Monkeypox (MPox) is a zoonotic infectious disease induced by the MPox Virus, part of the poxviridae orthopoxvirus group initially discovered in Africa and gained global attention in mid-2022 with cases reported outside endemic areas. Symptoms include headaches, chills, fever, smallpox, measles, and chickenpox-like skin manifestations and the WHO officially announced MPox as a global public health pandemic, in July 2022.Traditionally, PCR testing of skin lesions is considered a benchmark for the primary diagnosis by WHO, with symptom management as the primary treatment and antiviral drugs like tecovirimat for severe cases. However, manual analysis within hospitals poses a substantial challenge including the substantial burden on healthcare professionals, limited facilities, availability and fatigue among doctors, and human error during public health emergencies. Therefore, this survey paper provides an extensive and efficient analysis of deep learning (DL) methods for the automatic detection of MPox in skin lesion images. These DL techniques are broadly grouped into categories, including deep CNN, Deep CNNs ensemble, deep hybrid learning, the newly developed, and Vision transformer for diagnosing MPox. Moreover, this study offers a systematic exploration of the evolutionary progression of DL techniques and identifies, and addresses limitations in previous methods while highlighting the valuable contributions and innovation. Additionally, the paper addresses benchmark datasets and their collection from various authentic sources, pre-processing techniques, and evaluation metrics. The survey also briefly delves into emerging concepts, identifies research gaps, limitations, and applications, and outlines challenges in the diagnosis process. This survey furnishes valuable insights into the prospective areas of DL innovative ideas and is anticipated to serve as a path for researchers.
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Traumatic Brain Injury (TBI) presents a broad spectrum of clinical presentations and outcomes due to its inherent heterogeneity, leading to diverse recovery trajectories and varied therapeutic responses. While many studies have delved into TBI phenotyping for distinct patient populations, identifying TBI phenotypes that consistently generalize across various settings and populations remains a critical research gap. Our research addresses this by employing multivariate time-series clustering to unveil TBI's dynamic intricates. Utilizing a self-supervised learning-based approach to clustering multivariate time-Series data with missing values (SLAC-Time), we analyzed both the research-centric TRACK-TBI and the real-world MIMIC-IV datasets. Remarkably, the optimal hyperparameters of SLAC-Time and the ideal number of clusters remained consistent across these datasets, underscoring SLAC-Time's stability across heterogeneous datasets. Our analysis revealed three generalizable TBI phenotypes ({\alpha}, \b{eta}, and {\gamma}), each exhibiting distinct non-temporal features during emergency department visits, and temporal feature profiles throughout ICU stays. Specifically, phenotype {\alpha} represents mild TBI with a remarkably consistent clinical presentation. In contrast, phenotype \b{eta} signifies severe TBI with diverse clinical manifestations, and phenotype {\gamma} represents a moderate TBI profile in terms of severity and clinical diversity. Age is a significant determinant of TBI outcomes, with older cohorts recording higher mortality rates. Importantly, while certain features varied by age, the core characteristics of TBI manifestations tied to each phenotype remain consistent across diverse populations.
The inherent probabilistic nature of Large Language Models (LLMs) introduces an element of unpredictability, raising concerns about potential discrepancies in their output. This paper introduces an innovative approach aims to generate correct and optimal robotic task plans for diverse real-world demands and scenarios. LLMs have been used to generate task plans, but they are unreliable and may contain wrong, questionable, or high-cost steps. The proposed approach uses LLM to generate a number of task plans as trees and amalgamates them into a graph by removing questionable paths. Then an optimal task tree can be retrieved to circumvent questionable and high-cost nodes, thereby improving planning accuracy and execution efficiency. The approach is further improved by incorporating a large knowledge network. Leveraging GPT-4 further, the high-level task plan is converted into a low-level Planning Domain Definition Language (PDDL) plan executable by a robot. Evaluation results highlight the superior accuracy and efficiency of our approach compared to previous methodologies in the field of task planning.
The correlation between the sharpness of loss minima and generalisation in the context of deep neural networks has been subject to discussion for a long time. Whilst mostly investigated in the context of selected benchmark data sets in the area of computer vision, we explore this aspect for the acoustic scene classification task of the DCASE2020 challenge data. Our analysis is based on two-dimensional filter-normalised visualisations and a derived sharpness measure. Our exploratory analysis shows that sharper minima tend to show better generalisation than flat minima -even more so for out-of-domain data, recorded from previously unseen devices-, thus adding to the dispute about better generalisation capabilities of flat minima. We further find that, in particular, the choice of optimisers is a main driver of the sharpness of minima and we discuss resulting limitations with respect to comparability. Our code, trained model states and loss landscape visualisations are publicly available.
It is shown that a Hopfield recurrent neural network, informed by experimentally derived brain topology, recovers the scaling picture recently introduced by Deco et al., according to which the process of information transfer within the human brain shows spatially correlated patterns qualitatively similar to those displayed by turbulent flows. Although both models employ a coupling strength which decays exponentially with the euclidean distance between the nodes, their mathematical nature is widely different, Hopf oscillators versus Hopfield neural network. Hence, their convergence suggests a remarkable robustness of the aforementioned scaling picture. Furthermore, the present analysis shows that the Hopfield model brain remains functional by removing links above about five decay lengths, corresponding to about one sixth of the size of the global brain. This suggests that, in terms of connectivity decay length, the Hopfield brain functions in a sort of intermediate "turbulent liquid"-like state, whose essential connections are the intermediate ones between the connectivity decay length and the global brain size. This "turbulent-like liquid" appears to be more spiky than actual turbulent fluids, with a scaling exponent around $2/5$ instead of $2/3$.
Intensive longitudinal biomarker data are increasingly common in scientific studies that seek temporally granular understanding of the role of behavioral and physiological factors in relation to outcomes of interest. Intensive longitudinal biomarker data, such as those obtained from wearable devices, are often obtained at a high frequency typically resulting in several hundred to thousand observations per individual measured over minutes, hours, or days. Often in longitudinal studies, the primary focus is on relating the means of biomarker trajectories to an outcome, and the variances are treated as nuisance parameters, although they may also be informative for the outcomes. In this paper, we propose a Bayesian hierarchical model to jointly model a cross-sectional outcome and the intensive longitudinal biomarkers. To model the variability of biomarkers and deal with the high intensity of data, we develop subject-level cubic B-splines and allow the sharing of information across individuals for both the residual variability and the random effects variability. Then different levels of variability are extracted and incorporated into an outcome submodel for inferential and predictive purposes. We demonstrate the utility of the proposed model via an application involving bio-monitoring of hertz-level heart rate information from a study on social stress.
We explore leveraging corpus-specific vocabularies that improve both efficiency and effectiveness of learned sparse retrieval systems. We find that pre-training the underlying BERT model on the target corpus, specifically targeting different vocabulary sizes incorporated into the document expansion process, improves retrieval quality by up to 12% while in some scenarios decreasing latency by up to 50%. Our experiments show that adopting corpus-specific vocabulary and increasing vocabulary size decreases average postings list length which in turn reduces latency. Ablation studies show interesting interactions between custom vocabularies, document expansion techniques, and sparsification objectives of sparse models. Both effectiveness and efficiency improvements transfer to different retrieval approaches such as uniCOIL and SPLADE and offer a simple yet effective approach to providing new efficiency-effectiveness trade-offs for learned sparse retrieval systems.
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors -- the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network.
Solutions to vision tasks in gastrointestinal endoscopy (GIE) conventionally use image encoders pretrained in a supervised manner with ImageNet-1k as backbones. However, the use of modern self-supervised pretraining algorithms and a recent dataset of 100k unlabelled GIE images (Hyperkvasir-unlabelled) may allow for improvements. In this work, we study the fine-tuned performance of models with ResNet50 and ViT-B backbones pretrained in self-supervised and supervised manners with ImageNet-1k and Hyperkvasir-unlabelled (self-supervised only) in a range of GIE vision tasks. In addition to identifying the most suitable pretraining pipeline and backbone architecture for each task, out of those considered, our results suggest: that self-supervised pretraining generally produces more suitable backbones for GIE vision tasks than supervised pretraining; that self-supervised pretraining with ImageNet-1k is typically more suitable than pretraining with Hyperkvasir-unlabelled, with the notable exception of monocular depth estimation in colonoscopy; and that ViT-Bs are more suitable in polyp segmentation and monocular depth estimation in colonoscopy, ResNet50s are more suitable in polyp detection, and both architectures perform similarly in anatomical landmark recognition and pathological finding characterisation. We hope this work draws attention to the complexity of pretraining for GIE vision tasks, informs this development of more suitable approaches than the convention, and inspires further research on this topic to help advance this development. Code available: \underline{github.com/ESandML/SSL4GIE}
Purpose: Lymph nodes (LNs) in the chest have a tendency to enlarge due to various pathologies, such as lung cancer or pneumonia. Clinicians routinely measure nodal size to monitor disease progression, confirm metastatic cancer, and assess treatment response. However, variations in their shapes and appearances make it cumbersome to identify LNs, which reside outside of most organs. Methods: We propose to segment LNs in the mediastinum by leveraging the anatomical priors of 28 different structures (e.g., lung, trachea etc.) generated by the public TotalSegmentator tool. The CT volumes from 89 patients available in the public NIH CT Lymph Node dataset were used to train three 3D nnUNet models to segment LNs. The public St. Olavs dataset containing 15 patients (out-of-training-distribution) was used to evaluate the segmentation performance. Results: For the 15 test patients, the 3D cascade nnUNet model obtained the highest Dice score of 72.2 +- 22.3 for mediastinal LNs with short axis diameter $\geq$ 8mm and 54.8 +- 23.8 for all LNs respectively. These results represent an improvement of 10 points over a current approach that was evaluated on the same test dataset. Conclusion: To our knowledge, we are the first to harness 28 distinct anatomical priors to segment mediastinal LNs, and our work can be extended to other nodal zones in the body. The proposed method has immense potential for improved patient outcomes through the identification of enlarged nodes in initial staging CT scans.
Heuristics and cognitive biases are an integral part of human decision-making. Automatically detecting a particular cognitive bias could enable intelligent tools to provide better decision-support. Detecting the presence of a cognitive bias currently requires a hand-crafted experiment and human interpretation. Our research aims to explore conversational agents as an effective tool to measure various cognitive biases in different domains. Our proposed conversational agent incorporates a bias measurement mechanism that is informed by the existing experimental designs and various experimental tasks identified in the literature. Our initial experiments to measure framing and loss-aversion biases indicate that the conversational agents can be effectively used to measure the biases.
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