8,814 research outputs found
Consensus and meta-analysis regulatory networks for combining multiple microarray gene expression datasets
Microarray data is a key source of experimental data for modelling gene regulatory interactions from expression levels. With the rapid increase of publicly available microarray data comes the opportunity to produce regulatory network models based on multiple datasets. Such models are potentially more robust with greater confidence, and place less reliance on a single dataset. However, combining datasets directly can be difficult as experiments are often conducted on different microarray platforms, and in different laboratories leading to inherent biases in the data that are not always removed through pre-processing such as normalisation. In this paper we compare two frameworks for combining microarray datasets to model regulatory networks: pre- and post-learning aggregation. In pre-learning approaches, such as using simple scale-normalisation prior to the concatenation of datasets, a model is learnt from a combined dataset, whilst in post-learning aggregation individual models are learnt from each dataset and the models are combined. We present two novel approaches for post-learning aggregation, each based on aggregating high-level features of Bayesian network models that have been generated from different microarray expression datasets. Meta-analysis Bayesian networks are based on combining statistical confidences attached to network edges whilst Consensus Bayesian networks identify consistent network features across all datasets. We apply both approaches to multiple datasets from synthetic and real (Escherichia coli and yeast) networks and demonstrate that both methods can improve on networks learnt from a single dataset or an aggregated dataset formed using a standard scale-normalisation
The 1990 progress report and future plans
This document describes the progress and plans of the Artificial Intelligence Research Branch (RIA) at ARC in 1990. Activities span a range from basic scientific research to engineering development and to fielded NASA applications, particularly those applications that are enabled by basic research carried out at RIA. Work is conducted in-house and through collaborative partners in academia and industry. Our major focus is on a limited number of research themes with a dual commitment to technical excellence and proven applicability to NASA short, medium, and long-term problems. RIA acts as the Agency's lead organization for research aspects of artificial intelligence, working closely with a second research laboratory at JPL and AI applications groups at all NASA centers
Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models
The emergence and development of cancer is a consequence of the accumulation
over time of genomic mutations involving a specific set of genes, which
provides the cancer clones with a functional selective advantage. In this work,
we model the order of accumulation of such mutations during the progression,
which eventually leads to the disease, by means of probabilistic graphic
models, i.e., Bayesian Networks (BNs). We investigate how to perform the task
of learning the structure of such BNs, according to experimental evidence,
adopting a global optimization meta-heuristics. In particular, in this work we
rely on Genetic Algorithms, and to strongly reduce the execution time of the
inference -- which can also involve multiple repetitions to collect
statistically significant assessments of the data -- we distribute the
calculations using both multi-threading and a multi-node architecture. The
results show that our approach is characterized by good accuracy and
specificity; we also demonstrate its feasibility, thanks to a 84x reduction of
the overall execution time with respect to a traditional sequential
implementation
Context Based Visual Content Verification
In this paper the intermediary visual content verification method based on
multi-level co-occurrences is studied. The co-occurrence statistics are in
general used to determine relational properties between objects based on
information collected from data. As such these measures are heavily subject to
relative number of occurrences and give only limited amount of accuracy when
predicting objects in real world. In order to improve the accuracy of this
method in the verification task, we include the context information such as
location, type of environment etc. In order to train our model we provide new
annotated dataset the Advanced Attribute VOC (AAVOC) that contains additional
properties of the image. We show that the usage of context greatly improve the
accuracy of verification with up to 16% improvement.Comment: 6 pages, 6 Figures, Published in Proceedings of the Information and
Digital Technology Conference, 201
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Context-awareness for mobile sensing: a survey and future directions
The evolution of smartphones together with increasing computational power have empowered developers to create innovative context-aware applications for recognizing user related social and cognitive activities in any situation and at any location. The existence and awareness of the context provides the capability of being conscious of physical environments or situations around mobile device users. This allows network services to respond proactively and intelligently based on such awareness. The key idea behind context-aware applications is to encourage users to collect, analyze and share local sensory knowledge in the purpose for a large scale community use by creating a smart network. The desired network is capable of making autonomous logical decisions to actuate environmental objects, and also assist individuals. However, many open challenges remain, which are mostly arisen due to the middleware services provided in mobile devices have limited resources in terms of power, memory and bandwidth. Thus, it becomes critically important to study how the drawbacks can be elaborated and resolved, and at the same time better understand the opportunities for the research community to contribute to the context-awareness. To this end, this paper surveys the literature over the period of 1991-2014 from the emerging concepts to applications of context-awareness in mobile platforms by providing up-to-date research and future research directions. Moreover, it points out the challenges faced in this regard and enlighten them by proposing possible solutions
Literal Perceptual Inference
In this paper, I argue that theories of perception that appeal to Helmholtz’s idea of unconscious inference (“Helmholtzian” theories) should be taken literally, i.e. that the inferences appealed to in such theories are inferences in the full sense of the term, as employed elsewhere in philosophy and in ordinary discourse.
In the course of the argument, I consider constraints on inference based on the idea that inference is a deliberate acton, and on the idea that inferences depend on the syntactic structure of representations. I argue that inference is a personal-level but sometimes unconscious process that cannot in general be distinguished from association on the basis of the structures of the representations over which it’s defined. I also critique arguments against representationalist interpretations of Helmholtzian theories, and argue against the view that perceptual inference is encapsulated in a module
Efficient Benchmarking of Algorithm Configuration Procedures via Model-Based Surrogates
The optimization of algorithm (hyper-)parameters is crucial for achieving
peak performance across a wide range of domains, ranging from deep neural
networks to solvers for hard combinatorial problems. The resulting algorithm
configuration (AC) problem has attracted much attention from the machine
learning community. However, the proper evaluation of new AC procedures is
hindered by two key hurdles. First, AC benchmarks are hard to set up. Second
and even more significantly, they are computationally expensive: a single run
of an AC procedure involves many costly runs of the target algorithm whose
performance is to be optimized in a given AC benchmark scenario. One common
workaround is to optimize cheap-to-evaluate artificial benchmark functions
(e.g., Branin) instead of actual algorithms; however, these have different
properties than realistic AC problems. Here, we propose an alternative
benchmarking approach that is similarly cheap to evaluate but much closer to
the original AC problem: replacing expensive benchmarks by surrogate benchmarks
constructed from AC benchmarks. These surrogate benchmarks approximate the
response surface corresponding to true target algorithm performance using a
regression model, and the original and surrogate benchmark share the same
(hyper-)parameter space. In our experiments, we construct and evaluate
surrogate benchmarks for hyperparameter optimization as well as for AC problems
that involve performance optimization of solvers for hard combinatorial
problems, drawing training data from the runs of existing AC procedures. We
show that our surrogate benchmarks capture overall important characteristics of
the AC scenarios, such as high- and low-performing regions, from which they
were derived, while being much easier to use and orders of magnitude cheaper to
evaluate
The challenge of complexity for cognitive systems
Complex cognition addresses research on (a) high-level cognitive processes – mainly problem solving, reasoning, and decision making – and their interaction with more basic processes such as perception, learning, motivation and emotion and (b) cognitive processes which take place in a complex, typically dynamic, environment. Our focus is on AI systems and cognitive models dealing with complexity and on psychological findings which can inspire or challenge cognitive systems research. In this overview we first motivate why we have to go beyond models for rather simple cognitive processes and reductionist experiments. Afterwards, we give a characterization of complexity from our perspective. We introduce the triad of cognitive science methods – analytical, empirical, and engineering methods – which in our opinion have all to be utilized to tackle complex cognition. Afterwards we highlight three aspects of complex cognition – complex problem solving, dynamic decision making, and learning of concepts, skills and strategies. We conclude with some reflections about and challenges for future research
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