A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Neuron-level fuzzy memoization in RNNs

The final publication is available at ACM via http://dx.doi.org/10.1145/3352460.3358309Recurrent Neural Networks (RNNs) are a key technology for applications such as automatic speech recognition or machine translation. Unlike conventional feed-forward DNNs, RNNs remember past information to improve the accuracy of future predictions and, therefore, they are very effective for sequence processing problems. For each application run, each recurrent layer is executed many times for processing a potentially large sequence of inputs (words, images, audio frames, etc.). In this paper, we make the observation that the output of a neuron exhibits small changes in consecutive invocations. We exploit this property to build a neuron-level fuzzy memoization scheme, which dynamically caches the output of each neuron and reuses it whenever it is predicted that the current output will be similar to a previously computed result, avoiding in this way the output computations. The main challenge in this scheme is determining whether the new neuron's output for the current input in the sequence will be similar to a recently computed result. To this end, we extend the recurrent layer with a much simpler Bitwise Neural Network (BNN), and show that the BNN and RNN outputs are highly correlated: if two BNN outputs are very similar, the corresponding outputs in the original RNN layer are likely to exhibit negligible changes. The BNN provides a low-cost and effective mechanism for deciding when fuzzy memoization can be applied with a small impact on accuracy. We evaluate our memoization scheme on top of a state-of-the-art accelerator for RNNs, for a variety of different neural networks from multiple application domains. We show that our technique avoids more than 24.2% of computations, resulting in 18.5% energy savings and 1.35x speedup on average.Peer ReviewedPostprint (author's final draft

Autoencoding the Retrieval Relevance of Medical Images

Content-based image retrieval (CBIR) of medical images is a crucial task that can contribute to a more reliable diagnosis if applied to big data. Recent advances in feature extraction and classification have enormously improved CBIR results for digital images. However, considering the increasing accessibility of big data in medical imaging, we are still in need of reducing both memory requirements and computational expenses of image retrieval systems. This work proposes to exclude the features of image blocks that exhibit a low encoding error when learned by a $n/p/n$ autoencoder ($p\!<\!n$). We examine the histogram of autoendcoding errors of image blocks for each image class to facilitate the decision which image regions, or roughly what percentage of an image perhaps, shall be declared relevant for the retrieval task. This leads to reduction of feature dimensionality and speeds up the retrieval process. To validate the proposed scheme, we employ local binary patterns (LBP) and support vector machines (SVM) which are both well-established approaches in CBIR research community. As well, we use IRMA dataset with 14,410 x-ray images as test data. The results show that the dimensionality of annotated feature vectors can be reduced by up to 50% resulting in speedups greater than 27% at expense of less than 1% decrease in the accuracy of retrieval when validating the precision and recall of the top 20 hits.Comment: To appear in proceedings of The 5th International Conference on Image Processing Theory, Tools and Applications (IPTA'15), Nov 10-13, 2015, Orleans, Franc