In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a health-related entity mention in a free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language System (UMLS). This is a challenging task since medical terminology is very different when coming from health care professionals or from the general public in the form of social media texts. We approach it as a sequence learning problem with powerful neural networks such as recurrent neural networks and contextualized word representation models trained to obtain semantic representations of social media expressions. Our experimental evaluation over three different benchmarks shows that neural architectures leverage the semantic meaning of the entity mention and significantly outperform an existing state of the art models.

Data used in Flow Cytometry present pronounced variability due to biological and technical reasons. Biological variability is a well known phenomenon produced by measurements on different individuals, with different characteristics such as age, sex, etc... The use of different settings for measurement, the variation of the conditions during experiments or the different types of flow cytometers are some of the technical sources of variability. This high variability makes difficult the use of supervised machine learning for identification of cell populations. We propose optimalFlowTemplates, based on a similarity distance and Wasserstein barycenters, which clusterizes cytometries and produces prototype cytometries for the different groups. We show that supervised learning restricted to the new groups performs better than the same techniques applied to the whole collection. We also present optimalFlowClassification, which uses a database of gated cytometries and optimalFlowTemplates to assign cell types to a new cytometry. We show that this procedure can outperform state of the art techniques in the proposed datasets. Our code and data are freely available as R packages at https://github.com/HristoInouzhe/optimalFlow and https://github.com/HristoInouzhe/optimalFlowData.

In symbolic planning systems, the knowledge on the domain is commonly provided by an expert. Recently, an automatic abstraction procedure has been proposed in the literature to create a Planning Domain Definition Language (PDDL) representation, which is the most widely used input format for most off-the-shelf automated planners, starting from `options', a data structure used to represent actions within the hierarchical reinforcement learning framework. We propose an architecture that potentially removes the need for human intervention. In particular, the architecture first acquires options in a fully autonomous fashion on the basis of open-ended learning, then builds a PDDL domain based on symbols and operators that can be used to accomplish user-defined goals through a standard PDDL planner. We start from an implementation of the above mentioned procedure tested on a set of benchmark domains in which a humanoid robot can change the state of some objects through direct interaction with the environment. We then investigate some critical aspects of the information abstraction process that have been observed, and propose an extension that mitigates such criticalities, in particular by analysing the type of classifiers that allow a suitable grounding of symbols.

The term Neural Architecture Search (NAS) refers to the automatic optimization of network architectures for a new, previously unknown task. Since testing an architecture is computationally very expensive, many optimizers need days or even weeks to find suitable architectures. However, this search time can be significantly reduced if knowledge from previous searches on different tasks is reused. In this work, we propose a generally applicable framework that introduces only minor changes to existing optimizers to leverage this feature. As an example, we select an existing optimizer and demonstrate the complexity of the integration of the framework as well as its impact. In experiments on CIFAR-10 and CIFAR-100, we observe a reduction in the search time from 200 to only 6 GPU days, a speed up by a factor of 33. In addition, we observe new records of 1.99 and 14.06 for NAS optimizers on the CIFAR benchmarks, respectively. In a separate study, we analyze the impact of the amount of source and target data. Empirically, we demonstrate that the proposed framework generally gives better results and, in the worst case, is just as good as the unmodified optimizer.

Prevalent efforts have been put in automatically inferring genres of musical items. Yet, the propose solutions often rely on simplifications and fail to address the diversity and subjectivity of music genres. Accounting for these has, though, many benefits for aligning knowledge sources, integrating data and enriching musical items with tags. Here, we choose a new angle for the genre study by seeking to predict what would be the genres of musical items in a target tag system, knowing the genres assigned to them within source tag systems. We call this a translation task and identify three cases: 1) no common annotated corpus between source and target tag systems exists, 2) such a large corpus exists, 3) only few common annotations exist. We propose the related solutions: a knowledge-based translation modeled as taxonomy mapping, a statistical translation modeled with maximum likelihood logistic regression; a hybrid translation modeled with maximum a posteriori logistic regression with priors given by the knowledge-based translation. During evaluation, the solutions fit well the identified cases and the hybrid translation is systematically the most effective w.r.t. multilabel classification metrics. This is a first attempt to unify genre tag systems by leveraging both representation and interpretation diversity.

We study the problem of approximating orthogonal matrices so that their application is numerically fast and yet accurate. We find an approximation by solving an optimization problem over a set of structured matrices, that we call Givens transformations, including Givens rotations as a special case. We propose an efficient greedy algorithm to solve such a problem and show that it strikes a balance between approximation accuracy and speed of computation. The proposed approach is relevant in spectral methods and we illustrate its application to PCA.

Many software analysis methods have come to rely on machine learning approaches. Code segmentation - the process of decomposing source code into meaningful blocks - can augment these methods by featurizing code, reducing noise, and limiting the problem space. Traditionally, code segmentation has been done using syntactic cues; current approaches do not intentionally capture logical content. We develop a novel deep learning approach to generate logical code segments regardless of the language or syntactic correctness of the code. Due to the lack of logically segmented source code, we introduce a unique data set construction technique to approximate ground truth for logically segmented code. Logical code segmentation can improve tasks such as automatically commenting code, detecting software vulnerabilities, repairing bugs, labeling code functionality, and synthesizing new code.

We propose a probabilistic model for inferring the multivariate function from multiple areal data sets with various granularities. Here, the areal data are observed not at location points but at regions. Existing regression-based models require the fine-grained auxiliary data sets on the same domain. With the proposed model, the functions for respective areal data sets are assumed to be a multivariate dependent Gaussian process (GP) that is modeled as a linear mixing of independent latent GPs. Sharing of latent GPs across multiple areal data sets allows us to effectively estimate spatial correlation for each areal data set; moreover it can easily be extended to transfer learning across multiple domains. To handle the multivariate areal data, we design its observation model with a spatial aggregation process for each areal data set, which is an integral of the mixed GP over the corresponding region. By deriving the posterior GP, we can predict the data value at any location point by considering the spatial correlations and the dependences between areal data sets simultaneously. Our experiments on real-world data sets demonstrate that our model can 1) accurately refine the coarse-grained areal data, and 2) offer performance improvements by using the areal data sets from multiple domains.

Use of an autoencoder (AE) as a normal model is a state-of-the-art technique for unsupervised-anomaly detection in sounds (ADS). The AE is trained to minimize the sample mean of the anomaly score of normal sounds in a mini-batch. One problem with this approach is that the anomaly score of rare-normal sounds becomes higher than that of frequent-normal sounds, because the sample mean is strongly affected by frequent-normal samples, resulting in preferentially decreasing the anomaly score of frequent-normal samples. To decrease anomaly scores for both frequent- and rare-normal sounds, we propose batch uniformization, a training method for unsupervised-ADS for minimizing a weighted average of the anomaly score on each sample in a mini-batch. We used the reciprocal of the probabilistic density of each sample as the weight, more intuitively, a large weight is given for rare-normal sounds. Such a weight works to give a constant anomaly score for both frequent- and rare-normal sounds. Since the probabilistic density is unknown, we estimate it by using the kernel density estimation on each training mini-batch. Verification- and objective-experiments show that the proposed batch uniformization improves the performance of unsupervised-ADS.

With the rapid adoption of machine learning techniques for large-scale applications in science and engineering comes the convergence of two grand challenges in visualization. First, the utilization of black box models (e.g., deep neural networks) calls for advanced techniques in exploring and interpreting model behaviors. Second, the rapid growth in computing has produced enormous datasets that require techniques that can handle millions or more samples. Although some solutions to these interpretability challenges have been proposed, they typically do not scale beyond thousands of samples, nor do they provide the high-level intuition scientists are looking for. Here, we present the first scalable solution to explore and analyze high-dimensional functions often encountered in the scientific data analysis pipeline. By combining a new streaming neighborhood graph construction, the corresponding topology computation, and a novel data aggregation scheme, namely topology aware datacubes, we enable interactive exploration of both the topological and the geometric aspect of high-dimensional data. Following two use cases from high-energy-density (HED) physics and computational biology, we demonstrate how these capabilities have led to crucial new insights in both applications.