Artificial Neural Network Pruning to Extract Knowledge

Artificial Neural Networks (NN) are widely used for solving complex problems from medical diagnostics to face recognition. Despite notable successes, the main disadvantages of NN are also well known: the risk of overfitting, lack of explainability (inability to extract algorithms from trained NN), and high consumption of computing resources. Determining the appropriate specific NN structure for each problem can help overcome these difficulties: Too poor NN cannot be successfully trained, but too rich NN gives unexplainable results and may have a high chance of overfitting. Reducing precision of NN parameters simplifies the implementation of these NN, saves computing resources, and makes the NN skills more transparent. This paper lists the basic NN simplification problems and controlled pruning procedures to solve these problems. All the described pruning procedures can be implemented in one framework. The developed procedures, in particular, find the optimal structure of NN for each task, measure the influence of each input signal and NN parameter, and provide a detailed verbal description of the algorithms and skills of NN. The described methods are illustrated by a simple example: the generation of explicit algorithms for predicting the results of the US presidential election.Comment: IJCNN 202

Deep learning for extracting protein-protein interactions from biomedical literature

State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN compares favorably to the state-of-the-art rich-feature and single-kernel based methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on "difficult" instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.Comment: Accepted for publication in Proceedings of the 2017 Workshop on Biomedical Natural Language Processing, 10 pages, 2 figures, 6 table

A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community

In recent years, deep learning (DL), a re-branding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, natural language processing, etc. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV; e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should be aware of, if not at the leading edge of, of advancements like DL. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as it relates to (i) inadequate data sets, (ii) human-understandable solutions for modelling physical phenomena, (iii) Big Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote Sensin

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

DeeSIL: Deep-Shallow Incremental Learning

Incremental Learning (IL) is an interesting AI problem when the algorithm is assumed to work on a budget. This is especially true when IL is modeled using a deep learning approach, where two com- plex challenges arise due to limited memory, which induces catastrophic forgetting and delays related to the retraining needed in order to incorpo- rate new classes. Here we introduce DeeSIL, an adaptation of a known transfer learning scheme that combines a fixed deep representation used as feature extractor and learning independent shallow classifiers to in- crease recognition capacity. This scheme tackles the two aforementioned challenges since it works well with a limited memory budget and each new concept can be added within a minute. Moreover, since no deep re- training is needed when the model is incremented, DeeSIL can integrate larger amounts of initial data that provide more transferable features. Performance is evaluated on ImageNet LSVRC 2012 against three state of the art algorithms. Results show that, at scale, DeeSIL performance is 23 and 33 points higher than the best baseline when using the same and more initial data respectively

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