection. Apart from the roles, this study also revealed that the integration of deep learning in AVs faces challenges such as dataset uncertainty, sensor challenges, and model training intricacies. However, these issues can be addressed through the increased standardization of sensors and real-life testing for model training, and advancements in model compression technologies can optimize the performance of deep learning in AVs. This study concludes that deep learning plays a crucial role in enhancing the safety and reliability of AV navigation. This study contributes to the ongoing discourse on the optimal integration of deep learning in AVs, aiming to foster their safety, reliability, and societal acceptance.

Diagnostic Applications of AI in Sports: A Comprehensive Review of Injury Risk Prediction Methods

This review provides a comprehensive analysis of the transformative role of artificial intelligence (AI) in predicting and preventing sports injuries across various disciplines. By exploring the application of machine learning (ML) and deep learning (DL) techniques, such as random forests (RFs), convolutional neural networks (CNNs), and artificial neural networks (ANNs), this review highlights AI’s ability to analyze complex datasets, detect patterns, and generate predictive insights that enhance injury prevention strategies. AI models improve the accuracy and reliability of injury risk assessments by tailoring prevention strategies to individual athlete profiles and processing real-time data. A literature review was conducted through searches in PubMed, Google Scholar, Science Direct, and Web of Science, focusing on studies from 2014 to 2024 and using keywords such as ‘artificial intelligence’, ‘machine learning’, ‘sports injury’, and ‘risk prediction’. While AI’s predictive power supports both team and individual sports, its effectiveness varies based on the unique data requirements and injury risks of each, with team sports presenting additional complexity in data integration and injury tracking across multiple players. This review also addresses critical issues such as data quality, ethical concerns, privacy, and the need for transparency in AI applications. By shifting the focus from reactive to proactive injury management, AI technologies contribute to enhanced athlete safety, optimized performance, and reduced human error in medical decisions. As AI continues to evolve, its potential to revolutionize sports injury prediction and prevention promises further advancements in athlete health and performance while addressing current challenges.

Clinical application of machine-based deep learning in patients with radiologically presumed adult-type diffuse glioma grades 2 or 3

Abstract BACKGROUND Radiologically presumed diffuse lower-grade glioma (dLGG) are typically non or minimal enhancing tumors, with hyperintensity in T2w-images. The aim of this study was to test the clinical usefulness of deep learning (DL) in IDH mutation prediction in patients with radiologically presumed dLGG. METHODS 314 patients were retrospectively recruited from six neurosurgical departments in Sweden, Norway, France, Austria, and the United States. Collected data included patients’ age, sex, tumor molecular characteristics (IDH, and 1p19q), and routine preoperative radiological images. A clinical model was built using multivariable logistic regression with the variables age and tumor location. DL models were built using MRI data only, and four DL architectures used in glioma research. In the final validation test, the clinical model and the best DL model were scored on an external validation cohort with 155 patients from the Erasmus Glioma Dataset. RESULTS The mean age in the recruited and external cohorts was 45.0 (SD 14.3) and 44.3 years (SD 14.6). The cohorts were rather similar, except for sex distribution (53.5% vs 64.5% males, p-value 0.03) and IDH status (30.9% vs 12.9% IDH wild-type, p-value <0.01). Overall, the area under the curve for the prediction of IDH mutations in the external validation cohort was 0.86, 0.82, and 0.87 for the clinical model, the DL model, and the model combining both models’ probabilities. CONCLUSIONS In their current state, when these complex models were applied to our clinical scenario, they did not seem to provide a net gain compared to our baseline clinical model.

Open-world disaster information identification from multimodal social media

The application of multimodal deep learning for emergency response and recovery, specifically in disaster social media analysis, is of utmost importance. It is worth noting that in real-world scenarios, sudden disaster events may differ from the training data, which may require the multimodal network to predict them as unknown classes instead of misclassifying them to known ones. Previous studies have primarily focused on model accuracy in a closed environment and may not be able to directly detect unknown classes. Thus, we propose a novel multimodal model for categorizing social media related to disasters in an open-world environment. Our methodology entails utilizing pre-trained unimodal models as encoders for each modality and performing information fusion with a cross-attention module to obtain the joint representation. For open-world detection, we use a multitask classifier that encompasses both a closed-world and an open-world classifier. The closed-world classifier is trained on the original data to classify known classes, whereas the open-world classifier is used to determine whether the input belongs to a known class. Furthermore, we propose a sample generation strategy that models the distribution of unknown samples using known data, which allows the open-world classifier to identify unknown samples. Our experiments were conducted on two public datasets, namely CrisisMMD and MHII. According to the experimental results, the proposed method outperforms other baselines and approaches in crisis information classification.

Deep Learning for Text Sentiment Analysis: A Survey

Abstract. With the continuous improvement of many factors such as corpus, computing power, data scale, and laboratory conditions, how to quickly and accurately understand the emotional tendency in the text has become an important issue in many fields. The current state of affairs and the trajectory that deep learning is pursuing in the realm of text emotion analysis hold significant importance. This article first introduces the definition, importance and classification of emotional analysis, including the analysis of emotional polarity, emotional detection and fine-grained emotion. Subsequently, the key technologies of deep learning were discussed and the application of deep learning in natural language processing, especially LSTM, Bert, and their specific applications in emotional analysis within deep learning models. Then reveal the advantages and limitations of each model by comparing the performance of different deep learning models in emotional analysis tasks. Finally, in combination with current deep learning research, this study summarizes the challenges and research trends in the field of text emotional analysis.

Modified Multiresolution Convolutional Neural Network for Quasi-Periodic Noise Reduction in Phase Shifting Profilometry for 3D Reconstruction

Fringe profilometry is a method that obtains the 3D information of objects by projecting a pattern of fringes. The three-step technique uses only three images to acquire the 3D information from an object, and many studies have been conducted to improve this technique. However, there is a problem that is inherent to this technique, and that is the quasi-periodic noise that appears due to this technique and considerably affects the final 3D object reconstructed. Many studies have been carried out to tackle this problem to obtain a 3D object close to the original one. The application of deep learning in many areas of research presents a great opportunity to to reduce or eliminate the quasi-periodic noise that affects images. Therefore, a model of convolutional neural network along with four different patterns of frequencies projected in the three-step technique is researched in this work. The inferences produced by models trained with different frequencies are compared with the original ones both qualitatively and quantitatively.

The application of Deep Learning in the field of Robotics

Abstract. As a new field with rapid development in the past two decades, deep learning has received more and more attention from researchers. Neural network adopts widely interconnected structure and effective learning mechanisms to simulate the process of information processing in the human brain, which is an important method in the development of artificial intelligence. Compared with shallow models, deep learning can achieve stronger unsupervised autonomous learning capabilities by increasing the number of layers of the network. In the past, the robots needed to be controlled by the humans; they controlled the robot to finish different tasks. In recent years, the researchers have tried to apply deep learning in the field of robots. Deep neural networks can simulate the complex cognitive laws of the human brain, so many researchers apply deep learning to robots to make robots have the thinking ability of humans. This article will review the cases of combining robot and in-depth learning in recent decades, Summarizing the achievements and problems faced in the three fields of robot vision, trajectory planning and motion control.

Research on image recognition and processing application technology of unmanned vehicle based on deep learning

Abstract. Image recognition technology is critically important in various fields, including the rapidly advancing sector of autonomous vehicles. As one of the core components enabling driverless cars to perceive their environment and make informed decisions, image recognition has seen significant advancements due to deep learning. This paper focuses on the application of deep learning in image recognition for self-driving cars and explores its implications for the future of autonomous driving technology. To begin with, this paper examines the empirical evaluation of deep learning models in highway driving scenarios. By employing Convolutional Neural Networks (CNN), these models achieve high detection rates and superior accuracy in recognizing vehicles and lanes. The robustness of these models is tested under varying weather conditions and times, demonstrating their effectiveness compared to classical computer vision techniques. Next, the paper discusses radar-camera fusion technology, highlighting different fusion strategies such as data-level, feature-level, object-level, and hybrid-level. The findings suggest that while feature-level fusion excels in detecting small objects in complex scenes, hybrid-level fusion is optimal for diverse driving situations. This section provides valuable insights into the integration of multimodal data for improved object recognition and semantic segmentation. After discussing fusion technologies, the paper finally reviews the security challenges posed by adversarial attacks on deep learning-based unmanned systems.

Research on CAPTCHA recognition technology based on deep learning

Abstract. CAPTCHA (Completely Automated Public Turing test to tell Computers and Humans Apart), a security technique widely used on the Internet, can be utilized to distinguish human users from automated programs. The rapid development of deep learning technology has led to the emergence of graph-based recognition techniques that demonstrate excellent performance, which has prompted the investigation of CAPTCHA recognition based on deep learning as a research area of significant interest. This paper addresses the challenging problem of CAPTCHA recognition based on deep learning techniques, reviews the development and classification of CAPTCHA, examines traditional CAPTCHA recognition methods, and delves into the application of deep learning in CAPTCHA recognition. Therefore, a CAPTCHA recognition system is designed and its effectiveness is verified through experiments. This paper makes a significant contribution to the field of CAPTCHA recognition by proposing a deep learning-based approach, which not only enhances the accuracy and efficiency of CAPTCHA recognition, but also provides new ideas and methods for the further development. In the future, further research will be conducted in the field of CAPTCHA recognition to explore additional deep learning models and techniques with the aim of boosting the security and user experience of CAPTCHA.

The backpropagation algorithm implemented on spiking neuromorphic hardware

The capabilities of natural neural systems have inspired both new generations of machine learning algorithms as well as neuromorphic, very large-scale integrated circuits capable of fast, low-power information processing. However, it has been argued that most modern machine learning algorithms are not neurophysiologically plausible. In particular, the workhorse of modern deep learning, the backpropagation algorithm, has proven difficult to translate to neuromorphic hardware. This study presents a neuromorphic, spiking backpropagation algorithm based on synfire-gated dynamical information coordination and processing implemented on Intel’s Loihi neuromorphic research processor. We demonstrate a proof-of-principle three-layer circuit that learns to classify digits and clothing items from the MNIST and Fashion MNIST datasets. To our knowledge, this is the first work to show a Spiking Neural Network implementation of the exact backpropagation algorithm that is fully on-chip without a computer in the loop. It is competitive in accuracy with off-chip trained SNNs and achieves an energy-delay product suitable for edge computing. This implementation shows a path for using in-memory, massively parallel neuromorphic processors for low-power, low-latency implementation of modern deep learning applications.

A review of deep learning-based stereo vision techniques for phenotype feature and behavioral analysis of fish in aquaculture

The industrialization, high-density, and greener aquaculture requires a more precise and intelligent aquaculture management. Phenotypic and behavioral information of fish, which can reflect fish growth and welfare status, play a crucial role in aquaculture management. Stereo vision technology, which simulates parallax perception of the human eye, can obtain the three-dimensional phenotypic characteristics and movement trajectories of fish through different types of sensors. It can overcome the limitations in dealing with fish deformation, frequent occlusions and understanding three-dimension scenes compared to the traditional two-dimensional computer vision techniques. With the deep learning development and application in aquaculture, stereo vision has become a super computer vision technology that can provide more precise and interpretable information for intelligent aquaculture management, such as size estimation, counting and behavioral analysis of fish. Hence, it is very beneficial for researchers, managers, and entrepreneurs to possess a thorough comprehension about the fast-developing stereo vision technology for modern aquaculture. This study provides a critical review of relevant topics, including the four-layer application structure of stereo vision technology in aquaculture, various deep learning-based technologies used, and specific application scenarios. The review contributes to research development by identifying the current challenges and provide valuable suggestions for future research directions. This review can serve as a useful resource for developing future studies and applications of stereo vision technology in smart aquaculture, focusing on phenotype feature extraction and behavioral analysis of fish.

Machine Learning and Deep Learning Applications in Disinformation Detection: A Bibliometric Assessment

Fake news is one of the biggest challenging issues in today’s technological world and has a huge impact on the population’s decision-making and way of thinking. Disinformation can be classified as a subdivision of fake news, the main purpose of which is to manipulate and generate confusion among people in order to influence their opinion and obtain certain advantages in multiple domains (politics, economics, etc.). Propaganda, rumors, and conspiracy theories are just a few examples of common disinformation. Therefore, there is an urgent need to understand this phenomenon and offer the scientific community a paper that provides a comprehensive examination of the existing literature, lay the foundation for future research areas, and contribute to the fight against disinformation. The present manuscript provides a detailed bibliometric analysis of the articles oriented towards disinformation detection, involving high-performance machine learning and deep learning algorithms. The dataset has been collected from the popular Web of Science database, through the use of specific keywords such as “disinformation”, “machine learning”, or “deep learning”, followed by a manual check of the papers included in the dataset. The documents were examined using the popular R tool, Biblioshiny 4.2.0; the bibliometric analysis included multiple perspectives and various facets: dataset overview, sources, authors, papers, n-gram analysis, and mixed analysis. The results highlight an increased interest from the scientific community on disinformation topics in the context of machine learning and deep learning, supported by an annual growth rate of 96.1%. The insights gained from the research bring to light surprising details, while the study provides a solid basis for both future research in this area, as well for the development of new strategies addressing this complex issue of disinformation and ensuring a trustworthy and safe online environment.

A novel method for assessment rooftop PV potential based on remote sensing images

The assessment of rooftop photovoltaic (PV) potential is highly significant for energy policy formulation. With the rapid development of computer vision (CV) and remote sensing imagery, utilizing CV to extract rooftop information is an ideal approach. However, deep learning requires a large amount of accurately annotated data, and annotating remote sensing images is a labor-intensive task. This limitation hinders the application of deep learning in rooftop PV potential assessment. To address this issue, this paper proposes a semi-supervised learning (SSL)-based segmentation model to extract rooftop information from remote sensing images. Subsequently, a rooftop classification method is proposed to categorize rooftops into several classes and estimate their rooftop PV available area ratios. Finally, the total available rooftop PV area in urban areas is evaluated, and the potential rooftop PV installed capacity and power generation are calculated. This method is applied in the Longhu District of Shantou City, Guangdong Province. The evaluation results show that the total rooftop area in Longhu District is 17.2 km2, with a rooftop PV available area of 12.7 km2. It is estimated that the rooftop PV installed capacity in Longhu District is 1849.4 MW, with an annual power generation of 2219.3 GWh.

Self-supervised Learning Approach for Anomaly Detection in Rotating Machinery

Early fault detection in rotating machinery needs careful expert analysis of vibration data for monitoring a component state. Online methods that automatically set a threshold and raise an alarm when the vibration signature is anomalous are meant to efficiently manage key assets in a preventive maintenance plan. In recent years a focus has raised on data driven methods in parallel with the increasing attention towards machine learning and, particularly, deep learning models. In this regard, for rotating equipment components, an important aspect relates to labelled data scarcity for supervised training. On the other hand, the advent of the Internet of Things allows to gather data from multiple assets with relevant information on the asset state itself. Self-supervised learning methods in deep learning application are currently tackling this problem. Investigating Self-learning approaches to integrate domain knowledge and learn relevant features from unlabeled data is therefore important for condition monitoring applications. In this paper a methodology is proposed based on cycle consistency representation learning for training an embedder network on univariate unlabeled data. In order to learn a distance metric in the embedding space the original data are transformed to generate sequences of augmented inputs to enforce learnable pattern similarity in the augmented pairs. A differentiable cycle-consistency loss is chosen to maximize the numbers of augmented pairs in the learned embedding space that have minimum features distance. The pretext task in the described self-supervised setting aims to train a feature extractor for discriminating dissimilar samples in the embedding space by a distance metric and to provide a useful representation for down-stream tasks. The paper analyzes the performance of the approach for anomaly detection in rotating machinery. The methodology is tested on vibration data provided by the Center for Intelligent Maintenance Systems (IMS), University of Cincinnati, considering different accelerated life test campaigns. The data were collected to monitor the fault development in bearings and the model shows how the learned embedding space discriminates effectively anomalous samples from normal ones in the degradation stages of the bearings.

A review of multimodal deep learning methods for genomic-enabled prediction in plant breeding.

Deep learning methods have been applied when working to enhance the prediction accuracy of traditional statistical methods in the field of plant breeding. Although deep learning seems to be a promising approach for genomic prediction, it has proven to have some limitations, since its conventional methods fail to leverage all available information. Multimodal deep learning methods aim to improve the predictive power of their unimodal counterparts by introducing several modalities (sources) of input information. In this review, we introduce some theoretical basic concepts of multimodal deep learning and provide a list of the most widely used neural network architectures in deep learning, as well as the available strategies to fuse data from different modalities. We mention some of the available computational resources for the practical implementation of multimodal deep learning problems. We finally performed a review of applications of multimodal deep learning to genomic selection in plant breeding and other related fields. We present a meta-picture of the practical performance of multimodal deep learning methods to highlight how these tools can help address complex problems in the field of plant breeding. We discussed some relevant considerations that researchers should keep in mind when applying multimodal deep learning methods. Multimodal deep learning holds significant potential for various fields, including genomic selection. While multimodal deep learning displays enhanced prediction capabilities over unimodal deep learning and other machine learning methods, it demands more computational resources. Multimodal deep learning effectively captures intermodal interactions, especially when integrating data from different sources. To apply multimodal deep learning in genomic selection, suitable architectures and fusion strategies must be chosen. It is relevant to keep in mind that multimodal deep learning, like unimodal deep learning, is a powerful tool but should be carefully applied. Given its predictive edge over traditional methods, multimodal deep learning is valuable in addressing challenges in plant breeding and food security amid a growing global population.

Computer vision applications for the detection or analysis of tuberculosis using digitised human lung tissue images - a systematic review

ObjectiveTo conduct a systematic review of the computer vision applications that detect, diagnose, or analyse tuberculosis (TB) pathology or bacilli using digitised human lung tissue images either through automatic or semi-automatic methods. We categorised the computer vision platform into four technologies: image processing, object/pattern recognition, computer graphics, and deep learning. In this paper, the focus is on image processing and deep learning (DL) applications for either 2D or 3D digitised human lung tissue images. This review is useful for establishing a common practice in TB analysis using human lung tissue as well as identifying opportunities for further research in this space. The review brings attention to the state-of-art techniques for detecting TB, with emphasis on the challenges and limitations of the current techniques. The ultimate goal is to promote the development of more efficient and accurate algorithms for the detection or analysis of TB, and raise awareness about the importance of early detection.DesignWe searched five databases and Google Scholar for articles published between January 2017 and December 2022 that focus on Mycobacterium tuberculosis detection, or tuberculosis pathology using digitised human lung tissue images. Details regarding design, image processing and computer-aided techniques, deep learning models, and datasets were collected and summarised. Discussions, analysis, and comparisons of state-of-the-art methods are provided to help guide future research. Further, a brief update on the relevant techniques and their performance is provided.ResultsSeveral studies have been conducted to develop automated and AI-assisted methods for diagnosing Mtb and TB pathology from digitised human lung tissue images. Some studies presented a completely automated method of diagnosis, while other studies developed AI-assisted diagnostic methods. Low-level focus areas included the development of a novel μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}CT scanner for soft tissue image contract, and use of multiresolution computed tomography to analyse the 3D structure of the human lung. High-level focus areas included the investigation the effects of aging on the number and size of small airways in the lungs using CT and whole lung high-resolution μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}CT, and the 3D microanatomy characterisation of human tuberculosis lung using μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\upmu$$\\end{document}CT in conjunction with histology and immunohistochemistry. Additionally, a novel method for acquiring high-resolution 3D images of human lung structure and topology is also presented.ConclusionThe literature indicates that post 1950s, TB was predominantly studied using animal models even though no animal model reflects the full spectrum of human pulmonary TB disease and does not reproducibly transmit Mtb infection to other animals (Hunter, 2011). This explains why there are very few studies that used human lung tissue for detection or analysis of Mtb. Nonetheless, we found 10 studies that used human tissues (predominately lung) of which five studies proposed machine learning (ML) models for the detection of bacilli and the other five used CT on human lung tissue scanned ex-vivo.

Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach.

Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant challenges persist due to data inadequacies and statistical unidentifiability of key parameters. These issues are particularly pronounced in poorly resolved phylogenies, commonly observed in outbreaks such as SARS-CoV-2. In this study, we conducted a thorough evaluation of PhyloDeep, a deep learning inference tool for phylodynamics, assessing its performance on poorly resolved phylogenies. Our findings reveal the limited predictive accuracy of PhyloDeep (and other state-of-the-art approaches) in these scenarios. However, models trained on poorly resolved, realistically simulated trees demonstrate improved predictive power, despite not being infallible, especially in scenarios with superspreading dynamics, whose parameters are challenging to capture accurately. Notably, we observe markedly improved performance through the integration of minimal contact tracing data, which refines poorly resolved trees. Applying this approach to a sample of SARS-CoV-2 sequences partially matched to contact tracing from Hong Kong yields informative estimates of superspreading potential, extending beyond the scope of contact tracing data alone. Our findings demonstrate the potential for enhancing phylodynamic analysis through complementary data integration, ultimately increasing the precision of epidemiological predictions crucial for public health decision making and outbreak control.