DDA-SKF: Predicting Drug–Disease Associations Using Similarity Kernel Fusion

Drug repositioning provides a promising and efficient strategy to discover potential associations between drugs and diseases. Many systematic computational drug-repositioning methods have been introduced, which are based on various similarities of drugs and diseases. In this work, we proposed a new computational model, DDA-SKF (drug–disease associations prediction using similarity kernels fusion), which can predict novel drug indications by utilizing similarity kernel fusion (SKF) and Laplacian regularized least squares (LapRLS) algorithms. DDA-SKF integrated multiple similarities of drugs and diseases. The prediction performances of DDA-SKF are better, or at least comparable, to all state-of-the-art methods. The DDA-SKF can work without sufficient similarity information between drug indications. This allows us to predict new purpose for orphan drugs. The source code and benchmarking datasets are deposited in a GitHub repository (https://github.com/GCQ2119216031/DDA-SKF).

ILPMDA: Predicting miRNA–Disease Association Based on Improved Label Propagation

MicroRNAs (miRNAs) are small non-coding RNAs that have been demonstrated to be related to numerous complex human diseases. Considerable studies have suggested that miRNAs affect many complicated bioprocesses. Hence, the investigation of disease-related miRNAs by utilizing computational methods is warranted. In this study, we presented an improved label propagation for miRNA–disease association prediction (ILPMDA) method to observe disease-related miRNAs. First, we utilized similarity kernel fusion to integrate different types of biological information for generating miRNA and disease similarity networks. Second, we applied the weighted k-nearest known neighbor algorithm to update verified miRNA–disease association data. Third, we utilized improved label propagation in disease and miRNA similarity networks to make association prediction. Furthermore, we obtained final prediction scores by adopting an average ensemble method to integrate the two kinds of prediction results. To evaluate the prediction performance of ILPMDA, two types of cross-validation methods and case studies on three significant human diseases were implemented to determine the accuracy and effectiveness of ILPMDA. All results demonstrated that ILPMDA had the ability to discover potential miRNA–disease associations.

Task-Adaptive Embedding Learning with Dynamic Kernel Fusion for Few-Shot Remote Sensing Scene Classification

The central goal of few-shot scene classification is to learn a model that can generalize well to a novel scene category (UNSEEN) from only one or a few labeled examples. Recent works in the remote sensing (RS) community tackle this challenge by developing algorithms in a meta-learning manner. However, most prior approaches have either focused on rapidly optimizing a meta-learner or aimed at finding good similarity metrics while overlooking the embedding power. Here we propose a novel Task-Adaptive Embedding Learning (TAEL) framework that complements the existing methods by giving full play to feature embedding’s dual roles in few-shot scene classification - representing images and constructing classifiers in the embedding space. First, we design a lightweight network that enriches the diversity and expressive capacity of embeddings by dynamically fusing information from multiple kernels. Second, we present a task-adaptive strategy that helps to generate more discriminative representations by transforming the universal embeddings into task-specific embeddings via a self-attention mechanism. We evaluate our model in the standard few-shot learning setting on two challenging datasets: NWPU-RESISC4 and RSD46-WHU. Experimental results demonstrate that, on all tasks, our method achieves state-of-the-art performance by a significant margin.

Over 100x Faster Bootstrapping in Fully Homomorphic Encryption through Memory-centric Optimization with GPUs

Fully Homomorphic encryption (FHE) has been gaining in popularity as an emerging means of enabling an unlimited number of operations in an encrypted message without decryption. A major drawback of FHE is its high computational cost. Specifically, a bootstrapping step that refreshes the noise accumulated through consequent FHE operations on the ciphertext can even take minutes of time. This significantly limits the practical use of FHE in numerous real applications.By exploiting the massive parallelism available in FHE, we demonstrate the first instance of the implementation of a GPU for bootstrapping CKKS, one of the most promising FHE schemes supporting the arithmetic of approximate numbers. Through analyzing CKKS operations, we discover that the major performance bottleneck is their high main-memory bandwidth requirement, which is exacerbated by leveraging existing optimizations targeted to reduce the required computation. These observations motivate us to utilize memory-centric optimizations such as kernel fusion and reordering primary functions extensively.Our GPU implementation shows a 7.02× speedup for a single CKKS multiplication compared to the state-of-the-art GPU implementation and an amortized bootstrapping time of 0.423us per bit, which corresponds to a speedup of 257× over a single-threaded CPU implementation. By applying this to logistic regression model training, we achieved a 40.0× speedup compared to the previous 8-thread CPU implementation with the same data.

Discrete Multiple Kernel k-means

The multiple kernel k-means (MKKM) and its variants utilize complementary information from different kernels, achieving better performance than kernel k-means (KKM). However, the optimization procedures of previous works all comprise two stages, learning the continuous relaxed label matrix and obtaining the discrete one by extra discretization procedures. Such a two-stage strategy gives rise to a mismatched problem and severe information loss. To address this problem, we elaborate a novel Discrete Multiple Kernel k-means (DMKKM) model solved by an optimization algorithm that directly obtains the cluster indicator matrix without subsequent discretization procedures. Moreover, DMKKM can strictly measure the correlations among kernels, which is capable of enhancing kernel fusion by reducing redundancy and improving diversity. What’s more, DMKKM is parameter-free avoiding intractable hyperparameter tuning, which makes it feasible in practical applications. Extensive experiments illustrated the effectiveness and superiority of the proposed model.

An Accurate Tool for Uncovering Cancer Subtypes by Fast Kernel Learning Method to Integrate Multiple Profile Data

In recent years, cancer has become a severe threat to human health. If we can accurately identify the subtypes of cancer, it will be of great significance to the research of anti-cancer drugs, the development of personalized treatment methods, and finally conquer cancer. In this paper, we obtain three feature representation datasets (gene expression profile, isoform expression and DNA methylation data) on lung cancer and renal cancer from the Broad GDAC, which collects the standardized data extracted from The Cancer Genome Atlas (TCGA). Since the feature dimension is too large, Principal Component Analysis (PCA) is used to reduce the feature vector, thus eliminating the redundant features and speeding up the operation speed of the classification model. By multiple kernel learning (MKL), we use Kernel target alignment (KTA), fast kernel learning (FKL), Hilbert-Schmidt Independence Criterion (HSIC), Mean to calculate the weight of kernel fusion. Finally, we put the combined kernel function into the support vector machine (SVM) and get excellent results. Among them, in the classification of renal cell carcinoma subtypes, the maximum accuracy can reach 0.978 by using the method of MKL (HSIC calculation weight), while in the classification of lung cancer subtypes, the accuracy can even reach 0.990 with the same method (FKL calculation weight).