INESC-ID

About: INESC-ID is a nonprofit organization based out in Lisbon, Portugal. It is known for research contribution in the topics: Field-programmable gate array & Control theory. The organization has 932 authors who have published 2618 publications receiving 37658 citations.

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

Abstract: Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumoris a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses thestate-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross tota lresection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

An update to the systematic literature review of empirical evidence of the impacts and outcomes of computer games and serious games

Abstract: Continuing interest in digital games indicated that it would be useful to update Connolly et al.'s (2012) systematic literature review of empirical evidence about the positive impacts and outcomes of games. Since a large number of papers was identified in the period from 2009 to 2014, the current review focused on 143 papers that provided higher quality evidence about the positive outcomes of games. Connolly et al.'s multidimensional analysis of games and their outcomes provided a useful framework for organising the varied research in this area. The most frequently occurring outcome reported for games for learning was knowledge acquisition, while entertainment games addressed a broader range of affective, behaviour change, perceptual and cognitive and physiological outcomes. Games for learning were found across varied topics with STEM subjects and health the most popular. Future research on digital games would benefit from a systematic programme of experimental work, examining in detail which game features are most effective in promoting engagement and supporting learning. The current systematic literature review updates Author (date).The review looks at impacts and outcomes of playing digital games from 2009 to 2014.Multi-component coding of papers, games and learning outcomes was used.Many papers were found with 143 papers providing high quality evidence.Games for entertainment and learning addressed different outcomes.

Posterior Regularization for Structured Latent Variable Models

Abstract: We present posterior regularization, a probabilistic framework for structured, weakly supervised learning. Our framework efficiently incorporates indirect supervision via constraints on posterior distributions of probabilistic models with latent variables. Posterior regularization separates model complexity from the complexity of structural constraints it is desired to satisfy. By directly imposing decomposable regularization on the posterior moments of latent variables during learning, we retain the computational efficiency of the unconstrained model while ensuring desired constraints hold in expectation. We present an efficient algorithm for learning with posterior regularization and illustrate its versatility on a diverse set of structural constraints such as bijectivity, symmetry and group sparsity in several large scale experiments, including multi-view learning, cross-lingual dependency grammar induction, unsupervised part-of-speech induction, and bitext word alignment.

Finding Function in Form: Compositional Character Models for Open Vocabulary Word Representation

Abstract: We introduce a model for constructing vector representations of words by composing characters using bidirectional LSTMs. Relative to traditional word representation models that have independent vectors for each word type, our model requires only a single vector per character type and a fixed set of parameters for the compositional model. Despite the compactness of this model and, more importantly, the arbitrary nature of the form‐function relationship in language, our “composed” word representations yield state-of-the-art results in language modeling and part-of-speech tagging. Benefits over traditional baselines are particularly pronounced in morphologically rich languages (e.g., Turkish).

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Abstract: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net .