Type-2 Fuzzy PCA Approach in Extracting Salient Features for Molecular Cancer Diagnostics and Prognostics

Robust PCA with Lw,∗ and L2,1 Norms: A Novel Method for Low-Quality Retinal Image Enhancement

Nonmydriatic retinal fundus images often suffer from quality issues and artifacts due to ocular or systemic comorbidities, leading to potential inaccuracies in clinical diagnoses. In recent times, deep learning methods have been widely employed to improve retinal image quality. However, these methods often require large datasets and lack robustness in clinical settings. Conversely, the inherent stability and adaptability of traditional unsupervised learning methods, coupled with their reduced reliance on extensive data, render them more suitable for real-world clinical applications, particularly in the limited data context of high noise levels or a significant presence of artifacts. However, existing unsupervised learning methods encounter challenges such as sensitivity to noise and outliers, reliance on assumptions like cluster shapes, and difficulties with scalability and interpretability, particularly when utilized for retinal image enhancement. To tackle these challenges, we propose a novel robust PCA (RPCA) method with low-rank sparse decomposition that also integrates affine transformations τi, weighted nuclear norm, and the L2,1 norms, aiming to overcome existing method limitations and to achieve image quality improvement unseen by these methods. We employ the weighted nuclear norm (Lw,∗) to assign weights to singular values to each retinal images and utilize the L2,1 norm to eliminate correlated samples and outliers in the retinal images. Moreover, τi is employed to enhance retinal image alignment, making the new method more robust to variations, outliers, noise, and image blurring. The Alternating Direction Method of Multipliers (ADMM) method is used to optimally determine parameters, including τi, by solving an optimization problem. Each parameter is addressed separately, harnessing the benefits of ADMM. Our method introduces a novel parameter update approach and significantly improves retinal image quality, detecting cataracts, and diabetic retinopathy. Simulation results confirm our method's superiority over existing state-of-the-art methods across various datasets.

Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference

The normalization of RNA sequencing data is a primary step for downstream analysis. The most popular method used for the normalization is the trimmed mean of M values (TMM) and DESeq. The TMM tries to trim away extreme log fold changes of the data to normalize the raw read counts based on the remaining non-deferentially expressed genes. However, the major problem with the TMM is that the values of trimming factor M are heuristic. This paper tries to estimate the adaptive value of M in TMM based on Jaeckel's Estimator, and each sample acts as a reference to find the scale factor of each sample. The presented approach is validated on SEQC, MAQC2, MAQC3, PICKRELL and two simulated datasets with two-group and three-group conditions by varying the percentage of differential expression and the number of replicates. The performance of the present approach is compared with various state-of-the-art methods, and it is better in terms of area under the receiver operating characteristic curve and differential expression.

Survival prediction for oral tongue cancer patients via probabilistic genetic algorithm optimized neural network models

OBJECTIVES

High throughput pre-treatment imaging features may predict radiation treatment outcome and guide individualized treatment in radiotherapy (RT). Given relatively small patient sample (as compared with high dimensional imaging features), identifying potential prognostic imaging biomarkers is typically challenging. We aimed to develop robust machine learning methods for patient survival prediction using pre-treatment quantitative CT image features for a subgroup of head-and-neck cancer patients.

METHODS

Three neural network models, including back propagation (BP), Genetic Algorithm-Back Propagation (GA-BP), and Probabilistic Genetic Algorithm-Back Propagation (PGA-BP) neural networks were trained to simulate association between patient survival and radiomics data in radiotherapy. To evaluate the models, a subgroup of 59 head-and-neck patients with primary cancers in oral tongue area were utilized. Quantitative image features were extracted from planning CT images, a novel t-Distributed Stochastic Neighbor Embedding (t-SNE) method was used to remove irrelevant and redundant image features before fed into the network models. 80% patients were used to train the models, and remaining 20% were used for evaluation.

RESULTS

Of the three supervised machine-learning methods studied, PGA-BP yielded the best predictive performance. The reported actual patient survival interval of 30.5 ± 21.3 months, the predicted survival times were 47.3 ± 38.8, 38.5 ± 13.5 and 29.9 ± 15.3 months using the traditional PCA. Combining with the novel t-SNE dimensionality reduction algorithm, the predicted survival intervals are 35.8 ± 15.2, 32.3 ± 13.1 and 31.6 ± 15.8 months for the BP, GA-BP and PGA-BP neural network models, respectively.

CONCLUSION

The work demonstrated that the proposed probabilistic genetic algorithm optimized neural network models, integrating with the t-SNE dimensionality reduction algorithm, achieved accurate prediction of patient survival.

ADVANCES IN KNOWLEDGE

The proposed PGA-BP neural network, integrating with an advanced dimensionality reduction algorithm (t-SNE), improved patient survival prediction accuracy using pre-treatment quantitative CT image features of head-and-neck cancer patients.