The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both compounds and target proteins. While various prediction methods employ different feature combinations, both molecular-based and network-based models encounter the common obstacle of incomplete feature representations. Thus, a promising solution to this issue is to fully integrate all relevant CPI features. This study proposed a novel model named MCPI, which is designed to improve the prediction performance of CPI by integrating multiple sources of information, including the PPI network, CCI network, and structural features of CPI. The results of the study indicate that the MCPI model outperformed other existing methods for predicting CPI on public datasets. Furthermore, the study has practical implications for drug development, as the model was applied to search for potential inhibitors among FDA-approved drugs in response to the SARS-CoV-2 pandemic. The prediction results were then validated through the literature, suggesting that the MCPI model could be a useful tool for identifying potential drug candidates. Overall, this study has the potential to advance our understanding of CPI and guide drug development efforts.

Contrastive Language-Image Pretraining (CLIP) consists of two models trained in parallel. During training, (image, text) pairs are fed into the respective models, and both output a 512-dimensional vector embedding that represents the respective image/text in vector space. The contrastive component takes these two vector embeddings and calculates the model loss as the difference (e.g., contrast) between the two vectors. Both models are then optimized to minimize this difference and therefore learn how to embed similar (image, text) pairs into a similar vector space. After this contrastive pretraining process, we are left with CLIP, a multi-modal model capable of understanding both language and images via a shared vector space.

Random feature methods have been successful in various machine learning tasks, are easy to compute, and come with theoretical accuracy bounds. They serve as an alternative approach to standard neural networks since they can represent similar function spaces without a costly training phase. However, for accuracy, random feature methods require more measurements than trainable parameters, limiting their use for data-scarce applications or problems in scientific machine learning. This paper introduces the sparse random feature method that learns parsimonious random feature models utilizing techniques from compressive sensing. We provide uniform bounds on the approximation error for functions in a reproducing kernel Hilbert space depending on the number of samples and the distribution of features. The error bounds improve with additional structural conditions, such as coordinate sparsity, compact clusters of the spectrum, or rapid spectral decay.

We propose random ReLU features models in this work. Its motivation is rooted in both kernel methods and neural networks. We prove the universality and generalization performance of random ReLU features. Parallel to Barron's theorem, we consider the ReLU feature class, extended from the reproducing kernel Hilbert space of random ReLU features, and prove a strong quantitative approximation theorem, where both inner weights and outer weights of the the neural network with ReLU nodes as an approximator are bounded by constants. We also prove a similar approximation theorem for composition of functions in ReLU feature class by multi-layer ReLU networks. Separation theorem between ReLU feature class and their composition is proved as a consequence of separation between shallow and deep networks. These results reveal nice properties of ReLU nodes from the view of approximation theory, providing support for regularization on weights of ReLU networks and for the use of random ReLU features in practice. Our experiments confirm that the performance of random ReLU features is comparable with random Fourier features.

The random features method is an efficient method to approximate the kernel function. In this paper, we propose novel random features called "alternating circulant random features,'' which consist of a random mixture of independent random structured matrices. Existing fast random features exploit random sign flipping to reduce the correlation between features. Sign flipping works well on random Fourier features for real-valued shift-invariant kernels because the corresponding weight distribution is symmetric. However, this method cannot be applied to random Laplace features directly because the distribution is not symmetric. The method proposed herein yields alternating circulant random features, with the correlation between features being reduced through the random sampling of weights from multiple independent random structured matrices instead of via random sign flipping. The proposed method facilitates rapid calculation by employing structured matrices. In addition, the weight distribution is preserved because sign flipping is not implemented. The performance of the proposed alternating circulant random features method is theoretically and empirically evaluated.