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1.
BMC Bioinformatics ; 25(1): 185, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38730317

ABSTRACT

Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.


Subject(s)
Genotype , Machine Learning , DNA, Bacterial/genetics , Algorithms , Nucleic Acid Denaturation/genetics
2.
Front Aging Neurosci ; 16: 1285905, 2024.
Article in English | MEDLINE | ID: mdl-38685909

ABSTRACT

Introduction: Novelty detection (ND, also known as one-class classification) is a machine learning technique used to identify patterns that are typical of the majority class and can discriminate deviations as novelties. In the context of Alzheimer's disease (AD), ND could be employed to detect abnormal or atypical behavior that may indicate early signs of cognitive decline or the presence of the disease. To date, few research studies have used ND to discriminate the risk of developing AD and mild cognitive impairment (MCI) from healthy controls (HC). Methods: In this work, two distinct cohorts with highly heterogeneous data, derived from the Australian Imaging Biomarkers and Lifestyle (AIBL) Flagship Study of Ageing project and the Fujian Medical University Union Hospital (FMUUH) China, were employed. An innovative framework with built-in easily interpretable ND models constructed solely on HC data was introduced along with proposing a strategy of distance to boundary (DtB) to detect MCI and AD. Subsequently, a web-based graphical user interface (GUI) that incorporates the proposed framework was developed for non-technical stakeholders. Results: Our experimental results indicate that the best overall performance of detecting AD individuals in AIBL and FMUUH datasets was obtained by using the Mixture of Gaussian-based ND algorithm applied to single modality, with an AUC of 0.8757 and 0.9443, a sensitivity of 96.79% and 89.09%, and a specificity of 89.63% and 90.92%, respectively. Discussion: The GUI offers an interactive platform to aid stakeholders in making diagnoses of MCI and AD, enabling streamlined decision-making processes. More importantly, the proposed DtB strategy could visually and quantitatively identify individuals at risk of developing AD.

3.
Int. j. clin. health psychol. (Internet) ; 23(4)oct.-dic. 2023. ilus, tab, graf
Article in English | IBECS | ID: ibc-226378

ABSTRACT

Background/objective: Despite its obvious motivational impairment, anhedonia as a transdiagnostic psychopathological construct is accompanied by deficits in attention function. Previous studies have identified voluntary attention anomalies in anhedonia, but its involuntary attention has received less study. Method: Using a visual novelty oddball task, the current event-related potential study assessed electrophysical correlates underlying mismatch detection in anhedonia with a non-clinical sample. Well-matched healthy control (N = 28; CNT), social anhedonia (N = 27; SA), and physical anhedonia (N = 26; PA) groups were presented standard, target, and perceptually novel stimuli while their EEG was recording. Results: The PA group relative to the CNT group exhibited a reduced N2 to novel stimuli but not to target stimuli. In contrast, the SA group as compared to the other two groups showed comparable N2 responses to both target and novel stimuli. Control analyses indicated that these patterns were unaffected by depression symptoms. Conclusions: These findings suggest that anhedonia is a heterogenous construct associated with impairments in early detection of visual novelty in physical but not social anhedonia, highlighting that dysfunction in involuntary attention may play a mediating role in the development, maintenance, and consequences of anhedonia-related psychopathology. (AU)


Subject(s)
Humans , Anhedonia , Attention Deficit and Disruptive Behavior Disorders , Evoked Potentials , Attention , Electroencephalography
4.
Front Psychol ; 14: 1232262, 2023.
Article in English | MEDLINE | ID: mdl-38023001

ABSTRACT

Introduction: The perception of phonemes is guided by both low-level acoustic cues and high-level linguistic context. However, differentiating between these two types of processing can be challenging. In this study, we explore the utility of pupillometry as a tool to investigate both low- and high-level processing of phonological stimuli, with a particular focus on its ability to capture novelty detection and cognitive processing during speech perception. Methods: Pupillometric traces were recorded from a sample of 22 Danish-speaking adults, with self-reported normal hearing, while performing two phonological-contrast perception tasks: a nonword discrimination task, which included minimal-pair combinations specific to the Danish language, and a nonword detection task involving the detection of phonologically modified words within sentences. The study explored the perception of contrasts in both unprocessed speech and degraded speech input, processed with a vocoder. Results: No difference in peak pupil dilation was observed when the contrast occurred between two isolated nonwords in the nonword discrimination task. For unprocessed speech, higher peak pupil dilations were measured when phonologically modified words were detected within a sentence compared to sentences without the nonwords. For vocoded speech, higher peak pupil dilation was observed for sentence stimuli, but not for the isolated nonwords, although performance decreased similarly for both tasks. Conclusion: Our findings demonstrate the complexity of pupil dynamics in the presence of acoustic and phonological manipulation. Pupil responses seemed to reflect higher-level cognitive and lexical processing related to phonological perception rather than low-level perception of acoustic cues. However, the incorporation of multiple talkers in the stimuli, coupled with the relatively low task complexity, may have affected the pupil dilation.

5.
Int J Clin Health Psychol ; 23(4): 100407, 2023.
Article in English | MEDLINE | ID: mdl-37705683

ABSTRACT

Background/objective: Despite its obvious motivational impairment, anhedonia as a transdiagnostic psychopathological construct is accompanied by deficits in attention function. Previous studies have identified voluntary attention anomalies in anhedonia, but its involuntary attention has received less study. Method: Using a visual novelty oddball task, the current event-related potential study assessed electrophysical correlates underlying mismatch detection in anhedonia with a non-clinical sample. Well-matched healthy control (N = 28; CNT), social anhedonia (N = 27; SA), and physical anhedonia (N = 26; PA) groups were presented standard, target, and perceptually novel stimuli while their EEG was recording. Results: The PA group relative to the CNT group exhibited a reduced N2 to novel stimuli but not to target stimuli. In contrast, the SA group as compared to the other two groups showed comparable N2 responses to both target and novel stimuli. Control analyses indicated that these patterns were unaffected by depression symptoms. Conclusions: These findings suggest that anhedonia is a heterogenous construct associated with impairments in early detection of visual novelty in physical but not social anhedonia, highlighting that dysfunction in involuntary attention may play a mediating role in the development, maintenance, and consequences of anhedonia-related psychopathology.

6.
J Neurosci ; 43(44): 7307-7321, 2023 11 01.
Article in English | MEDLINE | ID: mdl-37714707

ABSTRACT

In mouse primary visual cortex (V1), familiar stimuli evoke significantly altered responses when compared with novel stimuli. This stimulus-selective response plasticity (SRP) was described originally as an increase in the magnitude of visual evoked potentials (VEPs) elicited in layer 4 (L4) by familiar phase-reversing grating stimuli. SRP is dependent on NMDA receptors (NMDARs) and has been hypothesized to reflect potentiation of thalamocortical (TC) synapses in L4. However, recent evidence indicates that the synaptic modifications that manifest as SRP do not occur on L4 principal cells. To shed light on where and how SRP is induced and expressed in male and female mice, the present study had three related aims: (1) to confirm that NMDAR are required specifically in glutamatergic principal neurons of V1, (2) to investigate the consequences of deleting NMDAR specifically in L6, and (3) to use translaminar electrophysiological recordings to characterize SRP expression in different layers of V1. We find that knock-out (KO) of NMDAR in L6 principal neurons disrupts SRP. Current-source density (CSD) analysis of the VEP depth profile shows augmentation of short latency current sinks in layers 3, 4, and 6 in response to phase reversals of familiar stimuli. Multiunit recordings demonstrate that increased peak firing occurs in response to phase reversals of familiar stimuli across all layers, but that activity between phase reversals is suppressed. Together, these data reveal important aspects of the underlying phenomenology of SRP and generate new hypotheses for the expression of experience-dependent plasticity in V1.SIGNIFICANCE STATEMENT Repeated exposure to stimuli that portend neither reward nor punishment leads to behavioral habituation, enabling organisms to dedicate attention to novel or otherwise significant features of the environment. The neural basis of this process, which is so often dysregulated in neurologic and psychiatric disorders, remains poorly understood. Learning and memory of stimulus familiarity can be studied in mouse visual cortex by measuring electrophysiological responses to simple phase-reversing grating stimuli. The current study advances knowledge of this process by documenting changes in visual evoked potentials (VEPs), neuronal spiking activity, and oscillations in the local field potentials (LFPs) across all layers of mouse visual cortex. In addition, we identify a key contribution of a specific population of neurons in layer 6 (L6) of visual cortex.


Subject(s)
Evoked Potentials, Visual , Visual Cortex , Humans , Mice , Male , Female , Animals , Learning/physiology , Neurons/physiology , Visual Cortex/physiology , Memory , Photic Stimulation
7.
J Imaging ; 9(7)2023 Jul 07.
Article in English | MEDLINE | ID: mdl-37504814

ABSTRACT

Reliable functionality in anomaly detection in thermal image datasets is crucial for defect detection of industrial products. Nevertheless, achieving reliable functionality is challenging, especially when datasets are image sequences captured during equipment runtime with a smooth transition from healthy to defective images. This causes contamination of healthy training data with defective samples. Anomaly detection methods based on autoencoders are susceptible to a slight violation of a clean training dataset and lead to challenging threshold determination for sample classification. This paper indicates that combining anomaly scores leads to better threshold determination that effectively separates healthy and defective data. Our research results show that our approach helps to overcome these challenges. The autoencoder models in our research are trained with healthy images optimizing two loss functions: mean squared error (MSE) and structural similarity index measure (SSIM). Anomaly score outputs are used for classification. Three anomaly scores are applied: MSE, SSIM, and kernel density estimation (KDE). The proposed method is trained and tested on the 32 × 32-sized thermal images, including one contaminated dataset. The model achieved the following average accuracies across the datasets: MSE, 95.33%; SSIM, 88.37%; and KDE, 92.81%. Using a combination of anomaly scores could assist in solving a low classification accuracy. The use of KDE improves performance when healthy training data are contaminated. The MSE+ and SSIM+ methods, as well as two parameters to control quantitative anomaly localization using SSIM, are introduced.

8.
Brain Topogr ; 36(5): 644-660, 2023 09.
Article in English | MEDLINE | ID: mdl-37382838

ABSTRACT

Radiologists routinely analyze hippocampal asymmetries in magnetic resonance (MR) images as a biomarker for neurodegenerative conditions like epilepsy and Alzheimer's Disease. However, current clinical tools rely on either subjective evaluations, basic volume measurements, or disease-specific models that fail to capture more complex differences in normal shape. In this paper, we overcome these limitations by introducing NORHA, a novel NORmal Hippocampal Asymmetry deviation index that uses machine learning novelty detection to objectively quantify it from MR scans. NORHA is based on a One-Class Support Vector Machine model learned from a set of morphological features extracted from automatically segmented hippocampi of healthy subjects. Hence, in test time, the model automatically measures how far a new unseen sample falls with respect to the feature space of normal individuals. This avoids biases produced by standard classification models, which require being trained using diseased cases and therefore learning to characterize changes produced only by the ones. We evaluated our new index in multiple clinical use cases using public and private MRI datasets comprising control individuals and subjects with different levels of dementia or epilepsy. The index reported high values for subjects with unilateral atrophies and remained low for controls or individuals with mild or severe symmetric bilateral changes. It also showed high AUC values for discriminating individuals with hippocampal sclerosis, further emphasizing its ability to characterize unilateral abnormalities. Finally, a positive correlation between NORHA and the functional cognitive test CDR-SB was observed, highlighting its promising application as a biomarker for dementia.


Subject(s)
Alzheimer Disease , Cognitive Dysfunction , Humans , Hippocampus/diagnostic imaging , Magnetic Resonance Imaging/methods , Alzheimer Disease/diagnostic imaging , Biomarkers
9.
Neuroimage ; 274: 120153, 2023 07 01.
Article in English | MEDLINE | ID: mdl-37146782

ABSTRACT

INTRODUCTION: Habituation and novelty detection are two fundamental and widely studied neurocognitive processes. Whilst neural responses to repetitive and novel sensory input have been well-documented across a range of neuroimaging modalities, it is not yet fully understood how well these different modalities are able to describe consistent neural response patterns. This is particularly true for infants and young children, as different assessment modalities might show differential sensitivity to underlying neural processes across age. Thus far, many neurodevelopmental studies are limited in either sample size, longitudinal scope or breadth of measures employed, impeding investigations of how well common developmental trends can be captured via different methods. METHOD: This study assessed habituation and novelty detection in N = 204 infants using EEG and fNIRS measured in two separate paradigms, but within the same study visit, at 1, 5 and 18 months of age in an infant cohort in rural Gambia. EEG was acquired during an auditory oddball paradigm during which infants were presented with Frequent, Infrequent and Trial Unique sounds. In the fNIRS paradigm, infants were familiarised to a sentence of infant-directed speech, novelty detection was assessed via a change in speaker. Indices for habituation and novelty detection were extracted for both EEG and NIRS RESULTS: We found evidence for weak to medium positive correlations between responses on the fNIRS and the EEG paradigms for indices of both habituation and novelty detection at most age points. Habituation indices correlated across modalities at 1 month and 5 months but not 18 months of age, and novelty responses were significantly correlated at 5 months and 18 months, but not at 1 month. Infants who showed robust habituation responses also showed robust novelty responses across both assessment modalities. DISCUSSION: This study is the first to examine concurrent correlations across two neuroimaging modalities across several longitudinal age points. Examining habituation and novelty detection, we show that despite the use of two different testing modalities, stimuli and timescale, it is possible to extract common neural metrics across a wide age range in infants. We suggest that these positive correlations might be strongest at times of greatest developmental change.


Subject(s)
Habituation, Psychophysiologic , Speech , Child , Humans , Infant , Child, Preschool , Habituation, Psychophysiologic/physiology , Spectrum Analysis , Sound , Electroencephalography/methods
10.
Neurosci Biobehav Rev ; 149: 105190, 2023 06.
Article in English | MEDLINE | ID: mdl-37085022

ABSTRACT

Rapid detection of novel stimuli that appear suddenly in the surrounding environment is crucial for an animal's survival. Stimulus-specific adaptation (SSA) may be an important mechanism underlying novelty detection. In this review, we discuss the latest advances in SSA research by addressing four main aspects: 1) the frequency dependence of SSA and the origin of SSA in the auditory cortex: 2) spatial SSA and its comparison with frequency SSA: 3) feature integration in SSA and its implications in novelty detection: 4) functional significance and the physiological mechanism of SSA. Although SSA has been extensively investigated, the cognitive insights from SSA studies are extremely limited. Future work should aim to bridge these gaps.


Subject(s)
Auditory Cortex , Evoked Potentials, Auditory , Animals , Acoustic Stimulation , Evoked Potentials, Auditory/physiology , Auditory Cortex/physiology , Adaptation, Physiological/physiology , Auditory Perception/physiology
11.
Sensors (Basel) ; 23(8)2023 Apr 20.
Article in English | MEDLINE | ID: mdl-37112482

ABSTRACT

Network intrusion detection technology is key to cybersecurity regarding the Internet of Things (IoT). The traditional intrusion detection system targeting Binary or Multi-Classification can detect known attacks, but it is difficult to resist unknown attacks (such as zero-day attacks). Unknown attacks require security experts to confirm and retrain the model, but new models do not keep up to date. This paper proposes a Lightweight Intelligent NIDS using a One-Class Bidirectional GRU Autoencoder and Ensemble Learning. It can not only accurately identify normal and abnormal data, but also identify unknown attacks as the type most similar to known attacks. First, a One-Class Classification model based on a Bidirectional GRU Autoencoder is introduced. This model is trained with normal data, and has high prediction accuracy in the case of abnormal data and unknown attack data. Second, a multi-classification recognition method based on ensemble learning is proposed. It uses Soft Voting to evaluate the results of various base classifiers, and identify unknown attacks (novelty data) as the type most similar to known attacks, so that exception classification becomes more accurate. Experiments are conducted on WSN-DS, UNSW-NB15, and KDD CUP99 datasets, and the recognition rates of the proposed models in the three datasets are raised to 97.91%, 98.92%, and 98.23% respectively. The results verify the feasibility, efficiency, and portability of the algorithm proposed in the paper.

12.
Metabolites ; 13(3)2023 Feb 27.
Article in English | MEDLINE | ID: mdl-36984792

ABSTRACT

The ability to monitor the dynamics of stem cell differentiation is a major goal for understanding biochemical evolution pathways. Automating the process of metabolic profiling using 2D NMR helps us to understand the various differentiation behaviors of stem cells, and therefore sheds light on the cellular pathways of development, and enhances our understanding of best practices for in vitro differentiation to guide cellular therapies. In this work, the dynamic evolution of adipose-tissue-derived human Mesenchymal stem cells (AT-derived hMSCs) after fourteen days of cultivation, adipocyte and osteocyte differentiation, was inspected based on 1H-1H TOCSY using machine learning. Multi-class classification in addition to the novelty detection of metabolites was established based on a control hMSC sample after four days' cultivation and we successively detected the changes of metabolites in differentiated MSCs following a set of 1H-1H TOCSY experiments. The classifiers Kernel Null Foley-Sammon Transform and Kernel Density Estimation achieved a total classification error between 0% and 3.6% and false positive and false negative rates of 0%. This approach was successfully able to automatically reveal metabolic changes that accompanied MSC cellular evolution starting from their undifferentiated status to their prolonged cultivation and differentiation into adipocytes and osteocytes using machine learning supporting the research in the field of metabolic pathways of stem cell differentiation.

13.
Sensors (Basel) ; 23(6)2023 Mar 07.
Article in English | MEDLINE | ID: mdl-36991619

ABSTRACT

Novelty detection is a statistical method that verifies new or unknown data, determines whether these data are inliers (within the norm) or outliers (outside the norm), and can be used, for example, in developing classification strategies in machine learning systems for industrial applications. To this end, two types of energy that have evolved over time are solar photovoltaic and wind power generation. Some organizations around the world have developed energy quality standards to avoid known electric disturbances; however, their detection is still a challenge. In this work, several techniques for novelty detection are implemented to detect different electric anomalies (disturbances), which are k-nearest neighbors, Gaussian mixture models, one-class support vector machines, self-organizing maps, stacked autoencoders, and isolation forests. These techniques are applied to signals from real power quality environments of renewable energy systems such as solar photovoltaic and wind power generation. The power disturbances that will be analyzed are considered in the standard IEEE-1159, such as sag, oscillatory transient, flicker, and a condition outside the standard attributed to meteorological conditions. The contribution of the work consists of the development of a methodology based on six techniques for novelty detection of power disturbances, under known and unknown conditions, over real signals in the power quality assessment. The merit of the methodology is a set of techniques that allow to obtain the best performance of each one under different conditions, which constitutes an important contribution to the renewable energy systems.

14.
Sensors (Basel) ; 23(6)2023 Mar 20.
Article in English | MEDLINE | ID: mdl-36992001

ABSTRACT

Structural damage detection using unsupervised learning methods has been a trending topic in the structural health monitoring (SHM) research community during the past decades. In the context of SHM, unsupervised learning methods rely only on data acquired from intact structures for training the statistical models. Consequently, they are often seen as more practical than their supervised counterpart in implementing an early-warning damage detection system in civil structures. In this article, we review publications on data-driven structural health monitoring from the last decade that relies on unsupervised learning methods with a focus on real-world application and practicality. Novelty detection using vibration data is by far the most common approach for unsupervised learning SHM and is, therefore, given more attention in this article. Following a brief introduction, we present the state-of-the-art studies in unsupervised-learning SHM, categorized by the types of used machine-learning methods. We then examine the benchmarks that are commonly used to validate unsupervised-learning SHM methods. We also discuss the main challenges and limitations in the existing literature that make it difficult to translate SHM methods from research to practical applications. Accordingly, we outline the current knowledge gaps and provide recommendations for future directions to assist researchers in developing more reliable SHM methods.

15.
Neural Comput Appl ; 35(2): 1157-1167, 2023.
Article in English | MEDLINE | ID: mdl-33723477

ABSTRACT

Anomaly detection is challenging, especially for large datasets in high dimensions. Here, we explore a general anomaly detection framework based on dimensionality reduction and unsupervised clustering. DRAMA is released as a general python package that implements the general framework with a wide range of built-in options. This approach identifies the primary prototypes in the data with anomalies detected by their large distances from the prototypes, either in the latent space or in the original, high-dimensional space. DRAMA is tested on a wide variety of simulated and real datasets, in up to 3000 dimensions, and is found to be robust and highly competitive with commonly used anomaly detection algorithms, especially in high dimensions. The flexibility of the DRAMA framework allows for significant optimization once some examples of anomalies are available, making it ideal for online anomaly detection, active learning, and highly unbalanced datasets. Besides, DRAMA naturally provides clustering of outliers for subsequent analysis.

16.
Clin Neurophysiol ; 145: 45-53, 2023 01.
Article in English | MEDLINE | ID: mdl-36423366

ABSTRACT

OBJECTIVE: Neurophysiological studies exploring involuntary attention have reported that electroencephalographic (EEG) measures can indicate impaired neural processing from initial stages of Parkinson's disease (PD). Since involuntary attention is regulated by right hemisphere networks and PD generally initiates its motor symptomatology unilaterally, whether involuntary attention is impaired depending on the onset side of PD remains unknown. METHODS: We compared the neurophysiological correlates of involuntary attention among a PD group with left-side onset (L-PD), a PD group with right-side onset (R-PD) symptomatology, and a healthy control group (HC). All participants performed an auditory involuntary attention task while a digital EEG was recorded. RESULTS: Our main finding was a reduction both in the P3a amplitude and evoked delta-theta phase alignment in the L-PD group compared to the HC. Further, there was a significant correlation between P3a amplitude and disease duration in the R-PD, but not in the L-PD group. Behaviorally, both clinical groups, and in particular L-PD, showed reduced orientation towards novel stimuli, and no reduction of distraction effects during the experiment. CONCLUSIONS: Our results indicate that involuntary attention is differentially impaired in patients with left side onset of symptoms. Involuntary attention impairment might be present from initial stages of left onset PD and become progressively compromised in patients with right onset PD. SIGNIFICANCE: The onset side of symptomatology should be considered for attentional impairment in PD.


Subject(s)
Cognitive Dysfunction , Parkinson Disease , Humans , Parkinson Disease/complications , Parkinson Disease/diagnosis , Electroencephalography , Attention/physiology , Neurophysiology
17.
Sensors (Basel) ; 22(21)2022 Nov 03.
Article in English | MEDLINE | ID: mdl-36366154

ABSTRACT

Sensor-based human activity recognition has been extensively studied. Systems learn from a set of training samples to classify actions into a pre-defined set of ground truth activities. However, human behaviours vary over time, and so a recognition system should ideally be able to continuously learn and adapt, while retaining the knowledge of previously learned activities, and without failing to highlight novel, and therefore potentially risky, behaviours. In this paper, we propose a method based on compression that can incrementally learn new behaviours, while retaining prior knowledge. Evaluation was conducted on three publicly available smart home datasets.


Subject(s)
Human Activities , Machine Learning , Humans
18.
Sensors (Basel) ; 22(19)2022 Oct 10.
Article in English | MEDLINE | ID: mdl-36236774

ABSTRACT

Image novelty detection is a repeating task in computer vision and describes the detection of anomalous images based on a training dataset consisting solely of normal reference data. It has been found that, in particular, neural networks are well-suited for the task. Our approach first transforms the training and test images into ensembles of patches, which enables the assessment of mean-shifts between normal data and outliers. As mean-shifts are only detectable when the outlier ensemble and inlier distribution are spatially separate from each other, a rich feature space, such as a pre-trained neural network, needs to be chosen to represent the extracted patches. For mean-shift estimation, the Hotelling T2 test is used. The size of the patches turned out to be a crucial hyperparameter that needs additional domain knowledge about the spatial size of the expected anomalies (local vs. global). This also affects model selection and the chosen feature space, as commonly used Convolutional Neural Networks or Vision Image Transformers have very different receptive field sizes. To showcase the state-of-the-art capabilities of our approach, we compare results with classical and deep learning methods on the popular dataset CIFAR-10, and demonstrate its real-world applicability in a large-scale industrial inspection scenario using the MVTec dataset. Because of the inexpensive design, our method can be implemented by a single additional 2D-convolution and pooling layer and allows particularly fast prediction times while being very data-efficient.


Subject(s)
Image Processing, Computer-Assisted , Neural Networks, Computer , Image Processing, Computer-Assisted/methods
19.
Comput Struct Biotechnol J ; 20: 5453-5465, 2022.
Article in English | MEDLINE | ID: mdl-36212538

ABSTRACT

Complex mixtures containing natural products are still an interesting source of novel drug candidates. High content screening (HCS) is a popular tool to screen for such. In particular, multiplexed HCS assays promise comprehensive bioactivity profiles, but generate also high amounts of data. Yet, only some machine learning (ML) applications for data analysis are available and these usually require a profound knowledge of the underlying cell biology. Unfortunately, there are no applications that simply predict if samples are biologically active or not (any kind of bioactivity). Within this work, we benchmark ML algorithms for binary classification, starting with classical ML models, which are the standard classifiers of the scikit-learn library or ensemble models of these classifiers (a total of 92 models tested). Followed by a partial least square regression (PLSR)-based classification (44 tested models in total) and simple artificial neural networks (ANNs) with dense layers (72 tested models in total). In addition, a novelty detection (ND) was examined, which is supposed to handle unknown patterns. For the final analysis the models, with and without upstream ND, were tested with two independent data sets. In our analysis, a stacking model, an ensamble model of class ML algorithms, performed best to predict new and unknown data. ND improved the predictions of the models and was useful to handle unknown patterns. Importantly, the classifier presented here can be easily rebuilt and be adapted to the data and demands of other groups. The hit detector (ND + stacking model) is universal and suitable for a broader application to support the search for new drug candidates.

20.
Front Robot AI ; 9: 974397, 2022.
Article in English | MEDLINE | ID: mdl-36313243

ABSTRACT

In the domain of planetary science, novelty detection is gaining attention because of the operational opportunities it offers, including annotated data products and downlink prioritization. Using a variational autoencoder (VAE), this work improves upon state-of-the-art novelty detection performance in the context of Martian exploration by > 7 % (measured by the area under the receiver operating characteristic curve (ROC AUC)). Autoencoders, especially VAEs, perform well across all classes of novelties defined for Martian exploration. VAEs are shown to have high recall in the Martian context, making them particularly useful for on-ground processing. Convolutional autoencoders (CAEs), on the other hand, demonstrate high precision making them good candidates for onboard downlink prioritization. In our implementation adversarial autoencoders (AAEs) are also shown to perform on par with state-of-the-art. Dimensionality reduction is a key feature of autoencoders for novelty detection. In this study the impact of dimensionality reduction on detection quality is explored, showing that both VAEs and AAEs achieve comparable ROC AUCs to CAEs despite observably poorer (blurred) image reconstructions; this is observed both in Martian data and in lunar analogue data.

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