67 research outputs found

    Neural plasma

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    This paper presents a novel type of artificial neural network, called neural plasma, which is tailored for classification tasks involving few observations with a large number of variables. Neural plasma learns to adapt its classification confidence by generating artificial training data as a function of its confidence in previous decisions. In contrast to multilayer perceptrons and similar techniques, which are inspired by topological and operational aspects of biological neural networks, neural plasma is motivated by aspects of high-level behavior and reasoning in the presence of uncertainty. The basic principles of the proposed model apply to other supervised learning algorithms that provide explicit classification confidence values. The empirical evaluation of this new technique is based on benchmarking experiments involving data sets from biotechnology that are characterized by the small-n-large-p problem. The presented study exposes a comprehensive methodology and is seen as a first step in exploring different aspects of this methodology.IFIP International Conference on Artificial Intelligence in Theory and Practice - Neural NetsRed de Universidades con Carreras en Informática (RedUNCI

    Instance-based concept learning from multiclass DNA microarray data

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    BACKGROUND: Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN) approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance. RESULTS: We investigated the performance of instance-based classifiers, including a NN classifier able to assign a degree of class membership to each sample. This model alleviates a major problem of conventional instance-based learners, namely the lack of confidence values for predictions. The model translates the distances to the nearest neighbors into 'confidence scores'; the higher the confidence score, the closer is the considered instance to a pre-defined class. We applied the models to three real gene expression data sets and compared them with state-of-the-art methods for classifying microarray data of multiple classes, assessing performance using a statistical significance test that took into account the data resampling strategy. Simple NN classifiers performed as well as, or significantly better than, their more intricate competitors. CONCLUSION: Given its highly intuitive underlying principles – simplicity, ease-of-use, and robustness – the k-NN classifier complemented by a suitable distance-weighting regime constitutes an excellent alternative to more complex models for multiclass microarray data sets. Instance-based classifiers using weighted distances are not limited to microarray data sets, but are likely to perform competitively in classifications of high-dimensional biological data sets such as those generated by high-throughput mass spectrometry

    Neural plasma

    Get PDF
    This paper presents a novel type of artificial neural network, called neural plasma, which is tailored for classification tasks involving few observations with a large number of variables. Neural plasma learns to adapt its classification confidence by generating artificial training data as a function of its confidence in previous decisions. In contrast to multilayer perceptrons and similar techniques, which are inspired by topological and operational aspects of biological neural networks, neural plasma is motivated by aspects of high-level behavior and reasoning in the presence of uncertainty. The basic principles of the proposed model apply to other supervised learning algorithms that provide explicit classification confidence values. The empirical evaluation of this new technique is based on benchmarking experiments involving data sets from biotechnology that are characterized by the small-n-large-p problem. The presented study exposes a comprehensive methodology and is seen as a first step in exploring different aspects of this methodology.IFIP International Conference on Artificial Intelligence in Theory and Practice - Neural NetsRed de Universidades con Carreras en Informática (RedUNCI

    Self-organizing incremental neural networks for continual learning

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    Continual learning systems can adapt to new tasks, changes in data distributions, and new information that becomes incrementally available over time. The key challenge for such systems is how to mitigate catastrophic forgetting, i.e., how to prevent the loss of previously learned knowledge when new tasks need to be solved. In our research, we investigate self-organizing incremental neural networks (SOINN) for continual learning from both stationary and non-stationary data. We have developed a new algorithm, SOINN+, that learns to forget irrelevant nodes and edges and is robust to noise

    Quo Vadis, Artificial Intelligence?

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    Since its conception in the mid 1950s, artificial intelligence with its great ambition to understand and emulate intelligence in natural and artificial environments alike is now a truly multidisciplinary field that reaches out and is inspired by a great diversity of other fields. Rapid advances in research and technology in various fields have created environments into which artificial intelligence could embed itself naturally and comfortably. Neuroscience with its desire to understand nervous systems of biological organisms and systems biology with its longing to comprehend, holistically, the multitude of complex interactions in biological systems are two such fields. They target ideals artificial intelligence has dreamt about for a long time including the computer simulation of an entire biological brain or the creation of new life forms from manipulations of cellular and genetic information in the laboratory. The scope for artificial intelligence in neuroscience and systems biology is extremely wide. This article investigates the standing of artificial intelligence in relation to neuroscience and systems biology and provides an outlook at new and exciting challenges for artificial intelligence in these fields. These challenges include, but are not necessarily limited to, the ability to learn from other projects and to be inventive, to understand the potential and exploit novel computing paradigms and environments, to specify and adhere to stringent standards and robust statistical frameworks, to be integrative, and to embrace openness principles

    Quo Vadis, Artificial Intelligence?

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    Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni

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    Schistosomiasis is a neglected tropical disease that currently affects over 250 million individuals worldwide. In the absence of an immunoprophylactic vaccine and the recognition that mono-chemotherapeutic control of schistosomiasis by praziquantel has limitations, new strategies for managing disease burden are urgently needed. A better understanding of schistosome biology could identify previously undocumented areas suitable for the development of novel interventions. Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within the Schistosoma mansoni genome. We find that G4 are present in both intragenic and intergenic regions of the seven autosomes as well as the sex-defining allosome pair. Amongst intragenic regions, G4 are particularly enriched in 3´ UTR regions. Gene Ontology (GO) term analysis evidenced significant G4 enrichment in the wnt signalling pathway (p<0.05) and PQS oligonucleotides synthetically derived from wnt-related genes resolve into parallel and anti-parallel G4 motifs as elucidated by circular dichroism (CD) spectroscopy. Finally, utilising a single chain anti-G4 antibody called BG4, we confirm the in situ presence of G4 within both adult female and male worm nuclei. These results collectively suggest that G4-targeted compounds could be tested as novel anthelmintic agents and highlights the possibility that G4-stabilizing molecules could be progressed as candidates for the treatment of schistosomiasi
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