A spectral dissimilarity constrained nonnegative matrix factorization based cancer screening algorithm from hyperspectral fluorescence images

Bioluminescence from living body can help screen cancers without penetrating the inside of living body. Hyperspectral imaging technique is a novel way to obtain physical meaningful signatures, providing very fine spectral resolution, that can be very used in distinguishing different kinds of materials, and have been widely used in remote sensing field. Fluorescence imaging has proved effective in monitoring probable cancer cells. Recent work has made great progress on the hyperspectral fluorescence imaging techniques, which makes the elaborate spectral observation of cancer areas possible. So how to propose the proper hyperspectral image processing methods to handle the hyperspectral medical images is of practical importance. Cancer cells would be distinguishable with normal ones when the living body is injected with fluorescence, which helps organs inside the living body emit lights, and then the signals can be catched by the passive imaging sensor. Spectral unmixing technique in hyperspectral remote sensing has been introduced to detect the probable cancer areas. However, since the cancer areas are small and the normal areas and the cancer ares may not pure pixels so that the predefined endmembers would not available. In this case, the classic blind signals separation methods are applicable. Considering the spectral dissimilarity between cancer and normal cells, a novel spectral dissimilarity constrained based NMF method is proposed in this paper for cancer screening from fluorescence hyperspectral images. Experiments evaluate the performance of variable NMF based method and our proposed spectral dissimilarity based NMF methods: 1) The NMF methods do perform well in detect the cancer areas inside the living body; 2) The spectral dissimilarity constrained NMF present more accurate cancer areas; 3) The spectral dissimilarity constraint presents better performance in different SNR and different purities of the mixing endmembers. © 2012 IEEE

Human Microbe-Disease Association Prediction With Graph Regularized Non-Negative Matrix Factorization

A microbe is a microscopic organism which may exists in its single-celled form or in a colony of cells. In recent years, accumulating researchers have been engaged in the field of uncovering microbe-disease associations since microbes are found to be closely related to the prevention, diagnosis, and treatment of many complex human diseases. As an effective supplement to the traditional experiment, more and more computational models based on various algorithms have been proposed for microbe-disease association prediction to improve efficiency and cost savings. In this work, we developed a novel predictive model of Graph Regularized Non-negative Matrix Factorization for Human Microbe-Disease Association prediction (GRNMFHMDA). Initially, microbe similarity and disease similarity were constructed on the basis of the symptom-based disease similarity and Gaussian interaction profile kernel similarity for microbes and diseases. Subsequently, it is worth noting that we utilized a preprocessing step in which unknown microbe-disease pairs were assigned associated likelihood scores to avoid the possible negative impact on the prediction performance. Finally, we implemented a graph regularized non-negative matrix factorization framework to identify potential associations for all diseases simultaneously. To assess the performance of our model, cross validations including global leave-one-out cross validation (LOOCV) and local LOOCV were implemented. The AUCs of 0.8715 (global LOOCV) and 0.7898 (local LOOCV) proved the reliable performance of our computational model. In addition, we carried out two types of case studies on three different human diseases to further analyze the prediction performance of GRNMFHMDA, in which most of the top 10 predicted disease-related microbes were verified by database HMDAD or experimental literatures

Multi-focus image fusion based on non-negative sparse representation and patch-level consistency rectification

Most existing sparse representation-based (SR) fusion methods consider the local information of each image patch independently during fusion. Some spatial artifacts are easily introduced to the fused image. A sliding window technology is often employed by these methods to overcome this issue. However, this comes at the cost of high computational complexity. Alternatively, we come up with a novel multi-focus image fusion method that takes full consideration of the strong correlations among spatially adjacent image patches with NO need for a sliding window. To this end, a non-negative SR model with local consistency constraint (CNNSR) on the representation coefficients is first constructed to encode each image patch. Then a patch-level consistency rectification strategy is presented to merge the input image patches, by which the spatial artifacts in the fused images are greatly reduced. As well, a compact non-negative dictionary is constructed for the CNNSR model. Experimental results demonstrate that the proposed fusion method outperforms some state-of-the art methods. Moreover, the proposed method is computationally efficient, thereby facilitating real-world applications

Manifold regularized discriminative nonnegative matrix factorization with fast gradient descent

Nonnegative matrix factorization (NMF) has become a popular data-representation method and has been widely used in image processing and pattern-recognition problems. This is because the learned bases can be interpreted as a natural parts-based representation of data and this interpretation is consistent with the psychological intuition of combining parts to form a whole. For practical classification tasks, however, NMF ignores both the local geometry of data and the discriminative information of different classes. In addition, existing research results show that the learned basis is unnecessarily parts-based because there is neither explicit nor implicit constraint to ensure the representation parts-based. In this paper, we introduce the manifold regularization and the margin maximization to NMF and obtain the manifold regularized discriminative NMF (MD-NMF) to overcome the aforementioned problems. The multiplicative update rule (MUR) can be applied to optimizing MD-NMF, but it converges slowly. In this paper, we propose a fast gradient descent (FGD) to optimize MD-NMF. FGD contains a Newton method that searches the optimal step length, and thus, FGD converges much faster than MUR. In addition, FGD includes MUR as a special case and can be applied to optimizing NMF and its variants. For a problem with 165 samples in R1600 , FGD converges in 28 s, while MUR requires 282 s. We also apply FGD in a variant of MD-NMF and experimental results confirm its efficiency. Experimental results on several face image datasets suggest the effectiveness of MD-NMF. © 2011 IEEE

NMF-based compositional models for audio source separation

학위논문 (박사)-- 서울대학교 대학원 : 전기·컴퓨터공학부, 2017. 2. 김남수.Many classes of data can be represented by constructive combinations of parts. Most signal and data from nature have nonnegative values and can be explained and reconstructed by constructive models. By the constructive models, only the additive combination is allowed and it does not result in subtraction of parts. The compositional models include dictionary learning, exemplar-based approaches, and nonnegative matrix factorization (NMF). Compositional models are desirable in many areas including image or visual signal processing, text information processing, audio signal processing, and music information retrieval. In this dissertation, we choose NMF for compositional models and NMF-based target source separation is performed for the application. The target source separation is the extraction or reconstruction of the target signals in the mixture signals which consists with the target and interfering signals. The target source separation can be thought as blind source separation (BSS). BSS aims that the original unknown source signals are extracted without knowing or with very limited information. However, in these days, much of prior information is frequently utilized, and various approaches have been proposed for single channel source separation. NMF basically approximates a nonnegative data matrix V with a product of nonnegative basis and encoding matrices W and H, i.e., V WH. Since both W and H are nonnegative, NMF often leads to a part based representation of the data. The methods based on NMF have shown impressive results in single channel source separation The objective function of NMF is generally presented Euclidean distant, Kullback-Leibler divergence, and Itakura-saito divergence. Many optimization methods have been proposed and utilized, e.g., multiplicative update rule, projected gradient descent and NeNMF. However, NMF-based audio source separation has some issues as follows: non-uniqueness of the bases, a high dependence to the prior information, the overlapped subspace between target bases and interfering bases, a disregard of the encoding vectors from the training phase, and insucient analysis of sparse NMF. In this dissertation, we propose new approaches to resolve the above issues. In section 4, we propose a novel speech enhancement method that combines the statistical model-based enhancement scheme with the NMF-based gain function. For a better performance in time-varying noise environments, both the speech and noise bases of NMF are adapted simultaneously with the help of the estimated speech presence probability. In section 5, we propose a discriminative NMF (DNMF) algorithm which exploits the reconstruction error for the interfering signals as well as the target signal based on target bases. In section 6, we propose an approach to robust bases estimation in which an incremental strategy is adopted. Based on an analogy between clustering and NMF analysis, we incrementally estimate the NMF bases similar to the modied k-means and Linde-Buzo-Gray algorithms popular in the data clustering area. In Section 7, the distribution of the encoding vector is modeled as a multivariate exponential PDF (MVE) with a single scaling factor for each source. In Section 8, several sparse penalty terms for NMF are analyzed and compared in terms of signal to distortion ratio, sparseness of encoding vectors, reconstruction error, and entropy of basis vectors. The new objective function which applied sparse representation and discriminative NMF (DNMF) is also proposed.1 Introduction 1 1.1 Audio source separation 1 1.2 Speech enhancement 3 1.3 Measurements 4 1.4 Outline of the dissertation 6 2 Compositional model and NMF 9 2.1 Compositional model 9 2.2 NMF 14 2.2.1 Update rules: MuR, PGD 16 2.2.2 Modied NMF 20 3 NMF-based audio source separation and issues 23 3.1 NMF-based audio source separation 23 3.2 Problems of NMF in audio source separation 26 3.2.1 A high dependency to the prior knowledge 26 3.2.2 A overlapped subspace between the target and interfering basis matrices 28 3.2.3 A non-uniqueness of the bases 29 3.2.4 A prior knowledge of the encoding vectors 30 3.2.5 Sparse NMF for the source separation 32 4 Online bases update 33 4.1 Introduction 33 4.2 NMF-based speech enhancement using spectral gain function 36 4.3 Speech enhancement combining statistical model-based and NMFbased methods with the on-line bases update 38 4.3.1 On-line update of speech and noise bases 40 4.3.2 Determining maximum update rates 42 4.4 Experiment result 43 5 Discriminative NMF 47 5.1 Introduction 47 5.2 Discriminative NMF utilizing cross reconstruction error 48 5.2.1 DNMF using the reconstruction error of the other source 49 5.2.2 DNMF using the interference factors 50 5.3 Experiment result 52 6 Incremental approach for bases estimate 57 6.1 Introduction 57 6.2 Incremental approach based on modied k-means clustering and Linde-Buzo-Gray algorithm 59 6.2.1 Based on modied k-means clustering 59 6.2.2 LBG based incremental approach 62 6.3 Experiment result 63 6.3.1 Modied k-means clustering based approach 63 6.3.2 LBG based approach 66 7 Prior model of encoding vectors 77 7.1 Introduction 77 7.2 Prior model of encoding vectors based on multivariate exponential distribution 78 7.3 Experiment result 82 8 Conclusions 87 Bibliography 91 국문초록 105Docto