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

Pruning Extreme Wavelets Learning Machine by Automatic Relevance Determination

Extreme learning machines are used for various contexts in artificial intelligence, such as for classifying patterns, performing time series prediction and regression problems, and being a more viable solution for training hidden layer weights to determine values of the learning model. However, the essence, the model determines that these weights should be determined randomly, and the Moore Penrose pseudoinverse will define only the weights that will act in the output layer. Random weights make this learning a black box because there is no relationship between the hidden layer weights and the problem data. This paper proposes the initialization of weights and bias in the hidden layer through the Wavelets transform that allows the two parameters, previously initialized at random, to be more representative about the problem domain, allowing the frequency range of the input patterns of the network to aid in the definition of weights of the ELM hidden layer. To assist in the representativeness of the data, a technique of selection of characteristics based on automatic relevance determination will be applied to the selection of the most characteristic dimensions of the problem. To compose the network structure, activation functions of the type rectified linear unit, also called ReLU, were used. The proposed model was submitted to the classification test of binary patterns in real classes, and the results show that the proposition of this work assists in bringing better accuracy to the classification results, and thus can be considered a feasible proposition to the training of neural networks that use extreme learning machine