•Novel devices are posing challenges to existing spike sorting pipelines.•Spike sorting methodology is expanding to handle thousands to millions of neurons.•Multi-stage procedures enhance robustness ...and reliability in sorting.•Evaluation without ground truth remains an issue but is receiving increased attention.
Engineering efforts are currently attempting to build devices capable of collecting neural activity from one million neurons in the brain. Part of this effort focuses on developing dense multiple-electrode arrays, which require post-processing via ‘spike sorting’ to extract neural spike trains from the raw signal. Gathering information at this scale will facilitate fascinating science, but these dreams are only realizable if the spike sorting procedure and data pipeline are computationally scalable, at or superior to hand processing, and scientifically reproducible. These challenges are all being amplified as the data scale continues to increase. In this review, recent efforts to attack these challenges are discussed, which have primarily focused on increasing accuracy and reliability while being computationally scalable. These goals are addressed by adding additional stages to the data processing pipeline and using divide-and-conquer algorithmic approaches. These recent developments should prove useful to most research groups regardless of data scale, not just for cutting-edge devices.
A non-parametric Bayesian factor model is proposed for joint analysis of multi-platform genomics data. The approach is based on factorizing the latent space (feature space) into a shared component ...and a data-specific component with the dimensionality of these components (spaces) inferred via a beta-Bernoulli process. The proposed approach is demonstrated by jointly analyzing gene expression/copy number variations and gene expression/methylation data for ovarian cancer patients, showing that the proposed model can potentially uncover key drivers related to cancer.
Availability and implementation: The source code for this model is written in MATLAB and has been made publicly available at https://sites.google.com/site/jointgenomics/
Contact:
catherine.ll.zheng@gmail.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
Background
The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) comprises 6 categories used for the diagnosis of thyroid fine‐needle aspiration biopsy (FNAB). Each category has an ...associated risk of malignancy, which is important in the management of a thyroid nodule. More accurate predictions of malignancy may help to reduce unnecessary surgery. A machine learning algorithm (MLA) was developed to evaluate thyroid FNAB via whole slide images (WSIs) to predict malignancy.
Methods
Files were searched for all thyroidectomy specimens with preceding FNAB over 8 years. All cytologic and surgical pathology diagnoses were recorded and correlated for each nodule. One representative slide from each case was scanned to create a WSI. An MLA was designed to identify follicular cells and predict the malignancy of the final pathology. The test set comprised cases blindly reviewed by a cytopathologist who assigned a TBSRTC category. The area under the receiver operating characteristic curve was used to assess the MLA performance.
Results
Nine hundred eight FNABs met the criteria. The MLA predicted malignancy with a sensitivity and specificity of 92.0% and 90.5%, respectively. The areas under the curve for the prediction of malignancy by the cytopathologist and the MLA were 0.931 and 0.932, respectively.
Conclusions
The performance of the MLA in predicting thyroid malignancy from FNAB WSIs is comparable to the performance of an expert cytopathologist. When the MLA and electronic medical record diagnoses are combined, the performance is superior to the performance of either alone. An MLA may be used as an adjunct to FNAB to assist in refining the indeterminate categories.
The machine learning algorithm performed at human levels in the prediction of thyroid malignancy using whole slide images of thyroid FNABs with an AUC of 0.931. When the machine predictions were combined with human decisions, the AUC increased to 0.962 and helped reduce the amount of indeterminate cases.
Background/AimsTo develop a convolutional neural network (CNN) to detect symptomatic Alzheimer’s disease (AD) using a combination of multimodal retinal images and patient data.MethodsColour maps of ...ganglion cell-inner plexiform layer (GC-IPL) thickness, superficial capillary plexus (SCP) optical coherence tomography angiography (OCTA) images, and ultra-widefield (UWF) colour and fundus autofluorescence (FAF) scanning laser ophthalmoscopy images were captured in individuals with AD or healthy cognition. A CNN to predict AD diagnosis was developed using multimodal retinal images, OCT and OCTA quantitative data, and patient data.Results284 eyes of 159 subjects (222 eyes from 123 cognitively healthy subjects and 62 eyes from 36 subjects with AD) were used to develop the model. Area under the receiving operating characteristic curve (AUC) values for predicted probability of AD for the independent test set varied by input used: UWF colour AUC 0.450 (95% CI 0.282, 0.592), OCTA SCP 0.582 (95% CI 0.440, 0.724), UWF FAF 0.618 (95% CI 0.462, 0.773), GC-IPL maps 0.809 (95% CI 0.700, 0.919). A model incorporating all images, quantitative data and patient data (AUC 0.836 (CI 0.729, 0.943)) performed similarly to models only incorporating all images (AUC 0.829 (95% CI 0.719, 0.939)). GC-IPL maps, quantitative data and patient data AUC 0.841 (95% CI 0.739, 0.943).ConclusionOur CNN used multimodal retinal images to successfully predict diagnosis of symptomatic AD in an independent test set. GC-IPL maps were the most useful single inputs for prediction. Models including only images performed similarly to models also including quantitative data and patient data.
There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and ...limitations of traditional pathogen-based testing for suspected upper respiratory viral infection. We inoculated human volunteers with either influenza A (A/Brisbane/59/2007 (H1N1) or A/Wisconsin/67/2005 (H3N2)), and assayed the peripheral blood transcriptome every 8 hours for 7 days. Of 41 inoculated volunteers, 18 (44%) developed symptomatic infection. Using unbiased sparse latent factor regression analysis, we generated a gene signature (or factor) for symptomatic influenza capable of detecting 94% of infected cases. This gene signature is detectable as early as 29 hours post-exposure and achieves maximal accuracy on average 43 hours (p = 0.003, H1N1) and 38 hours (p-value = 0.005, H3N2) before peak clinical symptoms. In order to test the relevance of these findings in naturally acquired disease, a composite influenza A signature built from these challenge studies was applied to Emergency Department patients where it discriminates between swine-origin influenza A/H1N1 (2009) infected and non-infected individuals with 92% accuracy. The host genomic response to Influenza infection is robust and may provide the means for detection before typical clinical symptoms are apparent.
Abstract
Glaucoma is the leading cause of irreversible blindness in the world, affecting over 70 million people. The cumbersome Standard Automated Perimetry (SAP) test is most frequently used to ...detect visual loss due to glaucoma. Due to the SAP test’s innate difficulty and its high test-retest variability, we propose the RetiNerveNet, a deep convolutional recursive neural network for obtaining estimates of the SAP visual field. RetiNerveNet uses information from the more objective Spectral-Domain Optical Coherence Tomography (SDOCT). RetiNerveNet attempts to trace-back the arcuate convergence of the retinal nerve fibers, starting from the Retinal Nerve Fiber Layer (RNFL) thickness around the optic disc, to estimate individual age-corrected 24-2 SAP values. Recursive passes through the proposed network sequentially yield estimates of the visual locations progressively farther from the optic disc. While all the methods used for our experiments exhibit lower performance for the advanced disease group (possibly due to the “floor effect” for the SDOCT test), the proposed network is observed to be more accurate than all the baselines for estimating the individual visual field values. We further augment the proposed network to additionally predict the SAP Mean Deviation values and also facilitate the assignment of higher weightage to the underrepresented groups in the data. We then study the resulting performance trade-offs of the RetiNerveNet on the early, moderate and severe disease groups.
•Machine-learning-based thyroid-malignancy prediction from cytopathology whole slides.•Beyond multiple instance learning: incorporating multiple global and local labels.•Weakly supervised method ...derived from a lower bound of a maximum likelihood estimator.•Ordinal regression framework for multi-label predictions augments human decisions.
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We consider machine-learning-based thyroid-malignancy prediction from cytopathology whole-slide images (WSI). Multiple instance learning (MIL) approaches, typically used for the analysis of WSIs, divide the image (bag) into patches (instances), which are used to predict a single bag-level label. These approaches perform poorly in cytopathology slides due to a unique bag structure: sparsely located informative instances with varying characteristics of abnormality. We address these challenges by considering multiple types of labels: bag-level malignancy and ordered diagnostic scores, as well as instance-level informativeness and abnormality labels. We study their contribution beyond the MIL setting by proposing a maximum likelihood estimation (MLE) framework, from which we derive a two-stage deep-learning-based algorithm. The algorithm identifies informative instances and assigns them local malignancy scores that are incorporated into a global malignancy prediction. We derive a lower bound of the MLE, leading to an improved training strategy based on weak supervision, that we motivate through statistical analysis. The lower bound further allows us to extend the proposed algorithm to simultaneously predict multiple bag and instance-level labels from a single output of a neural network. Experimental results demonstrate that the proposed algorithm provides competitive performance compared to several competing methods, achieves (expert) human-level performance, and allows augmentation of human decisions.
On Artificial Intelligence and Deep Learning Within Medical Education Carin, Lawrence
Academic medicine,
2020-November, 2020-11-00, Volume:
95, Issue:
11S Association of American Medical Colleges Learn Serve Lead: Proceedings of the 59th Annual Research in Medical Education Presentations
Journal Article
Peer reviewed
Open access
The methodology of deep learning, a component of machine learning and artificial intelligence, is introduced. The opportunity for this technology to automate some aspects of medical practice is ...reviewed. Finally, a discussion is provided on the integration of concepts from deep learning into medical education.
A method is presented for subpixel modeling, mapping, and classification in hyperspectral imagery using learned block-structured discriminative dictionaries, where each block is adapted and optimized ...to represent a material in a compact and sparse manner. The spectral pixels are modeled by linear combinations of subspaces defined by the learned dictionary atoms, allowing for linear mixture analysis. This model provides flexibility in source representation and selection, thus accounting for spectral variability, small-magnitude errors, and noise. A spatial-spectral coherence regularizer in the optimization allows pixel classification to be influenced by similar neighbors. We extend the proposed approach for cases for which there is no knowledge of the materials in the scene, unsupervised classification, and provide experiments and comparisons with simulated and real data. We also present results when the data have been significantly undersampled and then reconstructed, still retaining high-performance classification, showing the potential role of compressive sensing and sparse modeling techniques in efficient acquisition/transmission missions for hyperspectral imagery.
Brain-wide fluctuations in local field potential oscillations reflect emergent network-level signals that mediate behavior. Cracking the code whereby these oscillations coordinate in time and space ...(spatiotemporal dynamics) to represent complex behaviors would provide fundamental insights into how the brain signals emotional pathology. Using machine learning, we discover a spatiotemporal dynamic network that predicts the emergence of major depressive disorder (MDD)-related behavioral dysfunction in mice subjected to chronic social defeat stress. Activity patterns in this network originate in prefrontal cortex and ventral striatum, relay through amygdala and ventral tegmental area, and converge in ventral hippocampus. This network is increased by acute threat, and it is also enhanced in three independent models of MDD vulnerability. Finally, we demonstrate that this vulnerability network is biologically distinct from the networks that encode dysfunction after stress. Thus, these findings reveal a convergent mechanism through which MDD vulnerability is mediated in the brain.
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•Brain-wide electrical spatiotemporal dynamic map of stress states•Hippocampally directed network signals stress vulnerability in stress-naive animals•Early life stress increases activity in stress vulnerability network•Stress vulnerability network is mechanistically distinct from pathology networks
Patterns of brain activity predict vulnerability versus resilience to depression in response to stress.
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