While the publication of datasets in scientific repositories has become broadly recognised, the repositories tend to have increasing semantic-related problems. For instance, they present various data reuse obstacles for machine-actionable processes, especially in biological repositories, hampering the reproducibility of scientific experiments. An example of these shortcomings is the GenBank database. We propose GAP, an innovative data model to enhance the semantic data meaning to address these issues. The model focuses on converging related approaches like data provenance, semantic interoperability, FAIR principles, and nanopublications. Our experiments include a prototype to scrape genomic data and trace them to nanopublications as a proof of concept. For this, (meta)data are stored in a three-level nanopub data model. The first level is related to a target organism, specifying data in terms of biological taxonomy. The second level focuses on the biological strains of the target, the central part of our contribution. The strains express information related to deciphered (meta)data of the genetic variations of the genomic material. The third level stores related scientific papers (meta)data. We expect it will offer higher data storage flexibility and more extensive interoperability with other data sources by incorporating and adopting associated approaches to store genomic data in the proposed model.
In image denoising problems, the increasing density of available images makes an exhaustive visual inspection impossible and therefore automated methods based on machine-learning must be deployed for this purpose. This is particulary the case in seismic signal processing. Engineers/geophysicists have to deal with millions of seismic time series. Finding the sub-surface properties useful for the oil industry may take up to a year and is very costly in terms of computing/human resources. In particular, the data must go through different steps of noise attenuation. Each denoise step is then ideally followed by a quality control (QC) stage performed by means of human expertise. To learn a quality control classifier in a supervised manner, labeled training data must be available, but collecting the labels from human experts is extremely time-consuming. We therefore propose a novel active learning methodology to sequentially select the most relevant data, which are then given back to a human expert for labeling. Beyond the application in geophysics, the technique we promote in this paper, based on estimates of the local error and its uncertainty, is generic. Its performance is supported by strong empirical evidence, as illustrated by the numerical experiments presented in this article, where it is compared to alternative active learning strategies both on synthetic and real seismic datasets.
We propose modeling designer style in mixed-initiative game content creation tools as archetypical design traces. These design traces are formulated as transitions between design styles; these design styles are in turn found through clustering all intermediate designs along the way to making a complete design. This method is implemented in the Evolutionary Dungeon Designer, a research platform for mixed-initiative systems to create adventure and dungeon crawler games. We present results both in the form of design styles for rooms, which can be analyzed to better understand the kind of rooms designed by users, and in the form of archetypical sequences between these rooms, i.e., Designer Personas.
Real-world training data usually exhibits long-tailed distribution, where several majority classes have a significantly larger number of samples than the remaining minority classes. This imbalance degrades the performance of typical supervised learning algorithms designed for balanced training sets. In this paper, we address this issue by augmenting minority classes with a recently proposed implicit semantic data augmentation (ISDA) algorithm, which produces diversified augmented samples by translating deep features along many semantically meaningful directions. Importantly, given that ISDA estimates the class-conditional statistics to obtain semantic directions, we find it ineffective to do this on minority classes due to the insufficient training data. To this end, we propose a novel approach to learn transformed semantic directions with meta-learning automatically. In specific, the augmentation strategy during training is dynamically optimized, aiming to minimize the loss on a small balanced validation set, which is approximated via a meta update step. Extensive empirical results on CIFAR-LT-10/100, ImageNet-LT, and iNaturalist 2017/2018 validate the effectiveness of our method.
Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: //github.com/Luoxd1996/DTC
Cognitive task analysis (CTA) is a type of analysis in applied psychology aimed at eliciting and representing the knowledge and thought processes of domain experts. In CTA, often heavy human labor is involved to parse the interview transcript into structured knowledge (e.g., flowchart for different actions). To reduce human efforts and scale the process, automated CTA transcript parsing is desirable. However, this task has unique challenges as (1) it requires the understanding of long-range context information in conversational text; and (2) the amount of labeled data is limited and indirect---i.e., context-aware, noisy, and low-resource. In this paper, we propose a weakly-supervised information extraction framework for automated CTA transcript parsing. We partition the parsing process into a sequence labeling task and a text span-pair relation extraction task, with distant supervision from human-curated protocol files. To model long-range context information for extracting sentence relations, neighbor sentences are involved as a part of input. Different types of models for capturing context dependency are then applied. We manually annotate real-world CTA transcripts to facilitate the evaluation of the parsing tasks
Clustering is an essential data mining tool that aims to discover inherent cluster structure in data. For most applications, applying clustering is only appropriate when cluster structure is present. As such, the study of clusterability, which evaluates whether data possesses such structure, is an integral part of cluster analysis. However, methods for evaluating clusterability vary radically, making it challenging to select a suitable measure. In this paper, we perform an extensive comparison of measures of clusterability and provide guidelines that clustering users can reference to select suitable measures for their applications.
Over the past years, there has been a resurgence of Datalog-based systems in the database community as well as in industry. In this context, it has been recognized that to handle the complex knowl\-edge-based scenarios encountered today, such as reasoning over large knowledge graphs, Datalog has to be extended with features such as existential quantification. Yet, Datalog-based reasoning in the presence of existential quantification is in general undecidable. Many efforts have been made to define decidable fragments. Warded Datalog+/- is a very promising one, as it captures PTIME complexity while allowing ontological reasoning. Yet so far, no implementation of Warded Datalog+/- was available. In this paper we present the Vadalog system, a Datalog-based system for performing complex logic reasoning tasks, such as those required in advanced knowledge graphs. The Vadalog system is Oxford's contribution to the VADA research programme, a joint effort of the universities of Oxford, Manchester and Edinburgh and around 20 industrial partners. As the main contribution of this paper, we illustrate the first implementation of Warded Datalog+/-, a high-performance Datalog+/- system utilizing an aggressive termination control strategy. We also provide a comprehensive experimental evaluation.
Image captioning has been recently gaining a lot of attention thanks to the impressive achievements shown by deep captioning architectures, which combine Convolutional Neural Networks to extract image representations, and Recurrent Neural Networks to generate the corresponding captions. At the same time, a significant research effort has been dedicated to the development of saliency prediction models, which can predict human eye fixations. Even though saliency information could be useful to condition an image captioning architecture, by providing an indication of what is salient and what is not, research is still struggling to incorporate these two techniques. In this work, we propose an image captioning approach in which a generative recurrent neural network can focus on different parts of the input image during the generation of the caption, by exploiting the conditioning given by a saliency prediction model on which parts of the image are salient and which are contextual. We show, through extensive quantitative and qualitative experiments on large scale datasets, that our model achieves superior performances with respect to captioning baselines with and without saliency, and to different state of the art approaches combining saliency and captioning.
Visual question answering requires high-order reasoning about an image, which is a fundamental capability needed by machine systems to follow complex directives. Recently, modular networks have been shown to be an effective framework for performing visual reasoning tasks. While modular networks were initially designed with a degree of model transparency, their performance on complex visual reasoning benchmarks was lacking. Current state-of-the-art approaches do not provide an effective mechanism for understanding the reasoning process. In this paper, we close the performance gap between interpretable models and state-of-the-art visual reasoning methods. We propose a set of visual-reasoning primitives which, when composed, manifest as a model capable of performing complex reasoning tasks in an explicitly-interpretable manner. The fidelity and interpretability of the primitives' outputs enable an unparalleled ability to diagnose the strengths and weaknesses of the resulting model. Critically, we show that these primitives are highly performant, achieving state-of-the-art accuracy of 99.1% on the CLEVR dataset. We also show that our model is able to effectively learn generalized representations when provided a small amount of data containing novel object attributes. Using the CoGenT generalization task, we show more than a 20 percentage point improvement over the current state of the art.
Recommendation system is a common demand in daily life and matrix completion is a widely adopted technique for this task. However, most matrix completion methods lack semantic interpretation and usually result in weak-semantic recommendations. To this end, this paper proposes a $S$emantic $A$nalysis approach for $R$ecommendation systems $(SAR)$, which applies a two-level hierarchical generative process that assigns semantic properties and categories for user and item. $SAR$ learns semantic representations of users/items merely from user ratings on items, which offers a new path to recommendation by semantic matching with the learned representations. Extensive experiments demonstrate $SAR$ outperforms other state-of-the-art baselines substantially.