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This literature review explores the role of attractor neural networks (ANNs) in modeling psychological processes in artificial and biological systems. By synthesizing research from dynamical systems theory, psychology, and computational neuroscience, the review provides an overview of the current understanding of ANN function in memory formation, memory reinforcement, retrieval, and forgetting. Key mathematical foundations of ANNs, including dynamical systems theory and energy functions, are discussed to explain the behavior and stability of these networks. The review also examines empirical applications of ANNs in cognitive processes such as semantic memory and episodic recall, as well as highlighting the hippocampus' role in pattern separation and completion. The review addresses challenges like catastrophic forgetting and noise effects on memory retrieval. By identifying gaps between theoretical models and empirical findings, it highlights the interdisciplinary nature of ANN research and suggests future areas for exploration.

PURPOSE: This study uses deep neural network-generated rim-to-disc area ratio (RADAR) measurements and the disc damage likelihood scale (DDLS) to measure the rate of optic disc rim loss in a large cohort of glaucoma patients. METHODS: A deep neural network was used to calculate RADAR and DDLS for each optic disc photograph (ODP). Patient demographics, diagnosis, intraocular pressure (IOP), and mean deviation (MD) from perimetry were analyzed as risk factors for faster progression of RADAR. Receiver operating characteristic (ROC) curves were used to compare RADAR and DDLS in their utility to distinguish glaucoma from glaucoma suspect (GS) and for detecting glaucoma progression. RESULTS: A total of 13,679 ODPs with evidence of glaucomatous optic nerve damage from 4106 eyes of 2407 patients with glaucoma or GS were included. Of these eyes, 3264 (79.5%) had a diagnosis of glaucoma, and 842 (20.5%) eyes were GS. Mean ± SD baseline RADAR of GS and glaucoma were 0.67 ± 0.13 and 0.57 ± 0.18, respectively (P < 0.001). Older age, greater IOP fluctuation, baseline MD, right eye, and diagnosis of secondary open-angle glaucoma were associated with slope of RADAR. The mean baseline DDLS of GS and glaucoma were 3.78 and 4.39, respectively. Both RADAR and DDLS showed a less steep slope in advanced glaucoma. In glaucoma, the change of RADAR and DDLS correlated with the corresponding change in MD. RADAR and DDLS had a similar ability to discriminate glaucoma from GS and detect disease progression. Area under the ROC curve of RADAR and DDLS was 0.658 and 0.648. CONCLUSIONS: Automated calculation of RADAR and DDLS with a neural network can be used to evaluate the extent and long-term rate of optic disc rim loss and is further evidence of long-term nerve fiber loss in treated patients with glaucoma. TRANSLATIONAL RELEVANCE: Our study provides a large clinic-based experience for RADAR and DDLS measurements in GS and glaucoma with a neural network.

A real-time capable core Ion Cyclotron Range of Frequencies (ICRF) heating model on NSTX and WEST is developed. The model is based on two nonlinear regression algorithms, the random forest ensemble of decision trees and the multilayer perceptron neural network. The algorithms are trained on TORIC ICRF spectrum solver simulations of the expected flat-top operation scenarios in NSTX and WEST assuming Maxwellian plasmas. The surrogate models are shown to successfully capture the multi-species core ICRF power absorption predicted by the original model for the high harmonic fast wave and the ion cyclotron minority heating schemes while reducing the computational time by six orders of magnitude. Although these models can be expanded, the achieved regression scoring, computational efficiency and increased model robustness suggest these strategies can be implemented into integrated modeling frameworks for real-time control applications.

Objective. Physiological data are often low quality and thereby compromises the effectiveness of related health monitoring. The primary goal of this study is to develop a robust foundation model that can effectively handle low-quality issue in physiological data.Approach. We introduce SiamQuality, a self-supervised learning approach using convolutional neural networks (CNNs) as the backbone. SiamQuality learns to generate similar representations for both high and low quality photoplethysmography (PPG) signals that originate from similar physiological states. We leveraged a substantial dataset of PPG signals from hospitalized intensive care patients, comprised of over 36 million 30 s PPG pairs.Main results. After pre-training the SiamQuality model, it was fine-tuned and tested on six PPG downstream tasks focusing on cardiovascular monitoring. Notably, in tasks such as respiratory rate estimation and atrial fibrillation detection, the models performance exceeded the state-of-the-art by 75% and 5%, respectively. The results highlight the effectiveness of our model across all evaluated tasks, demonstrating significant improvements, especially in applications for heart monitoring on wearable devices.Significance. This study underscores the potential of CNNs as a robust backbone for foundation models tailored to physiological data, emphasizing their capability to maintain performance despite variations in data quality. The success of the SiamQuality model in handling real-world, variable-quality data opens new avenues for the development of more reliable and efficient healthcare monitoring technologies.

A neural network was developed to detect and characterize bowel obstruction, a common cause of acute abdominal pain. In this retrospective study, 202 CT scans of 165 patients with bowel obstruction from March to June 2022 were included and partitioned into training and test data sets. A multi-channel neural network was trained to segment the gastrointestinal tract, and to predict the diameter and the longitudinal position (longitude) along the gastrointestinal tract using a novel embedding. Its performance was compared to manual segmentations using the Dice score, and to manual measurements of the diameter and longitude using intraclass correlation coefficients (ICC). ROC curves as well as sensitivity and specificity were calculated for diameters above a clinical threshold for obstruction, and for longitudes corresponding to small bowel. In the test data set, Dice score for segmentation of the gastrointestinal tract was 78 ± 8%. ICC between measured and predicted diameters was 0.72, indicating moderate agreement. ICC between measured and predicted longitude was 0.85, indicating good agreement. AUROC was 0.90 for detection of dilated bowel, and was 0.95 and 0.90 for differentiation of the proximal and distal gastrointestinal tract respectively. Overall sensitivity and specificity for dilated small bowel were 0.83 and 0.90. Since obstruction is diagnosed based on the diameter and longitude of the bowel, this neural network and embedding may enable detection and characterization of this important disease on CT.

Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .

Message passing neural networks (MPNNs) on molecular graphs generate continuous and differentiable encodings of small molecules with state-of-the-art performance on protein-ligand complex scoring tasks. Here, we describe the proximity graph network (PGN) package, an open-source toolkit that constructs ligand-receptor graphs based on atom proximity and allows users to rapidly apply and evaluate MPNN architectures for a broad range of tasks. We demonstrate the utility of PGN by introducing benchmarks for affinity and docking score prediction tasks. Graph networks generalize better than fingerprint-based models and perform strongly for the docking score prediction task. Overall, MPNNs with proximity graph data structures augment the prediction of ligand-receptor complex properties when ligand-receptor data are available.

OBJECTIVE: Increased subcutaneous and visceral adipose tissue (SAT/VAT) volume is associated with risk for cardiometabolic diseases. This work aimed to develop and evaluate automated abdominal SAT/VAT segmentation on longitudinal MRI in adults with overweight/obesity using attention-based competitive dense (ACD) 3D U-Net and 3D nnU-Net with full field-of-view volumetric multi-contrast inputs. MATERIALS AND METHODS: 920 adults with overweight/obesity were scanned twice at multiple 3 T MRI scanners and institutions. The first scan was divided into training/validation/testing sets (n = 646/92/182). The second scan from the subjects in the testing set was used to evaluate the generalizability for longitudinal analysis. Segmentation performance was assessed by measuring Dice scores (DICE-SAT, DICE-VAT), false negatives (FN), and false positives (FP). Volume agreement was assessed using the intraclass correlation coefficient (ICC). RESULTS: ACD 3D U-Net achieved rapid ( 0.997) in longitudinal analysis. DISCUSSION: ACD 3D U-Net and 3D nnU-Net can be automated tools to quantify abdominal SAT/VAT volume rapidly, accurately, and longitudinally in adults with overweight/obesity.

Deep learning-based mammographic evaluations could noninvasively assess response to breast cancer chemoprevention. We evaluated change in a convolutional neural network-based breast cancer risk model applied to mammograms among women enrolled in SWOG S0812, which randomly assigned 208 premenopausal high-risk women to receive oral vitamin D3 20 000 IU weekly or placebo for 12 months. We applied the convolutional neural network model to mammograms collected at baseline (n = 109), 12 months (n = 97), and 24 months (n = 67) and compared changes in convolutional neural network-based risk score between treatment groups. Change in convolutional neural network-based risk score was not statistically significantly different between vitamin D and placebo groups at 12 months (0.005 vs 0.002, P = .875) or at 24 months (0.020 vs 0.001, P = .563). The findings are consistent with the primary analysis of S0812, which did not demonstrate statistically significant changes in mammographic density with vitamin D supplementation compared with placebo. There is an ongoing need to evaluate biomarkers of response to novel breast cancer chemopreventive agents.

Adaptation is a universal aspect of neural systems that changes circuit computations to match prevailing inputs. These changes facilitate efficient encoding of sensory inputs while avoiding saturation. Conventional artificial neural networks (ANNs) have limited adaptive capabilities, hindering their ability to reliably predict neural output under dynamic input conditions. Can embedding neural adaptive mechanisms in ANNs improve their performance? To answer this question, we develop a new deep learning model of the retina that incorporates the biophysics of photoreceptor adaptation at the front-end of conventional convolutional neural networks (CNNs). These conventional CNNs build on 'Deep Retina,' a previously developed model of retinal ganglion cell (RGC) activity. CNNs that include this new photoreceptor layer outperform conventional CNN models at predicting male and female primate and rat RGC responses to naturalistic stimuli that include dynamic local intensity changes and large changes in the ambient illumination. These improved predictions result directly from adaptation within the phototransduction cascade. This research underscores the potential of embedding models of neural adaptation in ANNs and using them to determine how neural circuits manage the complexities of encoding natural inputs that are dynamic and span a large range of light levels.

PurposeHigh quality scan prescription that optimally covers the area of interest with scan planes aligned to relevant anatomical structures is crucial for error-free radiologic interpretation. The goal of this project was to develop a machine learning pipeline for oblique scan prescription that could be trained on localizer images and metadata from previously acquired MR exams.MethodsA novel Multislice Rotational Region-based Convolutional Neural Network (MS-R2CNN) architecture was developed. Based on this architecture, models for automated prescription sagittal lumbar spine acquisitions from axial, sagittal, and coronal localizer slices were trained. The automated prescription pipeline was integrated with the scanner console software and evaluated in experiments with healthy volunteers (N = 3) and patients with lower-back pain (N = 20).ResultsExperiments in healthy volunteers demonstrated high accuracy of automated prescription in all subjects. There was good agreement between alignment and coverage of manual and automated prescriptions, as well as consistent views of the lumbar spine at different positions of the subjects within the scanner bore. In patients with lower-back pain, the generated prescription was applied in 18 cases (90% of the total number). None of the cases required major adjustment, while in 11 cases (55%) there were minor manual adjustments to the generated prescription.ConclusionsThis study demonstrates the ability of oriented object detection-based models to be trained to prescribe oblique lumbar spine MRI acquisitions without the need of manual annotation or feature engineering and the feasibility of using machine learning-based pipelines on the scanner for automated prescription of MRI acquisitions.

BACKGROUND: Language in nonmedical data sets is known to transmit human-like biases when used in natural language processing (NLP) algorithms that can reinforce disparities. It is unclear if NLP algorithms of medical notes could lead to similar transmissions of biases. RESEARCH QUESTION: Can we identify implicit bias in clinical notes, and are biases stable across time and geography? STUDY DESIGN AND METHODS: To determine whether different racial and ethnic descriptors are similar contextually to stigmatizing language in ICU notes and whether these relationships are stable across time and geography, we identified notes on critically ill adults admitted to the University of California, San Francisco (UCSF), from 2012 through 2022 and to Beth Israel Deaconess Hospital (BIDMC) from 2001 through 2012. Because word meaning is derived largely from context, we trained unsupervised word-embedding algorithms to measure the similarity (cosine similarity) quantitatively of the context between a racial or ethnic descriptor (eg, African-American) and a stigmatizing target word (eg, nonco-operative) or group of words (violence, passivity, noncompliance, nonadherence). RESULTS: In UCSF notes, Black descriptors were less likely to be similar contextually to violent words compared with White descriptors. Contrastingly, in BIDMC notes, Black descriptors were more likely to be similar contextually to violent words compared with White descriptors. The UCSF data set also showed that Black descriptors were more similar contextually to passivity and noncompliance words compared with Latinx descriptors. INTERPRETATION: Implicit bias is identifiable in ICU notes. Racial and ethnic group descriptors carry different contextual relationships to stigmatizing words, depending on when and where notes were written. Because NLP models seem able to transmit implicit bias from training data, use of NLP algorithms in clinical prediction could reinforce disparities. Active debiasing strategies may be necessary to achieve algorithmic fairness when using language models in clinical research.

To maximize the greenhouse gas (GHG) emission reduction potential of Battery Electric Vehicles (BEVs), it is critical to develop EV dynamic charging management strategies. These strategies leverage the temporal variability in emissions associated with generated electricity to align EV charging with periods of low-carbon power generation. This study introduces a deep neural network tool to enable BEV drivers to make charging sessions align with the availability of cleaner energy resources. This study leverages a Long Short-Term Memory network to forecast individual BEV vehicle miles traveled (VMT) up to two days ahead, using a year-long dataset of driving and charging patterns from 66 California-based BEVs. Based on the predicted VMT, the model then estimates the vehicle's energy needs and the necessity of a charging session. This allows drivers to charge theirvehicles strategically, prioritizing low-carbon electricity periods without risking incomplete journeys. This framework empowers drivers to actively contribute to cleaner electricity consumption with minimal disruption to their daily routines. The tool developed in this project outperforms benchmark models such as recurrent neural networks and autoregressive integrated moving averages, demonstrating its predictive capabilities. To enhance the reliability of predictions, confidence intervals are integrated into the model, ensuring that the model does not disrupt drivers' daily routine trips when skipping non-critical charging events. The potential benefits of the tool are demonstrated by applying it to real-world EV data, finding that if drivers follow the tool’s predictive suggestion, they can reduce overall GHG emissions by 41% without changing their driving patterns. This study also found that even charging in regions with higher carbon-intensity electricity than California can achieve Californian emission levels for EV charging in the short term through strategic management of non-critical charging events. This findingreveals new possibilities for further emissions reduction from EV charging, even before the full transition to a carbon-neutral grid. View the NCST Project Webpage

Artificial Intelligence (AI) has emerged as a complementary technology in supply chain research. However, the majority of AI approaches explored in this context afford little to no explainability, which is a significant barrier to a broader adoption of AI in supply chains. In recent years, the need for explainability has been a strong impetus for research in hybrid AI methodologies that combine neural architectures with logic-based reasoning, which are collectively referred to as Neurosymbolic AI. The aim of this paper is to provide a comprehensive overview of supply chain management literature that employs approaches within the neurosymbolic AI spectrum. To that end, a systematic review is conducted, followed by bibliometric, descriptive and thematic analyses on the identified studies. Our findings indicate that researchers have primarily focused on the limited subset of neurofuzzy approaches, while some supply chain applications, such as performance evaluation and sustainability, and sectors such as pharmaceutical and construction have received less attention. To help address these gaps, we propose five pillars of neurosymbolic AI research for supply chains and provide four use cases of applying unexplored neurosymbolic AI approaches to address typical problems in supply chain management, including a discussion of prerequisites for adopting such technologies. We envision that the findings and contributions of this survey will help encourage further research in neurosymbolic AI for supply chains and increase adoption of such technologies within supply chain practice. [ABSTRACT FROM AUTHOR]

Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for elucidating the molecular makeup of materials. It possesses the unique characteristics of single-molecule sensitivity and extremely high specificity. However, the true potential of SERS, particularly in capturing the biochemical content of particles, remains underexplored. In this study, we harnessed transformer neural networks to interpret SERS spectra, aiming to discern the amino acid profiles within proteins. By training the network on the SERS profiles of 20 amino acids of human proteins, we explore the feasibility of predicting the predominant proteins within the µL-scale detection volume of SERS. Our results highlight a consistent alignment between the models predictions and the proteins known amino acid compositions, deepening our understanding of the inherent information contained within SERS spectra. For instance, the model achieved low root mean square error (RMSE) scores and minimal deviation in the prediction of amino acid compositions for proteins such as Bovine Serum Albumin (BSA), ACE2 protein, and CD63 antigen. This novel methodology offers a robust avenue not only for protein analytics but also sets a precedent for the broader realm of spectral analyses across diverse material categories. It represents a solid step forward to establishing SERS-based proteomics.

An important difference between brains and deep neural networks is the way they learn. Nervous systems learn online where a stream of noisy data points are presented in a non-independent, identically distributed way. Further, synaptic plasticity in the brain depends only on information local to synapses. Deep networks, on the other hand, typically use non-local learning algorithms and are trained in an offline, non-noisy, independent, identically distributed setting. Understanding how neural networks learn under the same constraints as the brain is an open problem for neuroscience and neuromorphic computing. A standard approach to this problem has yet to be established. In this paper, we propose that discrete graphical models that learn via an online maximum a posteriori learning algorithm could provide such an approach. We implement this kind of model in a neural network called the Sparse Quantized Hopfield Network. We show our model outperforms state-of-the-art neural networks on associative memory tasks, outperforms these networks in online, continual settings, learns efficiently with noisy inputs, and is better than baselines on an episodic memory task.

BackgroundWhole brain delineation (WBD) is utilized in neuroimaging analysis for data preprocessing and deriving whole brain image metrics. Current automated WBD techniques for analysis of preclinical brain MRI data show limited accuracy when images present with significant neuropathology and anatomical deformations, such as that resulting from organophosphate intoxication (OPI) and Alzheimer's Disease (AD), and inadequate generalizability.MethodsA modified 2D U-Net framework was employed for WBD of MRI rodent brains, consisting of 27 convolutional layers, batch normalization, two dropout layers and data augmentation, after training parameter optimization. A total of 265 T2-weighted 7.0 T MRI scans were utilized for the study, including 125 scans of an OPI rat model for neural network training. For testing and validation, 20 OPI rat scans and 120 scans of an AD rat model were utilized. U-Net performance was evaluated using Dice coefficients (DC) and Hausdorff distances (HD) between the U-Net-generated and manually segmented WBDs.ResultsThe U-Net achieved a DC (median[range]) of 0.984[0.936-0.990] and HD of 1.69[1.01-6.78] mm for OPI rat model scans, and a DC (mean[range]) of 0.975[0.898-0.991] and HD of 1.49[0.86-3.89] for the AD rat model scans.Comparison with existing methodsThe proposed approach is fully automated and robust across two rat strains and longitudinal brain changes with a computational speed of 8 seconds/scan, overcoming limitations of manual segmentation.ConclusionsThe modified 2D U-Net provided a fully automated, efficient, and generalizable segmentation approach that achieved high accuracy across two disparate rat models of neurological diseases.

PurposeThis study aimed to compare a new Artificial Intelligence (AI) method to conventional mathematical warping in accurately overlaying peripheral retinal vessels from two different imaging devices: confocal scanning laser ophthalmoscope (cSLO) wide-field images and SLO ultra-wide field images.MethodsImages were captured using the Heidelberg Spectralis 55-degree field-of-view and Optos ultra-wide field. The conventional mathematical warping was performed using Random Sample Consensus-Sample and Consensus sets (RANSAC-SC). This was compared to an AI alignment algorithm based on a one-way forward registration procedure consisting of full Convolutional Neural Networks (CNNs) with Outlier Rejection (OR CNN), as well as an iterative 3D camera pose optimization process (OR CNN + Distortion Correction [DC]). Images were provided in a checkerboard pattern, and peripheral vessels were graded in four quadrants based on alignment to the adjacent box.ResultsA total of 660 boxes were analysed from 55 eyes. Dice scores were compared between the three methods (RANSAC-SC/OR CNN/OR CNN + DC): 0.3341/0.4665/4784 for fold 1-2 and 0.3315/0.4494/4596 for fold 2-1 in composite images. The images composed using the OR CNN + DC have a median rating of 4 (out of 5) versus 2 using RANSAC-SC. The odds of getting a higher grading level are 4.8 times higher using our OR CNN + DC than RANSAC-SC (p

Objective.Artificial neural networks (ANNs) are state-of-the-art tools for modeling and decoding neural activity, but deploying them in closed-loop experiments with tight timing constraints is challenging due to their limited support in existing real-time frameworks. Researchers need a platform that fully supports high-level languages for running ANNs (e.g. Python and Julia) while maintaining support for languages that are critical for low-latency data acquisition and processing (e.g. C and C++).Approach.To address these needs, we introduce the Backend for Realtime Asynchronous Neural Decoding (BRAND). BRAND comprises Linux processes, termednodes, which communicate with each other in agraphvia streams of data. Its asynchronous design allows for acquisition, control, and analysis to be executed in parallel on streams of data that may operate at different timescales. BRAND uses Redis, an in-memory database, to send data between nodes, which enables fast inter-process communication and supports 54 different programming languages. Thus, developers can easily deploy existing ANN models in BRAND with minimal implementation changes.Main results.In our tests, BRAND achieved

This study introduces a neural network-based approach to predict dust emissions, specifically PM2.5 particles, during almond harvesting in California. Using a feedforward neural network (FNN), this research predicted PM2.5 emissions by analyzing key operational parameters of an advanced almond harvester. Preprocessing steps like outlier removal and normalization were employed to refine the dataset for training. The networks architecture was designed with two hidden layers and optimized using tanh activation and MSE loss functions through the Adam algorithm, striking a balance between model complexity and predictive accuracy. The model was trained on extensive field data from an almond pickup system, including variables like brush speed, angular velocity, and harvester forward speed. The results demonstrate a notable predictive accuracy of the FNN model, with a mean squared error (MSE) of 0.02 and a mean absolute error (MAE) of 0.01, indicating high precision in forecasting PM2.5 levels. By integrating machine learning with agricultural practices, this research provides a significant tool for environmental management in almond production, offering a method to reduce harmful emissions while maintaining operational efficiency. This model presents a solution for the almond industry and sets a precedent for applying predictive analytics in sustainable agriculture.

Traditional histochemical staining of post-mortem samples often confronts inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, and such chemical staining procedures covering large tissue areas demand substantial labor, cost and time. Here, we demonstrate virtual staining of autopsy tissue using a trained neural network to rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images, matching hematoxylin and eosin (H&E) stained versions of the same samples. The trained model can effectively accentuate nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining fails to provide consistent staining quality. This virtual autopsy staining technique provides a rapid and resource-efficient solution to generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining.