Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

State-based decoding of force signals from multi-channel local field potentials

The functional use of brain-machine interfaces (BMIs) in everyday tasks requires the accurate decoding of both movement and force information. In real-word tasks such as reach-to-grasp movements, a prosthetic hand should be switched between reaching and grasping modes, depending on the detection of the user intents in the decoder part of the BMI. Therefore, it is important to detect the rest or active states of different actions in the decoder to produce the corresponding continuous command output during the estimated state. In this study, we demonstrated that the resting and force-generating time-segments in a key pressing task could be accurately detected from local field potentials (LFPs) in rat's primary motor cortex. Common spatial pattern (CSP) algorithm was applied on different spectral LFP sub-bands to maximize the difference between the two classes of force and rest. We also showed that combining a discrete state decoder with linear or non-linear continuous force variable decoders could lead to a higher force decoding performance compared with the case we use a continuous variable decoder only. Moreover, the results suggest that gamma LFP signals (50-100 Hz) could be used successfully for decoding the discrete rest/force states as well as continuous values of the force variable. The results of this study can offer substantial benefits for the implementation of a self-paced, force-related command generator in BMI experiments without the need for manual external signals to select the state of the decoder. © 2020 Institute of Electrical and Electronics Engineers Inc.. All rights reserved

Online mapping of EMG signals into kinematics by autoencoding

Background In this paper, we propose a nonlinear minimally supervised method based on auto-encoding (AEN) of EMG for myocontrol. The proposed method was tested against the state-of-the-art (SOA) control scheme using a Fitts’ law approach. Methods Seven able-bodied subjects performed a series of target acquisition myoelectric control tasks using the AEN and SOA algorithms for controlling two degrees-of-freedom (radial/ulnar deviation and flexion/extension of the wrist), and their online performance was characterized by six metrics. Results Both methods allowed a completion rate close to 100%, however AEN outperformed SOA for all other performance metrics, e.g. it allowed to perform the tasks on average in half the time with respect to SOA. Moreover, the amount of information transferred by the proposed method in bit/s was nearly twice the throughput of SOA. Conclusions These results show that autoencoders can map EMG signals into kinematics with the potential of providing intuitive and dexterous control of artificial limbs for amputees