Traditionally, pathological analysis and diagnosis are performed by manually eyeballing glass slide specimens under a microscope by an expert. The whole slide image is the digital specimen produced from the glass slide. Whole slide image enabled specimens to be observed on a computer screen and led to computational pathology where computer vision and artificial intelligence are utilized for automated analysis and diagnosis. With the current computational advancement, the entire whole slide image can be analyzed autonomously without human supervision. However, the analysis could fail or lead to wrong diagnosis if the whole slide image is affected by tissue artifacts such as tissue fold or air bubbles depending on the severity. Existing artifact detection methods rely on experts for severity assessment to eliminate artifact affected regions from the analysis. This process is time consuming, exhausting and undermines the goal of automated analysis or removal of artifacts without evaluating their severity, which could result in the loss of diagnostically important data. Therefore, it is necessary to detect artifacts and then assess their severity automatically. In this paper, we propose a system that incorporates severity evaluation with artifact detection utilizing convolutional neural networks. The proposed system uses DoubleUNet to segment artifacts and an ensemble network of six fine tuned convolutional neural network models to determine severity. This method outperformed current state of the art in accuracy by 9 percent for artifact segmentation and achieved a strong correlation of 97 percent with the evaluation of pathologists for severity assessment. The robustness of the system was demonstrated using our proposed heterogeneous dataset and practical usability was ensured by integrating it with an automated analysis system.
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Omics biomarkers play a pivotal role in personalized medicine by providing molecular-level insights into the etiology of diseases, guiding precise diagnostics, and facilitating targeted therapeutic interventions. Recent advancements in omics technologies have resulted in an increasing abundance of multimodal omics data, providing unprecedented opportunities for identifying novel omics biomarkers for human diseases. Mendelian randomization (MR) is a practically useful causal inference method that uses genetic variants as instrumental variables (IVs) to infer causal relationships between omics biomarkers and complex traits/diseases by removing hidden confounding bias. In this article, we first present current challenges in performing MR analysis with omics data, and then describe four MR methods for analyzing multi-omics data including epigenomics, transcriptomics, proteomics, and metabolomics data, all executable within the R software environment.
Chemical synthesis, which is crucial for advancing material synthesis and drug discovery, impacts various sectors including environmental science and healthcare. The rise of technology in chemistry has generated extensive chemical data, challenging researchers to discern patterns and refine synthesis processes. Artificial intelligence (AI) helps by analyzing data to optimize synthesis and increase yields. However, AI faces challenges in processing literature data due to the unstructured format and diverse writing style of chemical literature. To overcome these difficulties, we introduce an end-to-end AI agent framework capable of high-fidelity extraction from extensive chemical literature. This AI agent employs large language models (LLMs) for prompt generation and iterative optimization. It functions as a chemistry assistant, automating data collection and analysis, thereby saving manpower and enhancing performance. Our framework's efficacy is evaluated using accuracy, recall, and F1 score of reaction condition data, and we compared our method with human experts in terms of content correctness and time efficiency. The proposed approach marks a significant advancement in automating chemical literature extraction and demonstrates the potential for AI to revolutionize data management and utilization in chemistry.
Accurate frictional contact is critical in simulating the assembly of rod-like structures in the practical world, such as knots, hairs, flagella, and more. Due to their high geometric nonlinearity and elasticity, rod-on-rod contact remains a challenging problem tackled by researchers in both computational mechanics and computer graphics. Typically, frictional contact is regarded as constraints for the equations of motions of a system. Such constraints are often computed independently at every time step in a dynamic simulation, thus slowing down the simulation and possibly introducing numerical convergence issues. This paper proposes a fully implicit penalty-based frictional contact method, Implicit Contact Model (IMC), that efficiently and robustly captures accurate frictional contact responses. We showcase our algorithm's performance in achieving visually realistic results for the challenging and novel contact scenario of flagella bundling in fluid medium, a significant phenomenon in biology that motivates novel engineering applications in soft robotics. In addition to this, we offer a side-by-side comparison with Incremental Potential Contact (IPC), a state-of-the-art contact handling algorithm. We show that IMC possesses comparable performance to IPC while converging at a faster rate.
Surface vibration tactile feedback is capable of conveying various semantic information to humans via the handheld electronic devices, like smartphone, touch panel,and game controller. However, covering the whole device contacting surface with dense actuator arrangement can affect its normal use, how to produce desired vibration patterns at any contact point with only several sparse actuators deployed on the handled device surface remains a significant challenge. In this work, we develop a tactile feedback board with only five actuators in the size of a smartphone, and achieve the precise vibration pattern production that can focus at any desired position all over the board. Specifically, we investigate the vibration characteristics of single passive coil actuator, and construct its vibration pattern model at any position on the feedback board surface. Optimal phase and amplitude modulation, found with the simulated annealing algorithm, is employed with five actuators in a sparse array. And all actuators' vibration patterns are superimposed linearly to synthetically generate different onboard vibration energy distribution for tactile sensing. Experiments demonstrated that for point-wise vibration pattern production on our tactile board achieved an average level of about 0.9 in the Structural Similarity Index Measure (SSIM) evaluation, when compared to the ideal single-point-focused target vibration pattern. The sparse actuator array can be easily embedded into usual handheld electronic devices, which shows a good significant implication for enriching their haptic interaction functionalities.
To promote precision medicine, individualized treatment regimes (ITRs) are crucial for optimizing the expected clinical outcome based on patient-specific characteristics. However, existing ITR research has primarily focused on scenarios with categorical treatment options and a single outcome. In reality, clinicians often encounter scenarios with continuous treatment options and multiple, potentially competing outcomes, such as medicine efficacy and unavoidable toxicity. To balance these outcomes, a proper weight is necessary, which should be learned in a data-driven manner that considers both patient preference and clinician expertise. In this paper, we present a novel algorithm for developing individualized treatment regimes (ITRs) that incorporate continuous treatment options and multiple outcomes, utilizing observational data. Our approach assumes that clinicians are optimizing individualized patient utilities with sub-optimal treatment decisions that are at least better than random assignment. Treatment assignment is assumed to directly depend on the true underlying utility of the treatment rather than patient characteristics. The proposed method simultaneously estimates the weighting of composite outcomes and the decision-making process, allowing for construction of individualized treatment regimes with continuous doses. The proposed estimators can be used for inference and variable selection, facilitating the identification of informative treatment assignments and preference-associated variables. We evaluate the finite sample performance of our proposed method via simulation studies and apply it to a real data application of radiation oncology analysis.
Mental health conditions, prevalent across various demographics, necessitate efficient monitoring to mitigate their adverse impacts on life quality. The surge in data-driven methodologies for mental health monitoring has underscored the importance of privacy-preserving techniques in handling sensitive health data. Despite strides in federated learning for mental health monitoring, existing approaches struggle with vulnerabilities to certain cyber-attacks and data insufficiency in real-world applications. In this paper, we introduce a differential private federated transfer learning framework for mental health monitoring to enhance data privacy and enrich data sufficiency. To accomplish this, we integrate federated learning with two pivotal elements: (1) differential privacy, achieved by introducing noise into the updates, and (2) transfer learning, employing a pre-trained universal model to adeptly address issues of data imbalance and insufficiency. We evaluate the framework by a case study on stress detection, employing a dataset of physiological and contextual data from a longitudinal study. Our finding show that the proposed approach can attain a 10% boost in accuracy and a 21% enhancement in recall, while ensuring privacy protection.
Distinguishing sources of predictive uncertainty is of crucial importance in the application of forecasting models across various domains. Despite the presence of a great variety of proposed uncertainty measures, there are no strict definitions to disentangle them. Furthermore, the relationship between different measures of uncertainty quantification remains somewhat unclear. In this work, we introduce a general framework, rooted in statistical reasoning, which not only allows the creation of new uncertainty measures but also clarifies their interrelations. Our approach leverages statistical risk to distinguish aleatoric and epistemic uncertainty components and utilizes proper scoring rules to quantify them. To make it practically tractable, we propose an idea to incorporate Bayesian reasoning into this framework and discuss the properties of the proposed approximation.
Comparative diagnostic in brain tumor evaluation makes possible to use the available information of a medical center to compare similar cases when a new patient is evaluated. By leveraging Artificial Intelligence models, the proposed system is able of retrieving the most similar cases of brain tumors for a given query. The primary objective is to enhance the diagnostic process by generating more accurate representations of medical images, with a particular focus on patient-specific normal features and pathologies. A key distinction from previous models lies in its ability to produce enriched image descriptors solely from binary information, eliminating the need for costly and difficult to obtain tumor segmentation. The proposed model uses Artificial Intelligence to detect patient features to recommend the most similar cases from a database. The system not only suggests similar cases but also balances the representation of healthy and abnormal features in its design. This not only encourages the generalization of its use but also aids clinicians in their decision-making processes. This generalization makes possible for future research in different medical diagnosis areas with almost not any change in the system. We conducted a comparative analysis of our approach in relation to similar studies. The proposed architecture obtains a Dice coefficient of 0.474 in both tumoral and healthy regions of the patients, which outperforms previous literature. Our proposed model excels at extracting and combining anatomical and pathological features from brain scans, achieving state-of-the-art results while relying on less expensive label information. This substantially reduces the overall cost of the training process. Our findings highlight the significant potential for improving the efficiency and accuracy of comparative diagnostics and the treatment of tumoral pathologies.
Magnetic resonance imaging (MRI) is crucial for enhancing diagnostic accuracy in clinical settings. However, the inherent long scan time of MRI restricts its widespread applicability. Deep learning-based image super-resolution (SR) methods exhibit promise in improving MRI resolution without additional cost. Due to lacking of aligned high-resolution (HR) and low-resolution (LR) MRI image pairs, unsupervised approaches are widely adopted for SR reconstruction with unpaired MRI images. However, these methods still require a substantial number of HR MRI images for training, which can be difficult to acquire. To this end, we propose an unpaired MRI SR approach that employs contrastive learning to enhance SR performance with limited HR training data. Empirical results presented in this study underscore significant enhancements in the peak signal-to-noise ratio and structural similarity index, even when a paucity of HR images is available. These findings accentuate the potential of our approach in addressing the challenge of limited HR training data, thereby contributing to the advancement of MRI in clinical applications.
The rising global prevalence of skin conditions, some of which can escalate to life-threatening stages if not timely diagnosed and treated, presents a significant healthcare challenge. This issue is particularly acute in remote areas where limited access to healthcare often results in delayed treatment, allowing skin diseases to advance to more critical stages. One of the primary challenges in diagnosing skin diseases is their low inter-class variations, as many exhibit similar visual characteristics, making accurate classification challenging. This research introduces a novel multimodal method for classifying skin lesions, integrating smartphone-captured images with essential clinical and demographic information. This approach mimics the diagnostic process employed by medical professionals. A distinctive aspect of this method is the integration of an auxiliary task focused on super-resolution image prediction. This component plays a crucial role in refining visual details and enhancing feature extraction, leading to improved differentiation between classes and, consequently, elevating the overall effectiveness of the model. The experimental evaluations have been conducted using the PAD-UFES20 dataset, applying various deep-learning architectures. The results of these experiments not only demonstrate the effectiveness of the proposed method but also its potential applicability under-resourced healthcare environments.
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