... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics最新文献

Neuroimaging studies have demonstrated that Alzheimer's disease (AD) is closely related to changes in neuroanatomy in the form of damage to both grey matter and white matter. However, the exact nature of AD's relationship with white matter anatomical deterioration is not fully understood at a systemic level. To investigate this knowledge gap, we constructed structural brain networks from ADNI-GO/2 diffusion tensor imaging (DTI) images with brain regions of interest (ROIs) as nodes and white matter connections as edges weighted by fiber density. The cohort consists of healthy control (HC), mild cognitive impairment (MCI), and clinically diagnosed AD subjects. By optimizing consensus modularity of structural brain networks at a subpopulation level to investigate community structure throughout a range of resolution parameters (γ), we observed a split of the reward-based decision-making module in the AD group at γ = 1.3, thus finding a 7^th consensus community in the AD consensus brain network partition that was not present in that of MCI or HC populations. Upon further investigation, we found that thalamic and caudal regions were involved in the increased segregation of AD brain networks. These regions are implicated in regulation of decision-making processes, and their segregation from other decision-making regions is a novel finding in white matter biomarker studies of AD. Our study presents novel evidence that AD may be a disconnection syndrome at the mesoscopic structural level, with potential new avenues of exploration into the role of the thalamus and caudate that may reveal neural correlates of cognitive deficits in clinically diagnosed AD.

Autism and Attention-Deficit Hyperactivity Disorder (ADHD) are two of the most commonly observed neurodevelopmental conditions in childhood. Providing a specific computational assessment to distinguish between the two can prove difficult and time intensive. Given the high prevalence of their co-occurrence, there is a need for scalable and accessible methods for distinguishing the co-occurrence of autism and ADHD from individual diagnoses. The first step is to identify a core set of features that can serve as the basis for behavioral feature extraction. We trained machine learning models on data from the National Survey of Children's Health to identify behaviors to target as features in automated clinical decision support systems. A model trained on the binary task of distinguishing either developmental delay (autism or ADHD) vs. neither achieved sensitivity >92% and specificity >94%, while a model trained on the 4-way classification task of autism vs. ADHD vs. both vs. none demonstrated >65% sensitivity and >66% specificity. While the performance of the binary model was respectable, the relatively low performance in the differential classification of autism and ADHD highlights the challenges that persist in achieving specificity within clinical decision support tools for developmental delays. Nevertheless, this study demonstrates the potential of applying behavioral questionnaires not traditionally used for clinical purposes towards supporting digital screening assessments for pediatric developmental delays.

Detecting retinal image analysis, particularly the geometrical features of branching points, plays an essential role in diagnosing eye diseases. However, existing methods used for this purpose often are coarse-level and lack fine-grained analysis for efficient annotation. To mitigate these issues, this paper proposes a novel method for detecting retinal branching angles using a self-configured image processing technique. Additionally, we offer an open-source annotation tool and a benchmark dataset comprising 40 images annotated with retinal branching angles. Our methodology for retinal branching angle detection and calculation is detailed, followed by a benchmark analysis comparing our method with previous approaches. The results indicate that our method is robust under various conditions with high accuracy and efficiency, which offers a valuable instrument for ophthalmic research and clinical applications. The dataset and source codes are available at https://github.com/Retinal-Research/RBAD.

Opioid withdrawal's physiological effects are a major impediment to recovery from opioid use disorder (OUD). Prior work has demonstrated that transcutaneous cervical vagus nerve stimulation (tcVNS) can counteract some of opioid withdrawal's physiological effects by reducing heart rate and perceived symptoms. The purpose of this study was to assess the effects of tcVNS on respiratory manifestations of opioid withdrawal - specifically, respiratory timings and their variability. Patients with OUD (N = 21) underwent acute opioid withdrawal over the course of a two-hour protocol. The protocol involved opioid cues to induce opioid craving and neutral conditions for control purposes. Patients were randomly assigned to receive double-blind active tcVNS (n = 10) or sham stimulation (n = 11) throughout the protocol. Respiratory effort and electrocardiogram-derived respiration signals were used to estimate inspiration time (T_i), expiration time (T_e), and respiration rate (RR), along with each measure's variability quantified via interquartile range (IQR). Comparing the active and sham groups, active tcVNS significantly reduced IQR(T_i) - a variability measure - compared to sham stimulation (p = .02). Relative to baseline, the active group's median change in IQR(T_i) was 500 ms less than the sham group's median change in IQR(T_i). Notably, IQR(T_i) was found to be positively associated with post-traumatic stress disorder symptoms in prior work. Therefore, a reduction in IQR(T_i) suggests that tcVNS downregulates the respiratory stress response associated with opioid withdrawal. Although further investigations are necessary, these results promisingly suggest that tcVNS - a non-pharmacologic, non-invasive, readily implemented neuromodulation approach - can serve as a novel therapy to mitigate opioid withdrawal symptoms.

Parkinson's disease (PD) is the second most common neurodegenerative disease and presents a complex etiology with genomic and environmental factors and no recognized cures. Genotype data, such as single nucleotide polymorphisms (SNPs), could be used as a prodromal factor for early detection of PD. However, the polygenic nature of PD presents a challenge as the complex relationships between SNPs towards disease development are difficult to model. Traditional assessment methods such as polygenic risk scores and machine learning approaches struggle to capture the complex interactions present in the genotype data, thus limiting their discriminative capabilities in diagnosis. On the other hand, deep learning models are better suited for this task. Nevertheless, they encounter difficulties of their own such as a lack of interpretability. To overcome these limitations, in this work, a novel transformer encoder-based model is introduced to classify PD patients from healthy controls based on their genotype. This method is designed to effectively model complex global feature interactions and enable increased interpretability through the learned attention scores. The proposed framework outperformed traditional machine learning models and multilayer perceptron (MLP) baseline models. Moreover, visualization of the learned SNP-SNP associations provides not only interpretability to the model but also valuable insights into the biochemical pathways underlying PD development, which are corroborated by pathway enrichment analysis. Our results suggest novel SNP interactions to be further studied in wet lab and clinical settings.

To keep pace with the increased generation and digitization of documents, automated methods that can improve search, discovery and mining of the vast body of literature are essential. Keyphrases provide a concise representation by identifying salient concepts in a document. Various supervised approaches model keyphrase extraction using local context to predict the label for each token and perform much better than the unsupervised counterparts. However, existing supervised datasets have limited annotated examples to train better deep learning models. In contrast, many domains have large amount of un-annotated data that can be leveraged to improve model performance in keyphrase extraction. We introduce a self-learning based model that incorporates uncertainty estimates to select instances from large-scale unlabeled data to augment the small labeled training set. Performance evaluation on a publicly available biomedical dataset demonstrates that our method improves performance of keyphrase extraction over state of the art models.

High-throughput sequencing is widely used for strain detection and characterization of antibiotic resistance in microbial metagenomic samples. Current analytical tools use curated antibiotic resistance gene (ARG) databases to classify individual sequencing reads or assembled contigs. However, identifying ARGs from raw read data can be time consuming (especially if assembly or alignment is required) and challenging, due to genome rearrangements and mutations. Here, we present the k-mer-based antibiotic gene resistance analyzer (KARGA), a multi-platform Java toolkit for identifying ARGs from metagenomic short read data. KARGA does not perform alignment; it uses an efficient double-lookup strategy, statistical filtering on false positives, and provides individual read classification as well as covering of the database resistome. On simulated data, KARGA's antibiotic resistance class recall is 99.89% for error/mutation rates within 10%, and of 83.37% for error/mutation rates between 10% and 25%, while it is 99.92% on ARGs with rearrangements. On empirical data, KARGA provides higher hit score (≥1.5-fold) than AMRPlusPlus, DeepARG, and MetaMARC. KARGA has also faster runtimes than all other tools (2x faster than AMRPlusPlus, 7x than DeepARG, and over 100x than MetaMARC). KARGA is available under the MIT license at https://github.com/DataIntellSystLab/KARGA.