Learning a Patent-Informed Biomedical Knowledge Graph Reveals Technological Potential of Drug Repositioning Candidates

Drug repositioning-a promising strategy for discovering new therapeutic uses for existing drugs-has been increasingly explored in the computational science literature using biomedical databases. However, the technological potential of drug repositioning candidates has often been overlooked. This study presents a novel protocol to comprehensively analyse various sources such as pharmaceutical patents and biomedical databases, and identify drug repositioning candidates with both technological potential and scientific evidence. To this end, first, we constructed a scientific biomedical knowledge graph (s-BKG) comprising relationships between drugs, diseases, and genes derived from biomedical databases. Our protocol involves identifying drugs that exhibit limited association with the target disease but are closely located in the s-BKG, as potential drug candidates. We constructed a patent-informed biomedical knowledge graph (p-BKG) by adding pharmaceutical patent information. Finally, we developed a graph embedding protocol to ascertain the structure of the p-BKG, thereby calculating the relevance scores of those candidates with target disease-related patents to evaluate their technological potential. Our case study on Alzheimer's disease demonstrates its efficacy and feasibility, while the quantitative outcomes and systematic methods are expected to bridge the gap between computational discoveries and successful market applications in drug repositioning research.

Revisiting Image Pyramid Structure for High Resolution Salient Object Detection

Salient object detection (SOD) has been in the spotlight recently, yet has been studied less for high-resolution (HR) images. Unfortunately, HR images and their pixel-level annotations are certainly more labor-intensive and time-consuming compared to low-resolution (LR) images and annotations. Therefore, we propose an image pyramid-based SOD framework, Inverse Saliency Pyramid Reconstruction Network (InSPyReNet), for HR prediction without any of HR datasets. We design InSPyReNet to produce a strict image pyramid structure of saliency map, which enables to ensemble multiple results with pyramid-based image blending. For HR prediction, we design a pyramid blending method which synthesizes two different image pyramids from a pair of LR and HR scale from the same image to overcome effective receptive field (ERF) discrepancy. Our extensive evaluations on public LR and HR SOD benchmarks demonstrate that InSPyReNet surpasses the State-of-the-Art (SotA) methods on various SOD metrics and boundary accuracy.

Better Quality Estimation for Low Resource Corpus Mining

Quality Estimation (QE) models have the potential to change how we evaluate and maybe even train machine translation models. However, these models still lack the robustness to achieve general adoption. We show that State-of-the-art QE models, when tested in a Parallel Corpus Mining (PCM) setting, perform unexpectedly bad due to a lack of robustness to out-of-domain examples. We propose a combination of multitask training, data augmentation and contrastive learning to achieve better and more robust QE performance. We show that our method improves QE performance significantly in the MLQE challenge and the robustness of QE models when tested in the Parallel Corpus Mining setup. We increase the accuracy in PCM by more than 0.80, making it on par with state-of-the-art PCM methods that use millions of sentence pairs to train their models. In comparison, we use a thousand times less data, 7K parallel sentences in total, and propose a novel low resource PCM method.

Asymptotic Normality of Log Likelihood Ratio and Fundamental Limit of the Weak Detection for Spiked Wigner Matrices

We consider the problem of detecting the presence of a signal in a rank-one spiked Wigner model. Assuming that the signal is drawn from the Rademacher prior, we prove that the log likelihood ratio of the spiked model against the null model converges to a Gaussian when the signal-to-noise ratio is below a certain threshold. From the mean and the variance of the limiting Gaussian, we also compute the limit of the sum of the Type-I error and the Type-II error of the likelihood ratio test.

$α$-Stable convergence of heavy-tailed infinitely-wide neural networks

We consider infinitely-wide multi-layer perceptrons (MLPs) which are limits of standard deep feed-forward neural networks. We assume that, for each layer, the weights of an MLP are initialized with i.i.d. samples from either a light-tailed (finite variance) or heavy-tailed distribution in the domain of attraction of a symmetric $\alpha$-stable distribution, where $\alpha\in(0,2]$ may depend on the layer. For the bias terms of the layer, we assume i.i.d. initializations with a symmetric $\alpha$-stable distribution having the same $\alpha$ parameter of that layer. We then extend a recent result of Favaro, Fortini, and Peluchetti (2020), to show that the vector of pre-activation values at all nodes of a given hidden layer converges in the limit, under a suitable scaling, to a vector of i.i.d. random variables with symmetric $\alpha$-stable distributions.

Deep learning-based citation recommendation system for patents

In this study, we address the challenges in developing a deep learning-based automatic patent citation recommendation system. Although deep learning-based recommendation systems have exhibited outstanding performance in various domains (such as movies, products, and paper citations), their validity in patent citations has not been investigated, owing to the lack of a freely available high-quality dataset and relevant benchmark model. To solve these problems, we present a novel dataset called PatentNet that includes textual information and metadata for approximately 110,000 patents from the Google Big Query service. Further, we propose strong benchmark models considering the similarity of textual information and metadata (such as cooperative patent classification code). Compared with existing recommendation methods, the proposed benchmark method achieved a mean reciprocal rank of 0.2377 on the test set, whereas the existing state-of-the-art recommendation method achieved 0.2073.