Interpreting wide-band neural activity using convolutional neural networks.
Ontology highlight
ABSTRACT:
SUBMITTER: Frey M
PROVIDER: S-EPMC8328518 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:MotivationRecent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection.ResultsWe present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.
| S-EPMC10311404 | biostudies-literature
Project description:Recent advances in the field of artificial intelligence have revealed principles about neural processing, in particular about vision. Previous work demonstrated a direct correspondence between the hierarchy of the human visual areas and layers of deep convolutional neural networks (DCNN) trained on visual object recognition. We use DCNN to investigate which frequency bands correlate with feature transformations of increasing complexity along the ventral visual pathway. By capitalizing on intracranial depth recordings from 100 patients we assess the alignment between the DCNN and signals at different frequency bands. We find that gamma activity (30-70?Hz) matches the increasing complexity of visual feature representations in DCNN. These findings show that the activity of the DCNN captures the essential characteristics of biological object recognition not only in space and time, but also in the frequency domain. These results demonstrate the potential that artificial intelligence algorithms have in advancing our understanding of the brain.
| S-EPMC6123818 | biostudies-other
Project description:Keeping identity for a long term after occlusion is still an open problem in the video tracking of zebrafish-like model animals, and accurate animal trajectories are the foundation of behaviour analysis. We utilize the highly accurate object recognition capability of a convolutional neural network (CNN) to distinguish fish of the same congener, even though these animals are indistinguishable to the human eye. We used data augmentation and an iterative CNN training method to optimize the accuracy for our classification task, achieving surprisingly accurate trajectories of zebrafish of different size and age zebrafish groups over different time spans. This work will make further behaviour analysis more reliable.
| S-EPMC5314376 | biostudies-literature
Project description:Human activity recognition has become an obligatory necessity in day to day life and possible solutions can be provided with the technological advancement of sensing field. Radar based sensing with its unbeatable unique features has been a promising solution for identifying and distinguishing human activities in recent years. The ascent of loss of life among elderly people in care homes during COVID-19 is mainly due to poor monitoring services, that was not able to track their daily life activities. This has even more emphasized the need for savvy activity monitoring and tracking system. In this work, we have used a dataset that has captured six daily life activities of people from different locations during different times under realistic environments, unlike an regular controlled data collection environment. We have proposed a novel tower based convolutional neural network architecture that has employed parallel input layers with individual color channel images sent as inputs to the model. We have concatenated all the unique signature features from each channel to have better and robust feature representation to the model. We have analyzed the proposed model with different color spaces like RGB, LAB, HSV as inputs and found that our chosen input type performs better with the proposed model with significant test accuracy results. We have also compared our proposed model with other existing state of art architectures for radar based human activity recognition.
| S-EPMC8186827 | biostudies-literature
Project description:The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
| S-EPMC6010233 | biostudies-other
Project description:Chromatin immune-precipitation sequencing (ChIP-seq) experiments are commonly used to obtain genome-wide profiles of histone modifications associated with different types of functional genomic elements. However, the quality of histone ChIP-seq data is affected by many experimental parameters such as the amount of input DNA, antibody specificity, ChIP enrichment and sequencing depth. Making accurate inferences from chromatin profiling experiments that involve diverse experimental parameters is challenging.We introduce a convolutional denoising algorithm, Coda, that uses convolutional neural networks to learn a mapping from suboptimal to high-quality histone ChIP-seq data. This overcomes various sources of noise and variability, substantially enhancing and recovering signal when applied to low-quality chromatin profiling datasets across individuals, cell types and species. Our method has the potential to improve data quality at reduced costs. More broadly, this approach-using a high-dimensional discriminative model to encode a generative noise process-is generally applicable to other biological domains where it is easy to generate noisy data but difficult to analytically characterize the noise or underlying data distribution.https://github.com/kundajelab/coda .akundaje@stanford.edu.
| S-EPMC5870713 | biostudies-literature
Project description:Prostate cancer is one of the most common forms of cancer and the third leading cause of cancer death in North America. As an integrated part of computer-aided detection (CAD) tools, diffusion-weighted magnetic resonance imaging (DWI) has been intensively studied for accurate detection of prostate cancer. With deep convolutional neural networks (CNNs) significant success in computer vision tasks such as object detection and segmentation, different CNN architectures are increasingly investigated in medical imaging research community as promising solutions for designing more accurate CAD tools for cancer detection. In this work, we developed and implemented an automated CNN-based pipeline for detection of clinically significant prostate cancer (PCa) for a given axial DWI image and for each patient. DWI images of 427 patients were used as the dataset, which contained 175 patients with PCa and 252 patients without PCa. To measure the performance of the proposed pipeline, a test set of 108 (out of 427) patients were set aside and not used in the training phase. The proposed pipeline achieved area under the receiver operating characteristic curve (AUC) of 0.87 (95[Formula: see text] Confidence Interval (CI): 0.84-0.90) and 0.84 (95[Formula: see text] CI: 0.76-0.91) at slice level and patient level, respectively.
| S-EPMC6925141 | biostudies-literature
Project description:ObjectiveTo develop an automated vessel wall segmentation method using convolutional neural networks to facilitate the quantification on magnetic resonance (MR) vessel wall images of patients with intracranial atherosclerotic disease (ICAD).MethodsVessel wall images of 56 subjects were acquired with our recently developed whole-brain three-dimensional (3-D) MR vessel wall imaging (VWI) technique. An intracranial vessel analysis (IVA) framework was presented to extract, straighten, and resample the interested vessel segment into 2-D slices. A U-net-like fully convolutional networks (FCN) method was proposed for automated vessel wall segmentation by hierarchical extraction of low- and high-order convolutional features.ResultsThe network was trained and validated on 1160 slices and tested on 545 slices. The proposed segmentation method demonstrated satisfactory agreement with manual segmentations with Dice coefficient of 0.89 for the lumen and 0.77 for the vessel wall. The method was further applied to a clinical study of additional 12 symptomatic and 12 asymptomatic patients with >50% ICAD stenosis at the middle cerebral artery (MCA). Normalized wall index at the focal MCA ICAD lesions was found significantly larger in symptomatic patients compared to asymptomatic patients.ConclusionWe have presented an automated vessel wall segmentation method based on FCN as well as the IVA framework for 3-D intracranial MR VWI.SignificanceThis approach would make large-scale quantitative plaque analysis more realistic and promote the adoption of MR VWI in ICAD management.
| S-EPMC6788976 | biostudies-literature
Project description:The prediction of breeding values and phenotypes is of central importance for both livestock and crop breeding. In this study, we analyze the use of artificial neural networks (ANN) and, in particular, local convolutional neural networks (LCNN) for genomic prediction, as a region-specific filter corresponds much better with our prior genetic knowledge on the genetic architecture of traits than traditional convolutional neural networks. Model performances are evaluated on a simulated maize data panel (n = 10,000; p = 34,595) and real Arabidopsis data (n = 2,039; p = 180,000) for a variety of traits based on their predictive ability. The baseline LCNN, containing one local convolutional layer (kernel size: 10) and two fully connected layers with 64 nodes each, is outperforming commonly proposed ANNs (multi layer perceptrons and convolutional neural networks) for basically all considered traits. For traits with high heritability and large training population as present in the simulated data, LCNN are even outperforming state-of-the-art methods like genomic best linear unbiased prediction (GBLUP), Bayesian models and extended GBLUP, indicated by an increase in predictive ability of up to 24%. However, for small training populations, these state-of-the-art methods outperform all considered ANNs. Nevertheless, the LCNN still outperforms all other considered ANNs by around 10%. Minor improvements to the tested baseline network architecture of the LCNN were obtained by increasing the kernel size and of reducing the stride, whereas the number of subsequent fully connected layers and their node sizes had neglectable impact. Although gains in predictive ability were obtained for large scale data sets by using LCNNs, the practical use of ANNs comes with additional problems, such as the need of genotyping all considered individuals, the lack of estimation of heritability and reliability. Furthermore, breeding values are additive by design, whereas ANN-based estimates are not. However, ANNs also comes with new opportunities, as networks can easily be extended to account for additional inputs (omics, weather etc.) and outputs (multi-trait models), and computing time increases linearly with the number of individuals. With advances in high-throughput phenotyping and cheaper genotyping, ANNs can become a valid alternative for genomic prediction.
| S-EPMC7689358 | biostudies-literature
Project description:Footprints are left, or obtained, in a variety of scenarios from crime scenes to anthropological investigations. Determining the sex of a footprint can be useful in screening such impressions and attempts have been made to do so using single or multi landmark distances, shape analyses and via the density of friction ridges. Here we explore the relative importance of different components in sexing two-dimensional foot impressions namely, size, shape and texture. We use a machine learning approach and compare this to more traditional methods of discrimination. Two datasets are used, a pilot data set collected from students at Bournemouth University (N = 196) and a larger data set collected by podiatrists at Sheffield NHS Teaching Hospital (N = 2677). Our convolutional neural network can sex a footprint with accuracy of around 90% on a test set of N = 267 footprint images using all image components, which is better than an expert can achieve. However, the quality of the impressions impacts on this success rate, but the results are promising and in time it may be possible to create an automated screening algorithm in which practitioners of whatever sort (medical or forensic) can obtain a first order sexing of a two-dimensional footprint.
| S-EPMC8372903 | biostudies-literature