Hybrid Discrete Wavelet Transform and Gabor Filter Banks Processing for Features Extraction from Biomedical Images

A new methodology for automatic feature extraction from biomedical images and subsequent classification is presented. The approach exploits the spatial orientation of high-frequency textural features of the processed image as determined by a two-step process. First, the two-dimensional discrete wavelet transform(DWT) is applied to obtain the HH high-frequency subband image. Then, a Gabor filter bank is applied to the latter at different frequencies and spatial orientations to obtain new Gabor-filtered image whose entropy and uniformity are computed. Finally, the obtained statistics are fed to a support vector machine (SVM) binary classifier. The approach was validated on mammograms, retina, and brain magnetic resonance (MR) images.The obtained classification accuracies show better performance in comparison to common approaches that use only the DWT or Gabor filter banks for feature extraction

Image-Level and Group-Level Models for Drosophila Gene Expression Pattern Annotation

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison. Results: We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach. Conclusion: In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation

Image-level and group-level models for Drosophila gene expression pattern annotation

abstract: Background Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison. Results We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach. Conclusion In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.The electronic version of this article is the complete one and can be found online at: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-35

Hyperfeatures - Multilevel Local Coding for Visual Recognition

Histograms of local appearance descriptors are a popular representation for visual recognition. They are highly discriminant and they have good resistance to local occlusions and to geometric and photometric variations, but they are not able to exploit spatial co-occurrence statistics of features at scales larger than their local input patches. We present a new multilevel visual representation, `hyperfeatures', that is designed to remedy this. The basis of the work is the familiar notion that to detect object parts, in practice it often suffices to detect co-occurrences of more local object fragments a process that can be formalized as comparison (vector quantization) of image patches against a codebook of known fragments, followed by local aggregation of the resulting codebook membership vectors to detect co-occurrences. This process converts collections of local image descriptor vectors into slightly less local histogram vectors higher-level but spatially coarser descriptors. Our central observation is that it can therefore be iterated, and that doing so captures and codes ever larger assemblies of object parts and increasingly abstract or `semantic' image properties. This repeated nonlinear `folding' is essentially different from that of hierarchical models such as Convolutional Neural Networks and HMAX, being based on repeated comparison to local prototypes and accumulation of co-occurrence statistics rather than on repeated convolution and rectification. We formulate the hyperfeatures model and study its performance under several different image coding methods including clustering based Vector Quantization, Gaussian Mixtures, and combinations of these with Latent Discriminant Analysis. We find that the resulting high-level features provide improved performance in several object image and texture image classification tasks

Dynamic texture recognition using time-causal and time-recursive spatio-temporal receptive fields

This work presents a first evaluation of using spatio-temporal receptive fields from a recently proposed time-causal spatio-temporal scale-space framework as primitives for video analysis. We propose a new family of video descriptors based on regional statistics of spatio-temporal receptive field responses and evaluate this approach on the problem of dynamic texture recognition. Our approach generalises a previously used method, based on joint histograms of receptive field responses, from the spatial to the spatio-temporal domain and from object recognition to dynamic texture recognition. The time-recursive formulation enables computationally efficient time-causal recognition. The experimental evaluation demonstrates competitive performance compared to state-of-the-art. Especially, it is shown that binary versions of our dynamic texture descriptors achieve improved performance compared to a large range of similar methods using different primitives either handcrafted or learned from data. Further, our qualitative and quantitative investigation into parameter choices and the use of different sets of receptive fields highlights the robustness and flexibility of our approach. Together, these results support the descriptive power of this family of time-causal spatio-temporal receptive fields, validate our approach for dynamic texture recognition and point towards the possibility of designing a range of video analysis methods based on these new time-causal spatio-temporal primitives.Comment: 29 pages, 16 figure

Self-supervised Spatio-temporal Representation Learning for Videos by Predicting Motion and Appearance Statistics

We address the problem of video representation learning without human-annotated labels. While previous efforts address the problem by designing novel self-supervised tasks using video data, the learned features are merely on a frame-by-frame basis, which are not applicable to many video analytic tasks where spatio-temporal features are prevailing. In this paper we propose a novel self-supervised approach to learn spatio-temporal features for video representation. Inspired by the success of two-stream approaches in video classification, we propose to learn visual features by regressing both motion and appearance statistics along spatial and temporal dimensions, given only the input video data. Specifically, we extract statistical concepts (fast-motion region and the corresponding dominant direction, spatio-temporal color diversity, dominant color, etc.) from simple patterns in both spatial and temporal domains. Unlike prior puzzles that are even hard for humans to solve, the proposed approach is consistent with human inherent visual habits and therefore easy to answer. We conduct extensive experiments with C3D to validate the effectiveness of our proposed approach. The experiments show that our approach can significantly improve the performance of C3D when applied to video classification tasks. Code is available at https://github.com/laura-wang/video_repres_mas.Comment: CVPR 201