Dataset Information

Deep Learning of Nanopore Sensing Signals Using a Bi-Path Network.

ABSTRACT: Temporal changes in electrical resistance of a nanopore sensor caused by translocating target analytes are recorded as a sequence of pulses on current traces. Prevalent algorithms for feature extraction in pulse-like signals lack objectivity because empirical amplitude thresholds are user-defined to single out the pulses from the noisy background. Here, we use deep learning for feature extraction based on a bi-path network (B-Net). After training, the B-Net acquires the prototypical pulses and the ability of both pulse recognition and feature extraction without a priori assigned parameters. The B-Net is evaluated on simulated data sets and further applied to experimental data of DNA and protein translocation. The B-Net results are characterized by small relative errors and stable trends. The B-Net is further shown capable of processing data with a signal-to-noise ratio equal to 1, an impossibility for threshold-based algorithms. The B-Net presents a generic architecture applicable to pulse-like signals beyond nanopore currents.

SUBMITTER: Dematties D

PROVIDER: S-EPMC8482760 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Deep Learning of Nanopore Sensing Signals Using a Bi-Path Network.

Dematties Dario D Wen Chenyu C Pérez Mauricio David MD Zhou Dian D Zhang Shi-Li SL

ACS nano 20210817 9

Temporal changes in electrical resistance of a nanopore sensor caused by translocating target analytes are recorded as a sequence of pulses on current traces. Prevalent algorithms for feature extraction in pulse-like signals lack objectivity because empirical amplitude thresholds are user-defined to single out the pulses from the noisy background. Here, we use deep learning for feature extraction based on a bi-path network (B-Net). After training, the B-Net acquires the prototypical pulses and t ...[more]

PMID: 34583465

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Project description:Social robotics represents a branch of human-robot interaction dedicated to developing systems to control the robots to operate in unstructured environments with the presence of human beings. Social robots must interact with human beings by understanding social signals and responding appropriately to them. Most social robots are still pre-programmed, not having great ability to learn and respond with actions adequate during an interaction with humans. Recently more elaborate methods use body movements, gaze direction, and body language. However, these methods generally neglect vital signs present during an interaction, such as the human emotional state. In this article, we address the problem of developing a system to turn a robot able to decide, autonomously, what behaviors to emit in the function of the human emotional state. From one side, the use of Reinforcement Learning (RL) represents a way for social robots to learn advanced models of social cognition, following a self-learning paradigm, using characteristics automatically extracted from high-dimensional sensory information. On the other side, Deep Learning (DL) models can help the robots to capture information from the environment, abstracting complex patterns from the visual information. The combination of these two techniques is known as Deep Reinforcement Learning (DRL). The purpose of this work is the development of a DRL system to promote a natural and socially acceptable interaction among humans and robots. For this, we propose an architecture, Social Robotics Deep Q-Network (SocialDQN), for teaching social robots to behave and interact appropriately with humans based on social signals, especially on human emotional states. This constitutes a relevant contribution for the area since the social signals must not only be recognized by the robot but help him to take action appropriated according to the situation presented. Characteristics extracted from people's faces are considered for extracting the human emotional state aiming to improve the robot perception. The development and validation of the system are carried out with the support of SimDRLSR simulator. Results obtained through several tests demonstrate that the system learned satisfactorily to maximize the rewards, and consequently, the robot behaves in a socially acceptable way.

Dataset Information

Deep Learning of Nanopore Sensing Signals Using a Bi-Path Network.

Publications

Deep Learning of Nanopore Sensing Signals Using a Bi-Path Network.

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