IEEE Journal of Biomedical and Health Informatics

The crisis of antibiotic resistance has become a significant global threat to human health. Understanding properties of antibiotic resistance genes (ARGs) is the first step to mitigate this issue. Although many methods have been proposed for predicting properties of ARGs, most of these methods focus only on predicting antibiotic classes, while ignoring other properties of ARGs, such as resistance mechanisms and transferability. However, acquiring all of these properties of ARGs can help researchers gain a more comprehensive understanding of the essence of antibiotic resistance, which will facilitate the development of antibiotics...

Accurately delineating and categorizing individual hand bones in 3D ultrasound (US) is a promising technology for precise digital diagnostic analysis. However, this is a challenging task due to the inherent imaging limitations of the US and the insignificant feature differences among numerous bones. In this study, we have proposed a novel deep learning-based solution for pediatric hand bone segmentation in the US. Our method is unique in that it allows for effective detailed feature mining through an adaptive multi-dimensional weighting attention mechanism...

Multimodal medical image fusion aims to integrate complementary information from different modalities of medical images. Deep learning methods, especially recent vision Transformers, have effectively improved image fusion performance. However, there are limitations for Transformers in image fusion, such as lacks of local feature extraction and cross-modal feature interaction, resulting in insufficient multimodal feature extraction and integration. In addition, the computational cost of Transformers is higher...

The identification of EEG biomarkers to discriminate Subjective Cognitive Decline (SCD) from Mild Cognitive Impairment (MCI) conditions is a complex task which requires great clinical effort and expertise. We exploit the self-attention component of the Transformer architecture to obtain physiological explanations of the model's decisions in the discrimination of 56 SCD and 45 MCI patients using resting-state EEG. Specifically, an interpretability workflow leveraging attention scores and time-frequency analysis of EEG epochs through Continuous Wavelet Transform is proposed...

Congenital heart disease (CHD) is the most frequent birth defect and a leading cause of infant mortality, emphasizing the crucial need for its early diagnosis. Ultrasound is the primary imaging modality for prenatal CHD screening. As a complement to the four-chamber view, the three-vessel view (3VV) plays a vital role in detecting anomalies in the great vessels. However, the interpretation of fetal cardiac ultrasound images is subjective and relies heavily on operator experience, leading to variability in CHD detection rates, particularly in resource-constrained regions...

Despite the vast potential for insights and value present in Electronic Health Records (EHRs), it is challenging to fully leverage all the available information, particularly that contained in the free-text data written by clinicians describing the health status of patients. The utilization of Named Entity Recognition and Linking tools allows not only for the structuring of information contained within free-text data, but also for the integration with medical ontologies, which may prove highly beneficial for the analysis of patient medical histories with the aim of forecasting future medical outcomes, such as the diagnosis of a new disorder...

Diffuse large B-cell lymphoma (DLBCL), a cancer of B cells, has been one of the most challenging and complicated diseases because of its considerable variation in clinical behavior, response to therapy, and prognosis. Radiomic features from medical images, such as PET images, have become one of the most valuable features for disease classification or prognosis prediction using learning-based methods. In this paper, a new flexible ensemble deep learning model is proposed for the prognosis prediction of the DLBCL in 18 F-FDG PET images...

The B-mode ultrasound based computer-aided diagnosis (CAD) has demonstrated its effectiveness for diagnosis of Developmental Dysplasia of the Hip (DDH) in infants, which can conduct the Graf's method by detecting landmarks in hip ultrasound images. However, it is still necessary to explore more valuable information around these landmarks to enhance feature representation for improving detection performance in the detection model. To this end, a novel Involution Transformer based U-Net (IT-UNet) network is proposed for hip landmark detection...

Identifying links within biological networks is important in various biomedical applications. Recent studies have revealed that each node in a network may play a unique role in different links, but most link prediction methods overlook distinctive node roles, hindering the acquisition of effective link representations. Subgraph-based methods have been introduced as solutions but often ignore shared information among subgraphs. To address these limitations, we propose a Subgraph-aware Graph Kernel Neural Network (SubKNet) for link prediction in biological networks...

Transcranial focused ultrasound (tFUS) has emerged as a new mode of non-invasive brain stimulation (NIBS), with its exquisite spatial precision and capacity to reach the deep regions of the brain. The placement of the acoustic focus onto the desired part of the brain is critical for successful tFUS procedures; however, acoustic wave propagation is severely affected by the skull, distorting the focal location/shape and the pressure level. High-resolution (HR) numerical simulation allows for monitoring of acoustic pressure within the skull but with a considerable computational burden...

Interpersonal communication facilitates symptom measures of autistic sociability to enhance clinical decision-making in identifying children with autism spectrum disorder (ASD). Traditional methods are carried out by clinical practitioners with assessment scales, which are subjective to quantify. Recent studies employ engineering technologies to analyze children's behaviors with quantitative indicators, but these methods only generate specific rule-driven indicators that are not adaptable to diverse interaction scenarios...

High- throughput screening technology has enabled the generation of large-scale drug responses across hundreds of cancer cell lines. There remains a significant gap between in vitro cell lines and actual tumors in vivo in terms of their response to drug treatments yet. This is because tumors consist of a complex cellular composition and histopathology structure, known as the tumor microenvironment (TME), which greatly impacts the drug cytotoxicity against tumor cells. To date, no study has focused on modeling the impact of the TME on clinical drug response...

Inferring potential drug indications plays a vital role in the drug discovery process. It can be time-consuming and costly to discover novel drug indications through biological experiments. Recently, graph learning-based methods have gained popularity for this task. These methods typically treat the prediction task as a binary classification problem, focusing on modeling associations between drugs and diseases within a graph. However, labeled data for drug indication prediction is often limited and expensive to acquire...

Predicting the binding affinity of drug target is essential to reduce drug development costs and cycles. Recently, several deep learning-based methods have been proposed to utilize the structural or sequential information of drugs and targets to predict the drug-target binding affinity (DTA). However, methods that rely solely on sequence features do not consider hydrogen atom data, which may result in information loss. Graph-based methods may contain information that is not directly related to the prediction process...

Blood pressure (BP) is predicted by this effort based on photoplethysmography (PPG) data to provide effective pre-warning of possible preeclampsia of pregnant women. Towards frequent BP measurement, a PPG sensor device is utilized in this study as a solution to offer continuous, cuffless blood pressure monitoring frequently for pregnant women. PPG data were collected using a flexible sensor patch from the wrist arteries of 194 subjects, which included 154 normal individuals and 40 pregnant women. Deep-learning models in 3 stages were built and trained to predict BP...

Sleep onset latency (SOL) is an important factor relating to the sleep quality of a subject. Therefore, accurate prediction of SOL is useful to identify individuals at risk of sleep disorders and to improve sleep quality. In this study, we estimate SOL distribution and falling asleep function using an electroencephalogram (EEG), which can measure the electric field of brain activity. We proposed a Multi Ensemble Distribution model for estimating Sleep Onset Latency (MEDi-SOL), consisting of a temporal encoder and a time distribution decoder...

Although deep networks have succeeded in various signal classification tasks, the time sequence samples used to train the deep models are usually required to reach a certain length. Especially, in brain computer interface (BCI) research, around 3.5s-long motor imagery (MI) Electroencephalography (EEG) samples are needed to obtain satisfactory classification performance. This time-span requirement of the training samples makes real-time MI BCI systems impossible to implement based on deep networks, which restricts the related researches within laboratory and makes practical application hard to accomplish...

Detecting Alzheimer's disease (AD) accurately at an early stage is critical for planning and implementing disease-modifying treatments that can help prevent the progression to severe stages of the disease. In the existing literature, diagnostic test scores and clinical status have been provided for specific time points, and predicting the disease progression poses a significant challenge. However, few studies focus on longitudinal data to build deep-learning models for AD detection. These models are not stable to be relied upon in real medical settings due to a lack of adaptive training and testing...

In the field of pathology, the scarcity of certain diseases and the difficulty of annotating images hinder the development of large, high-quality datasets, which in turn affects the advancement of deep learning-assisted diagnostics. Few-shot learning has demonstrated unique advantages in modeling tasks with limited data, yet explorations of this method in the field of pathology remain in the early stages. To address this issue, we present a dual-channel prototype network (DCPN), a novel few-shot learning approach for efficiently classifying pathology images with limited data...

Artificial intelligence (AI) in healthcare, especially in medical imaging, faces challenges due to data scarcity and privacy concerns. Addressing these, we introduce Med-DDPM, a diffusion model designed for 3D semantic brain MRI synthesis. This model effectively tackles data scarcity and privacy issues by integrating semantic conditioning. This involves the channel-wise concatenation of a conditioning image to the model input, enabling control in image generation. Med-DDPM demonstrates superior stability and performance compared to existing 3D brain imaging synthesis methods...