Samaneh Kouchaki

University of Surrey · Centre for Vision, Speech and Signal Processing (CVSSP)

Background Agitation affects around 30% of people living with dementia (PLwD), increasing carer burden and straining care services. Agitation screening typically relies on subjective clinical scales and direct patient observation, which are resource-intensive and challenging to incorporate into routine care. Clinical applicability of data-driven me...

Sensor-based remote healthcare monitoring is a promising approach for timely detection of adverse health events such as falls or infections in people living with dementia (PLwD) in the home, and reducing preventable hospital admissions. Current anomaly detection approaches in the home setting are hindered by challenges such as noisy, multivariate d...

Sensor-based remote healthcare monitoring can be used for the timely detection of adverse health events in people living with long-term health conditions, and help reduce preventable hospitalization. Current anomaly detection approaches in a real-world setting are challenged by noisy data and unreliable event annotation. Inspired by the conceptual...

Sensor-based remote health monitoring can be used for prompt detection of adverse health in people living with dementia in the home. Current anomaly detection approaches are challenged by noisy data, unreliable event annotation and wide variability in home settings. We hypothesized that a downturn in health would present as a discernible shift in s...

Urinary Tract Infections (UTIs) are one of the most prevalent bacterial infections in older adults and a significant contributor to unplanned hospital admissions in People Living with Dementia (PLWD), with early detection being crucial due to the predicament of reporting symptoms and limited help-seeking behaviour. The most common diagnostic tool i...

The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed mode...

Specialised pre-trained language models are becoming more frequent in Natural language Processing (NLP) since they can potentially outperform models trained on generic texts. BioBERT (Sanh et al., Distilbert, a distilled version of bert: smaller, faster, cheaper and lighter. arXiv preprint arXiv: 1910.01108 , 2019) and BioClinicalBERT (Alsentzer et...

Background Sensor‐based remote health monitoring of persons living with dementia (PLwD) can be used to monitor the progression of their condition with minimal intrusion. This helps minimize preventable hospital admissions, while allowing researchers to improve their understanding of dementia. Existing approaches for detecting anomalies in activity...

Background Sensor‐based remote health monitoring of persons living with dementia (PLwD) can be used to monitor the progression of their condition with minimal intrusion. This helps minimize preventable hospital admissions, while allowing researchers to improve their understanding of dementia. Existing approaches for detecting anomalies in activity...

Dementia is a progressive condition that affects cognitive and functional abilities. There is a need for reliable and continuous health monitoring of People Living with Dementia (PLWD) to improve their quality of life and support their independent living. Healthcare services often focus on addressing and treating already established health conditio...

Background Sleep disturbances are both risk factors for and symptoms of dementia. Current methods for assessing sleep disturbances are largely based on either polysomnography (PSG) which is costly and inconvenient, or self‐ or care‐giver reports which are prone to measurement error. Low‐cost methods to monitor sleep disturbances longitudinally and...

Background Sensor‐based remote health monitoring of persons living with dementia (PLwD) can be used to gain insights into their health and monitor the progression of their condition, with minimal intrusion. This helps minimize preventable hospital admissions, while allowing researchers to improve their understanding of dementia. Existing approaches...

Background: Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, the understanding of resistance mechanisms is poor, which is hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine resistance determinants, we co...

Motivation: Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy owing to factors such as embedding size, hidden dimension, and number of layers. The natural lang...

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Kno...

Early detection of COVID-19 is an ongoing area of research that can help with triage, monitoring and general health assessment of potential patients and may reduce operational strain on hospitals that cope with the coronavirus pandemic. Different machine learning techniques have been used in the literature to detect potential cases of coronavirus u...

Sensor-based remote health monitoring is used in industrial, urban and healthcare settings to monitor ongoing operation of equipment and human health. An important aim is to intervene early if anomalous events or adverse health is detected. In the wild, these anomaly detection approaches are challenged by noise, label scarcity, high dimensionality,...

Oncology patients experience numerous co-occurring symptoms during their treatment. The identification of sentinel/core symptoms is a vital prerequisite for therapeutic interventions. In this study, using Network Analysis, we investigated the inter-relationships among 38 common symptoms over time (i.e., a total of six time points over two cycles of...

Pre-trained Language Models (LMs) have become an integral part of Natural Language Processing (NLP) in recent years, due to their superior performance in downstream applications. In spite of this resounding success, the usability of LMs is constrained by computational and time complexity, along with their increasing size; an issue that has been ref...

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy owing to factors such as embedding size, hidden dimension, and number of layers. The natural language processi...

Background: Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB...

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally this is done by culturing a clinical sample and then exposing aliquots to a panel of anti...

BACKGROUND Sensor-based remote health monitoring can be used for timely detection of health deterioration in people living with dementia with minimal impact on their day-to-day living. Anomaly detection approaches have been widely applied in various domains including remote health monitoring. However, current approaches are challenged by noisy and...

Background: Sensor-based remote health monitoring can be used for the timely detection of health deterioration in people living with dementia with minimal impact on their day-to-day living. Anomaly detection approaches have been widely applied in various domains, including remote health monitoring. However, current approaches are challenged by noi...

Background Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Method...

Phosphorylation of proteins is one of the most significant post-translational modifications (PTMs) and plays a crucial role in plant functionality due to its impact on signaling, gene expression, enzyme kinetics, protein stability and interactions. Accurate prediction of plant phosphorylation sites (p-sites) is vital as abnormal regulation of phosp...

Early detection of COVID-19 is an ongoing area of research that can help with triage, monitoring and general health assessment of potential patients and may reduce operational strain on hospitals that cope with the coronavirus pandemic. Different machine learning techniques have been used in the literature to detect coronavirus using routine clinic...

Due to the inevitable role of emotions in human learning and decision-making, different types of emotions in the form of emotional weights/neurons have also been considered in shallow neural networks. Emotional neural networks suffer from a low convergence rate as well as batch learning instability mainly because of the improper tuning of learning...

Background Behavioural changes and neuropsychiatric symptoms such as agitation are common in people with dementia. These symptoms impact the quality of life of people with dementia and can increase the stress on caregivers. This study aims to identify the likelihood of having agitation in people affected by dementia (i.e., patients and carers) usin...

Antimicrobial resistance (AMR) poses a threat to global public health. To mitigate the impacts of AMR, it is important to identify the molecular mechanisms of AMR and thereby determine optimal therapy as early as possible. Conventional machine learning-based drug-resistance analyses assume genetic variations to be homogeneous, thus not distinguishi...

Agitation is one of the neuropsychiatric symptoms with high prevalence in dementia which can negatively impact the Activities of Daily Living (ADL) and the independence of individuals. Detecting agitation episodes can assist in providing People Living with Dementia (PLWD) with early and timely interventions. Analysing agitation episodes will also h...

Agitation is one of the neuropsychiatric symptoms with high prevalence in de-mentia which can negatively impact the Activities of Daily Living (ADL) and the independence of individuals. Detecting agitation episodes can assist in providing People Living with Dementia (PLWD) with early and timely interventions. Analysing agitation episodes will also...

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally this is done by culturing a clinical sample and then exposing aliquots to a panel of anti...

COVID-19 is a major, urgent, and ongoing threat to global health. Globally more than 24 million have been infected and the disease has claimed more than a million lives as of November 2020. Predicting which patients will need respiratory support is important to guiding individual patient treatment and also to ensuring sufficient resources are avail...

Interpreting the environmental, behavioural and psychological data from in-home sensory observations and measurements can provide valuable insights into the health and well-being of individuals. Presents of neuropsychiatric and psychological symptoms in people with dementia have a significant impact on their well-being and disease prognosis. Agitat...

Missing values exist in nearly all clinical studies because data for a variable or question are not collected or not available. Inadequate handling of missing values can lead to biased results and loss of statistical power in analysis. Existing models usually do not consider privacy concerns or do not utilise the inherent correlations across multip...

Early prediction of pathogen infestation is a key factor to reduce the disease spread in plants. Macrophomina phaseolina (Tassi) Goid, as one of the main causes of charcoal rot disease, suppresses the plant productivity significantly. Charcoal rot disease is one of the most severe threats to soybean productivity. Prediction of this disease in soybe...

Early prediction of pathogen infestation is a key factor to reduce the disease spread in plants. Macrophomina phaseolina (Tassi) Goid, as one of the main causes of charcoal rot disease, suppresses the plant productivity significantly. Charcoal rot disease is one of the most severe threats to soybean productivity. Prediction of this disease in soybe...

Background The early clinical course of COVID-19 can be difficult to distinguish from other illnesses driving presentation to hospital. However, viral-specific PCR testing has limited sensitivity and results can take up to 72 h for operational reasons. We aimed to develop and validate two early-detection models for COVID-19, screening for the disea...

COVID-19 is a major, urgent, and ongoing threat to global health. Globally more than 24 million have been infected and the disease has claimed more than a million lives as of October 2020. Predicting which patients will need respiratory support is important to guiding individual patient treatment and also to ensuring sufficient resources are availa...

Background Rapid identification of COVID-19 is important for delivering care expediently and maintaining infection control. The early clinical course of SARS-CoV-2 infection can be difficult to distinguish from other undifferentiated medical presentations to hospital, however for operational reasons SARS-CoV-2 PCR testing can take up to 48 hours. A...

Resistance prediction and mutation ranking are important tasks in the analysis of Tuberculosis sequence data. Due to standard regimens for the use of first-line antibiotics, resistance co-occurrence, in which samples are resistant to multiple drugs, is common. Analysing all drugs simultaneously should therefore enable patterns reflecting resistance...

In this study, a novel sleep pose identification method has been proposed for classifying 12 different sleep postures using a two-step deep learning process. For this purpose, transfer learning as an initial stage retrains a well-known CNN network (VGG-19) to categorise the data into four main pose classes, namely: supine, left, right, and prone. A...

Advances in DNA sequencing technology are facilitating genomic analyses of unprecedented scope and scale, widening the gap between our abilities to generate and fully exploit biological sequence data. Comparable analytical challenges are encountered in other data-intensive fields involving sequential data, such as signal processing, in which dimens...

Advances in DNA sequencing technology are facilitating genomic analyses of unprecedented scope and scale, widening the gap between our abilities to generate and fully exploit biological sequence data. Comparable analytical challenges are encountered in other data-intensive fields involving sequential data, such as signal processing, in which dimens...

We introduce a new method to tag Multiword Expressions (MWEs) using a linguistically interpretable language-independent deep learning architecture. We specifically target discontinuity, an under-explored aspect that poses a significant challenge to computational treatment of MWEs. Two neural architectures are explored: Graph Convolutional Network (...

Algorithms in bioinformatics use textual representations of genetic information, sequences of the characters A, T, G and C represented computationally as strings or sub-strings. Signal and related image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for e...

Motivation: Timely identification of Mycobacterium tuberculosis (MTB) resistance to existing drugs is vital to decrease mortality and prevent the amplification of existing antibiotic resistance. Machine learning methods have been widely applied for timely predicting resistance of MTB given a specific drug and identifying resistance markers. Howeve...

Wastewater Treatment (WWT) for water reuse applications has been accepted as a strategic solution in improving water supplies across the globe; however, there are still various challenges that should be overcome. Selection of practical solutions is then required whilst considering technical, environmental, socio-cultural, and financial factors. In...

It is evident that biological signals of each subject (e.g., electrocardiogram signal) carry his/her unique signature; consequently, several attempts have been made to extract subject-dependent features from these signals with application to human verification. Despite numerous efforts to characterize electrocardiogram (ECG) signals and provide pro...

It is evident that the electroencephalogram (EEG) rhythms are slightly changed when the efficacy of mental activity declines (brain fatigue). Nonetheless, this slight change is not easily detectable by the so far suggested scalp EEG features. The goal of this paper is to propose an EEG-based biomarker, which has a congruity to the mental fatigue va...

Electroencephalography (EEG) signals arise as mixtures of various neural processes which occur in particular spatial, frequency, and temporal brain locations. In classification paradigms, algorithms are developed that can distinguish between these processes. In this work, we apply tensor factorisation to a set of EEG data from a group of epileptic...

Bioinformatics methods typically use textual representations of genetic information, represented computationally as strings or sub-strings of the characters A, T, G and C. Image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for exact matching. We introdu...

In many subspace signal decomposition methods such as principal component analysis (PCA) or its extension, singular spectrum analysis (SSA), is particularly meant for processing of single channel signals, there is need for a robust determination and validation of the number of sources. Here, we attempt to find a relation between the number of sourc...

Due to the chronic nature of diabetes, patient self-care factors play an important role in any treatment plan. In order to understand the behaviour of patients in response to medical advice on self-care, clinicians often conduct cross-sectional surveys. When analysing the survey data, statistical machine learning methods can potentially provide add...

Due to the chronic nature of diabetes, patient self-care factors play an important role in any treatment plan. In order to understand the behaviour of patients in response to medical advice on self-care, clinicians often conduct cross-sectional surveys. When analysing the survey data, statistical machine learning methods can potentially provide add...

Background: Manual sleep scoring is deemed to be tedious and time consuming. Even among automatic methods such as Time-Frequency (T-F) representations, there is still room for more improvement. New method: To optimise the efficiency of T-F domain analysis of sleep electroencephalography (EEG) a novel approach for automatically identifying the br...