arXiv subjects

David Ahmedt-Aristizabal

Publications and source records attributed to David Ahmedt-Aristizabal.

45 records · Page 3Linked to original sources

arXiv2022

In-Bed Human Pose Estimation from Unseen and Privacy-Preserving Image Domains

Medical applications have benefited greatly from the rapid advancement in computer vision. Considering patient monitoring in particular, in-bed human posture estimation offers important health-related metrics with potential value in medical condition assessments. Despite great progress in this domain, it remains challenging due to substantial ambiguity during occlusions, and the lack of large corpora of manually labeled data for model training, particularly with domains such as thermal infrared imaging which are privacy-preserving, and thus of great interest. Motivated by the effectiveness of self-supervised methods in learning features directly from data, we propose a multi-modal conditional variational autoencoder (MC-VAE) capable of reconstructing features from missing modalities seen during training. This approach is used with HRNet to enable single modality inference for in-bed pose estimation. Through extensive evaluations, we demonstrate that body positions can be effectively recognized from the available modality, achieving on par results with baseline models that are highly dependent on having access to multiple modes at inference time. The proposed framework supports future research towards self-supervised learning that generates a robust model from a single source, and expects it to generalize over many unknown distributions in clinical environments.

cs.CV↗

arXiv2021

The CSIRO Crown-of-Thorn Starfish Detection Dataset

Crown-of-Thorn Starfish (COTS) outbreaks are a major cause of coral loss on the Great Barrier Reef (GBR) and substantial surveillance and control programs are underway in an attempt to manage COTS populations to ecologically sustainable levels. We release a large-scale, annotated underwater image dataset from a COTS outbreak area on the GBR, to encourage research on Machine Learning and AI-driven technologies to improve the detection, monitoring, and management of COTS populations at reef scale. The dataset is released and hosted in a Kaggle competition that challenges the international Machine Learning community with the task of COTS detection from these underwater images.

cs.CV↗

arXiv2021

A Survey on Graph-Based Deep Learning for Computational Histopathology

With the remarkable success of representation learning for prediction problems, we have witnessed a rapid expansion of the use of machine learning and deep learning for the analysis of digital pathology and biopsy image patches. However, learning over patch-wise features using convolutional neural networks limits the ability of the model to capture global contextual information and comprehensively model tissue composition. The phenotypical and topological distribution of constituent histological entities play a critical role in tissue diagnosis. As such, graph data representations and deep learning have attracted significant attention for encoding tissue representations, and capturing intra- and inter- entity level interactions. In this review, we provide a conceptual grounding for graph analytics in digital pathology, including entity-graph construction and graph architectures, and present their current success for tumor localization and classification, tumor invasion and staging, image retrieval, and survival prediction. We provide an overview of these methods in a systematic manner organized by the graph representation of the input image, scale, and organ on which they operate. We also outline the limitations of existing techniques, and suggest potential future research directions in this domain.

cs.LG↗

arXiv2021

Towards Interpretable Attention Networks for Cervical Cancer Analysis

Recent advances in deep learning have enabled the development of automated frameworks for analysing medical images and signals, including analysis of cervical cancer. Many previous works focus on the analysis of isolated cervical cells, or do not offer sufficient methods to explain and understand how the proposed models reach their classification decisions on multi-cell images. Here, we evaluate various state-of-the-art deep learning models and attention-based frameworks for the classification of images of multiple cervical cells. As we aim to provide interpretable deep learning models to address this task, we also compare their explainability through the visualization of their gradients. We demonstrate the importance of using images that contain multiple cells over using isolated single-cell images. We show the effectiveness of the residual channel attention model for extracting important features from a group of cells, and demonstrate this model's efficiency for this classification task. This work highlights the benefits of channel attention mechanisms in analyzing multiple-cell images for potential relations and distributions within a group of cells. It also provides interpretable models to address the classification of cervical cells.

cs.CV↗

arXiv2021

Video-Based Inpatient Fall Risk Assessment: A Case Study

Inpatient falls are a serious safety issue in hospitals and healthcare facilities. Recent advances in video analytics for patient monitoring provide a non-intrusive avenue to reduce this risk through continuous activity monitoring. However, in-bed fall risk assessment systems have received less attention in the literature. The majority of prior studies have focused on fall event detection, and do not consider the circumstances that may indicate an imminent inpatient fall. Here, we propose a video-based system that can monitor the risk of a patient falling, and alert staff of unsafe behaviour to help prevent falls before they occur. We propose an approach that leverages recent advances in human localisation and skeleton pose estimation to extract spatial features from video frames recorded in a simulated environment. We demonstrate that body positions can be effectively recognised and provide useful evidence for fall risk assessment. This work highlights the benefits of video-based models for analysing behaviours of interest, and demonstrates how such a system could enable sufficient lead time for healthcare professionals to respond and address patient needs, which is necessary for the development of fall intervention programs.

cs.CV↗

arXiv2021

Graph-Based Deep Learning for Medical Diagnosis and Analysis: Past, Present and Future

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

cs.LG↗

arXiv2020

Neural Memory Networks for Seizure Type Classification

Classification of seizure type is a key step in the clinical process for evaluating an individual who presents with seizures. It determines the course of clinical diagnosis and treatment, and its impact stretches beyond the clinical domain to epilepsy research and the development of novel therapies. Automated identification of seizure type may facilitate understanding of the disease, and seizure detection and prediction has been the focus of recent research that has sought to exploit the benefits of machine learning and deep learning architectures. Nevertheless, there is not yet a definitive solution for automating the classification of seizure type, a task that must currently be performed by an expert epileptologist. Inspired by recent advances in neural memory networks (NMNs), we introduce a novel approach for the classification of seizure type using electrophysiological data. We first explore the performance of traditional deep learning techniques which use convolutional and recurrent neural networks, and enhance these architectures by using external memory modules with trainable neural plasticity. We show that our model achieves a state-of-the-art weighted F1 score of 0.945 for seizure type classification on the TUH EEG Seizure Corpus with the IBM TUSZ preprocessed data. This work highlights the potential of neural memory networks to support the field of epilepsy research, along with biomedical research and signal analysis more broadly.

eess.SP↗

arXiv2019

Neural Memory Plasticity for Anomaly Detection

In the domain of machine learning, Neural Memory Networks (NMNs) have recently achieved impressive results in a variety of application areas including visual question answering, trajectory prediction, object tracking, and language modelling. However, we observe that the attention based knowledge retrieval mechanisms used in current NMNs restricts them from achieving their full potential as the attention process retrieves information based on a set of static connection weights. This is suboptimal in a setting where there are vast differences among samples in the data domain; such as anomaly detection where there is no consistent criteria for what constitutes an anomaly. In this paper, we propose a plastic neural memory access mechanism which exploits both static and dynamic connection weights in the memory read, write and output generation procedures. We demonstrate the effectiveness and flexibility of the proposed memory model in three challenging anomaly detection tasks in the medical domain: abnormal EEG identification, MRI tumour type classification and schizophrenia risk detection in children. In all settings, the proposed approach outperforms the current state-of-the-art. Furthermore, we perform an in-depth analysis demonstrating the utility of neural plasticity for the knowledge retrieval process and provide evidence on how the proposed memory model generates sparse yet informative memory outputs.

cs.NE↗

arXiv2018

Deep Classification of Epileptic Signals

Electrophysiological observation plays a major role in epilepsy evaluation. However, human interpretation of brain signals is subjective and prone to misdiagnosis. Automating this process, especially seizure detection relying on scalp-based Electroencephalography (EEG) and intracranial EEG, has been the focus of research over recent decades. Nevertheless, its numerous challenges have inhibited a definitive solution. Inspired by recent advances in deep learning, we propose a new classification approach for EEG time series based on Recurrent Neural Networks (RNNs) via the use of Long-Short Term Memory (LSTM) networks. The proposed deep network effectively learns and models discriminative temporal patterns from EEG sequential data. Especially, the features are automatically discovered from the raw EEG data without any pre-processing step, eliminating humans from laborious feature design task. We also show that, in the epilepsy scenario, simple architectures can achieve competitive performance. Using simple architectures significantly benefits in the practical scenario considering their low computation complexity and reduced requirement for large training datasets. Using a public dataset, a multi-fold cross-validation scheme exhibited an average validation accuracy of 95.54\% and an average AUC of 0.9582 of the ROC curve among all sets defined in the experiment. This work reinforces the benefits of deep learning to be further attended in clinical applications and neuroscientific research.

cs.LG↗