The identification of drug side-effects is considered to be an important step in drug design, which could not only shorten the time but also reduce the cost of drug development. In this paper, we investigate the relationship between the potential side-effects of drug candidates and their chemical structures. The preliminary Regularized Regression (RR) model for drug side-effects prediction has promising features in the efficiency of model training and the existence of a closed form solution. It performs better than other state-of-the-art methods, in terms of minimum accuracy and average accuracy. In order to dig inside how drug structure will associate with side effect, we propose weighted GTS (Generalized T-Student Kernel: WGTS) SVM model from a structural risk minimization perspective. The SVM model proposed in this paper provide a better understanding of drug side-effects in the process of drug development. The usefulness of the WGTS model lies in the superior performance in a cross validation setting on a 1385 side-effects profiling from SIDER database and the chemical structures of 888 approved drugs and independent side-effect profile predictions. This work is expected to shed light on intriguing studies that predict potential un-identifying side-effects and suggest how we can avoid drug side-effects by the removal of some distinguished chemical structures.

Metabolism is a vital cellular process, and its malfunction can be a major contributor to many human diseases. Metabolites can serve as a metabolic disease biomarker. An detection of such biomarkers plays a significant role in the study of biochemical reaction and signaling networks. Early research mainly focused on the analysis of the metabolic networks. The issue of integrating metabolite networks with other available biological data to reveal the mechanics of disease-metabolite associations is an important and interesting challenge.

Motivation: Continuous advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled researchers to further explore the study of cell heterogeneity, trajectory inference, identification of rare cell types, and neurology. Accurate scRNA-seq data clustering is crucial in single-cell sequencing data analysis. However, the high dimensionality, sparsity, and presence of “false” zero values in the data can pose challenges to clustering. Furthermore, current unsupervised clustering algorithms have not effectively leveraged prior biological knowledge, making cell clustering even more challenging.Results: This study investigates a semisupervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint, and cross-entropy constraint based on deep learning. Specifically, the model begins by pretraining a denoising autoencoder based on a zero-inflated negative binomial distribution. Deep clustering is then performed in the learned latent feature space using triplet constraints and pairwise constraints generated from partial labeled cells. Finally, to address imbalanced cell-type datasets, a weighted cross-entropy loss is introduced to optimize the model. A series of experimental results on 10 real scRNA-seq datasets and five simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework.Availability and implementation: scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.

In this study, we investigate the accelerated learning control schemes for point-to-point tracking systems (PTSs) with measurement noise. The asymptotic convergence of the generated input sequence has been a long-standing open issue for point-to-point tracking problems because there are infinite possible input candidates that can drive the system dynamics to track the desired reference at specified time instants. An accelerated gradient algorithm and its generalized version with a novel direction regulation matrix are proposed, with the learning gain is adaptively triggered by the practical tracking errors. The learning gain remains constant at the early stage and begins to decrease after a certain number of iterations. The input sequence generated by the proposed scheme converges to a specified limit for any fixed initial input, with the limit being closest to the initial input, in a certain sense. Numerical simulations are provided to verify the theoretical results.

This article studies the conflicting goals of high-precision tracking and quick convergence speed, which is a longstanding problem in the learning control of stochastic systems. In such systems, a decreasing gain sequence is necessary to ensure the asymptotic convergence of the generated input sequence to a fixed limit. However, the convergence speed is adversely affected by gain sequences of this nature. In this article, we propose a novel multistage learning control strategy to resolve this conflict, where each stage consists of several iterations. The learning gain remains constant in each stage but is reduced at the transition from a given stage to the subsequent stage. The switching iteration between two stages is determined by the tracking performance index of the contracted input error and the accumulated noise drift. Furthermore, an improved mechanism is proposed to optimize the lengths of the different stages. The asymptotic convergence of the input sequence generated by the newly proposed strategy is strictly established by thoroughly analyzing the properties of the proposed gain sequence. Numerical simulations are presented to verify the theoretical results.