The quantification of biomarkers on immunohistochemistry breast cancer images is essential for defining appropriate therapy for breast cancer patients, as well as for extracting relevant information on disease prognosis. This is an arduous and time-consuming task that may introduce a bias in the results due to intra- and inter-observer variability which could be alleviated by making use of automatic quantification tools. However, this is not a simple processing task given the heterogeneity of breast tumors that results in non-uniformly distributed tumor cells exhibiting different staining colors and intensity, size, shape, and texture, of the nucleus, cytoplasm and membrane. In this research work, we demonstrate the feasibility of using a deep learning-based instance segmentation architecture for the automatic quantification of both nuclear and membrane biomarkers applied to IHC-stained slides. We have solved the cumbersome task of training set generation with the design and implementation of a web platform, which has served as a hub for communication and feedback between researchers and pathologists as well as a system for the validation of the automatic image processing models. Through this tool, we have collected annotations over samples of HE, ER and Ki-67 (nuclear biomarkers) and HER2 (membrane biomarker) IHC-stained images. Using the same deep learning network architecture, we have trained two models, so-called nuclei- and membrane-aware segmentation models, which, once successfully validated, have revealed to be a promising method to segment nuclei instances in IHC-stained images. The quantification method proposed in this work has been integrated into the developed web platform and is currently being used as a decision-support tool by pathologists.

In this article, we propose two kinds of neural networks inspired by power method and inverse power method to solve linear eigenvalue problems. These neural networks share similar ideas with traditional methods, in which the differential operator is realized by automatic differentiation. The eigenfunction of the eigenvalue problem is learned by the neural network and the iterative algorithms are implemented by optimizing the specially defined loss function. The largest positive eigenvalue, smallest eigenvalue and interior eigenvalues with the given prior knowledge can be solved efficiently. We examine the applicability and accuracy of our methods in the numerical experiments in one dimension, two dimensions and higher dimensions. Numerical results show that accurate eigenvalue and eigenfunction approximations can be obtained by our methods.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., the Medical Subject Headings (MeSH) thesaurus), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This article investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. In this context, we devise lexical and pre-trained language models based methods. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We further contribute an extensive analysis of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

The development of models for learning music similarity and feature extraction from audio media files is an increasingly important task for the entertainment industry. This work proposes a novel music classification model based on metric learning and feature extraction from MP3 audio files. The metric learning process considers the learning of a set of parameterized distances employing a structured prediction approach from a set of MP3 audio files containing several music genres. The main objective of this work is to make possible learning a personalized metric for each customer. To extract the acoustic information we use the Mel-Frequency Cepstral Coefficient (MFCC) and make a dimensionality reduction with the use of Principal Components Analysis. We attest the model validity performing a set of experiments and comparing the training and testing results with baseline algorithms, such as K-means and Soft Margin Linear Support Vector Machine (SVM). Experiments show promising results and encourage the future development of an online version of the learning model.