Severe acute respiratory disease SARS-CoV-2 has had a found impact on public health systems and healthcare emergency response especially with respect to making decisions on the most effective measures to be taken at any given time. As demonstrated throughout the last three years with COVID-19, the prediction of the number of positive cases can be an effective way to facilitate decision-making. However, the limited availability of data and the highly dynamic and uncertain nature of the virus transmissibility makes this task very challenging. Aiming at investigating these challenges and in order to address this problem, this work studies data-driven (learning, statistical) methods for incrementally training models to adapt to these nonstationary conditions. An extensive empirical study is conducted to examine various characteristics, such as, performance analysis on a per virus wave basis, feature extraction, "lookback" window size, memory size, all for next-, 7-, and 14-day forecasting tasks. We demonstrate that the incremental learning framework can successfully address the aforementioned challenges and perform well during outbreaks, providing accurate predictions.
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Photon counting radiation detectors have become an integral part of medical imaging modalities such as Positron Emission Tomography or Computed Tomography. One of the most promising detectors is the wide bandgap room temperature semiconductor detectors, which depends on the interaction gamma/x-ray photons with the detector material involves Compton scattering which leads to multiple interaction photon events (MIPEs) of a single photon. For semiconductor detectors like CdZnTeSe (CZTS), which have a high overlap of detected energies between Compton and photoelectric events, it is nearly impossible to distinguish between Compton scattered events from photoelectric events using conventional readout electronics or signal processing algorithms. Herein, we report a deep learning classifier CoPhNet that distinguishes between Compton scattering and photoelectric interactions of gamma/x-ray photons with CdZnTeSe (CZTS) semiconductor detectors. Our CoPhNet model was trained using simulated data to resemble actual CZTS detector pulses and validated using both simulated and experimental data. These results demonstrated that our CoPhNet model can achieve high classification accuracy over the simulated test set. It also holds its performance robustness under operating parameter shifts such as Signal-Noise-Ratio (SNR) and incident energy. Our work thus laid solid foundation for developing next-generation high energy gamma-rays detectors for better biomedical imaging.
Large Language Models (LLMs) have introduced a new era of proficiency in comprehending complex healthcare and biomedical topics. However, there is a noticeable lack of models in languages other than English and models that can interpret multi-modal input, which is crucial for global healthcare accessibility. In response, this study introduces Qilin-Med-VL, the first Chinese large vision-language model designed to integrate the analysis of textual and visual data. Qilin-Med-VL combines a pre-trained Vision Transformer (ViT) with a foundational LLM. It undergoes a thorough two-stage curriculum training process that includes feature alignment and instruction tuning. This method enhances the model's ability to generate medical captions and answer complex medical queries. We also release ChiMed-VL, a dataset consisting of more than 1M image-text pairs. This dataset has been carefully curated to enable detailed and comprehensive interpretation of medical data using various types of images.
Pathological captioning of Whole Slide Images (WSIs), though is essential in computer-aided pathological diagnosis, has rarely been studied due to the limitations in datasets and model training efficacy. In this paper, we propose a new paradigm Subtype-guided Masked Transformer (SGMT) for pathological captioning based on Transformers, which treats a WSI as a sequence of sparse patches and generates an overall caption sentence from the sequence. An accompanying subtype prediction is introduced into SGMT to guide the training process and enhance the captioning accuracy. We also present an Asymmetric Masked Mechansim approach to tackle the large size constraint of pathological image captioning, where the numbers of sequencing patches in SGMT are sampled differently in the training and inferring phases, respectively. Experiments on the PatchGastricADC22 dataset demonstrate that our approach effectively adapts to the task with a transformer-based model and achieves superior performance than traditional RNN-based methods. Our codes are to be made available for further research and development.
In the era of the Internet of Things (IoT), the retrieval of relevant medical information has become essential for efficient clinical decision-making. This paper introduces MedFusionRank, a novel approach to zero-shot medical information retrieval (MIR) that combines the strengths of pre-trained language models and statistical methods while addressing their limitations. The proposed approach leverages a pre-trained BERT-style model to extract compact yet informative keywords. These keywords are then enriched with domain knowledge by linking them to conceptual entities within a medical knowledge graph. Experimental evaluations on medical datasets demonstrate MedFusion Rank's superior performance over existing methods, with promising results with a variety of evaluation metrics. MedFusionRank demonstrates efficacy in retrieving relevant information, even from short or single-term queries.
An objective measurement of chronic itch is necessary for improvements in patient care for numerous medical conditions. While wearables have shown promise for scratch detection, they are currently unable to estimate scratch intensity, preventing a comprehensive understanding of the effect of itch on an individual. In this work, we present a framework for the estimation of scratch intensity in addition to the detection of scratch. This is accomplished with a multimodal ring device, consisting of an accelerometer and a contact microphone, a pressure-sensitive tablet for capturing ground truth intensity values, and machine learning algorithms for regression of scratch intensity on a 0-600 milliwatts (mW) power scale that can be mapped to a 0-10 continuous scale. We evaluate the performance of our algorithms on 20 individuals using leave one subject out cross-validation and using data from 14 additional participants, we show that our algorithms achieve clinically-relevant discrimination of scratching intensity levels. By doing so, our device enables the quantification of the substantial variations in the interpretation of the 0-10 scale frequently utilized in patient self-reported clinical assessments. This work demonstrates that a finger-worn device can provide multidimensional, objective, real-time measures for the action of scratching.
Objectives: Artificial intelligence (AI) applications utilizing electronic health records (EHRs) have gained popularity, but they also introduce various types of bias. This study aims to systematically review the literature that address bias in AI research utilizing EHR data. Methods: A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guideline. We retrieved articles published between January 1, 2010, and October 31, 2022, from PubMed, Web of Science, and the Institute of Electrical and Electronics Engineers. We defined six major types of bias and summarized the existing approaches in bias handling. Results: Out of the 252 retrieved articles, 20 met the inclusion criteria for the final review. Five out of six bias were covered in this review: eight studies analyzed selection bias; six on implicit bias; five on confounding bias; four on measurement bias; two on algorithmic bias. For bias handling approaches, ten studies identified bias during model development, while seventeen presented methods to mitigate the bias. Discussion: Bias may infiltrate the AI application development process at various stages. Although this review discusses methods for addressing bias at different development stages, there is room for implementing additional effective approaches. Conclusion: Despite growing attention to bias in healthcare AI, research using EHR data on this topic is still limited. Detecting and mitigating AI bias with EHR data continues to pose challenges. Further research is needed to raise a standardized method that is generalizable and interpretable to detect, mitigate and evaluate bias in medical AI.
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein pathways are key drivers of embryogenesis and physiological processes. Comprehending their diverse behaviors is essential for tackling diseases, including cancer, as well as for engineering novel biological constructs. Despite the availability of extensive mathematical models represented in Systems Biology Markup Language (SBML), researchers face significant challenges in exploring the full spectrum of behaviors and optimizing interventions to efficiently shape those behaviors. Existing tools designed for simulation of biological network models are not tailored to facilitate interventions on network dynamics nor to facilitate automated discovery. Leveraging recent developments in machine learning (ML), this paper introduces SBMLtoODEjax, a lightweight library designed to seamlessly integrate SBML models with ML-supported pipelines, powered by JAX. SBMLtoODEjax facilitates the reuse and customization of SBML-based models, harnessing JAX's capabilities for efficient parallel simulations and optimization, with the aim to accelerate research in biological network analysis.
Anomaly detection in imbalanced datasets is a frequent and crucial problem, especially in the medical domain where retrieving and labeling irregularities is often expensive. By combining the generative stability of a $\beta$-variational autoencoder (VAE) with the discriminative strengths of generative adversarial networks (GANs), we propose a novel model, $\beta$-VAEGAN. We investigate methods for composing anomaly scores based on the discriminative and reconstructive capabilities of our model. Existing work focuses on linear combinations of these components to determine if data is anomalous. We advance existing work by training a kernelized support vector machine (SVM) on the respective error components to also consider nonlinear relationships. This improves anomaly detection performance, while allowing faster optimization. Lastly, we use the deviations from the Gaussian prior of $\beta$-VAEGAN to form a novel anomaly score component. In comparison to state-of-the-art work, we improve the $F_1$ score during anomaly detection from 0.85 to 0.92 on the widely used MITBIH Arrhythmia Database.
Breast Cancer (BC) is among women's most lethal health concerns. Early diagnosis can alleviate the mortality rate by helping patients make efficient treatment decisions. Human Epidermal Growth Factor Receptor (HER2) has become one the most lethal subtype of BC. According to the College of American Pathologists American Society of Clinical Oncology (CAP/ASCO), the severity level of HER2 expression can be classified between 0 and 3+ range. HER2 can be detected effectively from immunohistochemical (IHC) and, hematoxylin & eosin (HE) images of different classes such as 0, 1+, 2+, and 3+. An ensemble approach integrated with threshold filtered single instance evaluation (SIE) technique has been proposed in this study to diagnose BC from the multi-categorical expression of HER2 subtypes. Initially, DenseNet201 and Xception have been ensembled into a single classifier as feature extractors with an effective combination of global average pooling, dropout layer, dense layer with a swish activation function, and l2 regularizer, batch normalization, etc. After that, extracted features has been processed through single instance evaluation (SIE) to determine different confidence levels and adjust decision boundary among the imbalanced classes. This study has been conducted on the BC immunohistochemical (BCI) dataset, which is classified by pathologists into four stages of HER2 BC. This proposed approach known as DenseNet201-Xception-SIE with a threshold value of 0.7 surpassed all other existing state-of-art models with an accuracy of 97.12%, precision of 97.15%, and recall of 97.68% on H&E data and, accuracy of 97.56%, precision of 97.57%, and recall of 98.00% on IHC data respectively, maintaining momentous improvement. Finally, Grad-CAM and Guided Grad-CAM have been employed in this study to interpret, how TL-based model works on the histopathology dataset and make decisions from the data.
What is learned by sophisticated neural network agents such as AlphaZero? This question is of both scientific and practical interest. If the representations of strong neural networks bear no resemblance to human concepts, our ability to understand faithful explanations of their decisions will be restricted, ultimately limiting what we can achieve with neural network interpretability. In this work we provide evidence that human knowledge is acquired by the AlphaZero neural network as it trains on the game of chess. By probing for a broad range of human chess concepts we show when and where these concepts are represented in the AlphaZero network. We also provide a behavioural analysis focusing on opening play, including qualitative analysis from chess Grandmaster Vladimir Kramnik. Finally, we carry out a preliminary investigation looking at the low-level details of AlphaZero's representations, and make the resulting behavioural and representational analyses available online.
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