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Characterization of deep neural network features by decodability from human brain activity.

ABSTRACT: Achievements of near human-level performance in object recognition by deep neural networks (DNNs) have triggered a flood of comparative studies between the brain and DNNs. Using a DNN as a proxy for hierarchical visual representations, our recent study found that human brain activity patterns measured by functional magnetic resonance imaging (fMRI) can be decoded (translated) into DNN feature values given the same inputs. However, not all DNN features are equally decoded, indicating a gap between the DNN and human vision. Here, we present a dataset derived from DNN feature decoding analyses, which includes fMRI signals of five human subjects during image viewing, decoded feature values of DNNs (AlexNet and VGG19), and decoding accuracies of individual DNN features with their rankings. The decoding accuracies of individual features were highly correlated between subjects, suggesting the systematic differences between the brain and DNNs. We hope the present dataset will contribute to revealing the gap between the brain and DNNs and provide an opportunity to make use of the decoded features for further applications.

SUBMITTER: Horikawa T

PROVIDER: S-EPMC6371890 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Characterization of deep neural network features by decodability from human brain activity.

Horikawa Tomoyasu T Aoki Shuntaro C SC Tsukamoto Mitsuaki M Kamitani Yukiyasu Y

Scientific data 20190212

Achievements of near human-level performance in object recognition by deep neural networks (DNNs) have triggered a flood of comparative studies between the brain and DNNs. Using a DNN as a proxy for hierarchical visual representations, our recent study found that human brain activity patterns measured by functional magnetic resonance imaging (fMRI) can be decoded (translated) into DNN feature values given the same inputs. However, not all DNN features are equally decoded, indicating a gap betwee ...[more]

PMID: 30747910

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Project description:The effective decoding of movement from non-invasive electroencephalography (EEG) is essential for informing several therapeutic interventions, from neurorehabilitation robots to neural prosthetics. Deep neural networks are most suitable for decoding real-time data but their use in EEG is hindered by the gross classes of motor tasks in the currently available datasets, which are solvable even with network architectures that do not require specialized design considerations. Moreover, the weak association with the underlying neurophysiology limits the generalizability of modern networks for EEG inference. Here, we present a neurophysiologically interpretable 3-dimensional convolutional neural network (3D-CNN) that captured the spatiotemporal dependencies in brain areas that get co-activated during movement. The 3D-CNN received topography-preserving EEG inputs, and predicted complex components of hand movements performed on a plane using a back-drivable rehabilitation robot, namely (a) the reaction time (RT) for responding to stimulus (slow or fast), (b) the mode of movement (active or passive, depending on whether there was an assistive force provided by the apparatus), and (c) the orthogonal directions of the movement (left, right, up, or down). We validated the 3D-CNN on a new dataset that we acquired from an in-house motor experiment, where it achieved average leave-one-subject-out test accuracies of 79.81%, 81.23%, and 82.00% for RT, active vs. passive, and direction classifications, respectively. Our proposed method outperformed the modern 2D-CNN architecture by a range of 1.1% to 6.74% depending on the classification task. Further, we identified the EEG sensors and time segments crucial to the classification decisions of the network, which aligned well with the current neurophysiological knowledge on brain activity in motor planning and execution tasks. Our results demonstrate the importance of biological relevance in networks for an accurate decoding of EEG, suggesting that the real-time classification of other complex brain activities may now be within our reach.

Project description:BackgroundCircular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the regulation of various diseases and cancers. Determining the functions of circRNAs in mammalian cells is of great significance for revealing their mechanism of action in physiological and pathological processes, diagnosis and treatment of diseases. However, determining the functions of circRNAs on a large scale is a challenging task because of the high experimental costs.ResultsIn this paper, we present a hierarchical deep learning model, DeepciRGO, which can effectively predict gene ontology functions of circRNAs. We build a heterogeneous network containing circRNA co-expressions, protein-protein interactions and protein-circRNA interactions. The topology features of proteins and circRNAs are calculated using a novel representation learning approach HIN2Vec across the heterogeneous network. Then, a deep multi-label hierarchical classification model is trained with the topology features to predict the biological process function in the gene ontology for each circRNA. In particular, we manually curated a benchmark dataset containing 185 GO annotations for 62 circRNAs, namely, circRNA2GO-62. The DeepciRGO achieves promising performance on the circRNA2GO-62 dataset with a maximum F-measure of 0.412, a recall score of 0.400, and an accuracy of 0.425, which are significantly better than other state-of-the-art RNA function prediction methods. In addition, we demonstrate the considerable potential of integrating multiple interactions and association networks.ConclusionsDeepciRGO will be a useful tool for accurately annotating circRNAs. The experimental results show that integrating multi-source data can help to improve the predictive performance of DeepciRGO. Moreover, The model also can combine RNA structure and sequence information to further optimize predictive performance.

Dataset Information

Characterization of deep neural network features by decodability from human brain activity.

Publications

Characterization of deep neural network features by decodability from human brain activity.

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