Jian Chu

Xinxing Yang, Genke Yang, Jian Chu

Drug-target binding affinity prediction plays an important role in the early stages of drug discovery, which can infer the strength of interactions between new drugs and new targets. However, the performance of previous computational models is limited by the following drawbacks. The learning of drug representation relies only on supervised data, without taking into account the information contained in the molecular graph itself. Moreover, most previous studies tended to design complicated representation learning module, while uniformity, which is used to measure representation quality, is ignored. In this study, we propose GraphCL-DTA, a graph contrastive learning with molecular semantics for drug-target binding affinity prediction. In GraphCL-DTA, we design a graph contrastive learning framework for molecular graphs to learn drug representations, so that the semantics of molecular graphs are preserved. Through this graph contrastive framework, a more essential and effective drug representation can be learned without additional supervised data. Next, we design a new loss function that can be directly used to smoothly adjust the uniformity of drug and target representations. By directly optimizing the uniformity of representations, the representation quality of drugs and targets can be improved. The effectiveness of the above innovative elements is verified on two real datasets, KIBA and Davis. The excellent performance of GraphCL-DTA on the above datasets suggests its superiority to the state-of-the-art model.

Xinxing Yang, Genke Yang, Jian Chu

The computational drug repositioning aims to discover new uses for marketed drugs, which can accelerate the drug development process and play an important role in the existing drug discovery system. However, the number of validated drug-disease associations is scarce compared to the number of drugs and diseases in the real world. Too few labeled samples will make the classification model unable to learn effective latent factors of drugs, resulting in poor generalization performance. In this work, we propose a multi-task self-supervised learning framework for computational drug repositioning. The framework tackles label sparsity by learning a better drug representation. Specifically, we take the drug-disease association prediction problem as the main task, and the auxiliary task is to use data augmentation strategies and contrast learning to mine the internal relationships of the original drug features, so as to automatically learn a better drug representation without supervised labels. And through joint training, it is ensured that the auxiliary task can improve the prediction accuracy of the main task. More precisely, the auxiliary task improves drug representation and serving as additional regularization to improve generalization. Furthermore, we design a multi-input decoding network to improve the reconstruction ability of the autoencoder model. We evaluate our model using three real-world datasets. The experimental results demonstrate the effectiveness of the multi-task self-supervised learning framework, and its predictive ability is superior to the state-of-the-art model.

Song Chen, Shengze Cai, Tehuan Chen et al.

In this paper, we propose a novel nonlinear observer based on neural networks, called neural observer, for observation tasks of linear time-invariant (LTI) systems and uncertain nonlinear systems. In particular, the neural observer designed for uncertain systems is inspired by the active disturbance rejection control, which can measure the uncertainty in real-time. The stability analysis (e.g., exponential convergence rate) of LTI and uncertain nonlinear systems (involving neural observers) are presented and guaranteed, where it is shown that the observation problems can be solved only using the linear matrix inequalities (LMIs). Also, it is revealed that the observability and controllability of the system matrices are required to demonstrate the existence of solutions of LMIs. Finally, the effectiveness of neural observers is verified on three simulation cases, including the X-29A aircraft model, the nonlinear pendulum, and the four-wheel steering vehicle.

Xinxing Yang, Jiachen Li, Xiao Kang et al.

Drug combination refers to the use of two or more drugs to treat a specific disease at the same time. It is currently the mainstream way to treat complex diseases. Compared with single drugs, drug combinations have better efficacy and can better inhibit toxicity and drug resistance. The computational model based on deep learning concatenates the representation of multiple drugs and the corresponding cell line feature as input, and the output is whether the drug combination can have an inhibitory effect on the cell line. However, this strategy of concatenating multiple representations has the following defects: the alignment of drug representation and cell line representation is ignored, resulting in the synergistic relationship not being reflected positionally in the embedding space. Moreover, the alignment measurement function in deep learning cannot be suitable for drug synergy prediction tasks due to differences in input types. Therefore, in this work, we propose ALNSynergy, a graph convolutional network with multi-representation alignment for predicting drug synergy. In the ALNSynergy model, we designed a multi-representation alignment function suitable for the drug synergy prediction task so that the positional relationship between drug representations and cell line representation is reflected in the embedding space. In addition, the vector modulus of drug representations and cell line representation is considered to improve the accuracy of calculation results and accelerate model convergence. Finally, many relevant experiments were run on multiple drug synergy datasets to verify the effectiveness of the above innovative elements and the excellence of the ALNSynergy model.

Jiachen Li, Soovadeep Bakshi, Jian Chu et al.

This paper presents a hierarchical two-stage framework for multi-robot task allocation and trajectory optimization in asymmetric task spaces: (1) a sequential auction allocates tasks using closed-form bid functions, and (2) each robot independently solves an optimal control problem for energy-minimal trajectories with a physics-based battery model, followed by a collision avoidance refinement step using pairwise proximity penalties. Event-triggered warm-start rescheduling with bounded trigger frequency handles robot faults, priority arrivals, and energy deviations. Across 505 scenarios with 2-20 robots and up to 100 tasks on three factory layouts, both energy- and distance-based auction variants achieve 11.8% average energy savings over nearest-task allocation, with rescheduling latency under 10 ms. The central finding is that bid-metric performance is regime-dependent: in uniform workspaces, distance bids outperform energy bids by 3.5% (p < 0.05, Wilcoxon) because a 15.7% closed-form approximation error degrades bid ranking accuracy to 87%; however, when workspace friction heterogeneity is sufficient (r < 0.85 energy-distance correlation), a zone-aware energy bid outperforms distance bids by 2-2.4%. These results provide practitioner guidance: use distance bids in near-uniform terrain and energy-aware bids when friction variation is significant.

Jiachen Li, Shihao Li, Jian Chu et al.

Autonomous mobile robot fleets must coordinate task allocation and charging under limited shared resources, yet most battery aware planning methods address only a single robot. This paper extends degradation cost aware task planning to a multi robot setting by jointly optimizing task assignment, service sequencing, optional charging decisions, charging mode selection, and charger access while balancing degradation across the fleet. The formulation relies on reduced form degradation proxies grounded in the empirical battery aging literature, capturing both charging mode dependent wear and idle state of charge dependent aging; the bilinear idle aging term is linearized through a disaggregated piecewise McCormick formulation. Tight big M values derived from instance data strengthen the LP relaxation. To manage scalability, we propose a hierarchical matheuristic in which a fleet level master problem coordinates assignments, routes, and charger usage, while robot level subproblems whose integer part decomposes into trivially small independent partition selection problems compute route conditioned degradation schedules. Systematic experiments compare the proposed method against three baselines: a rule based nearest available dispatcher, an energy aware formulation that enforces battery feasibility without modeling degradation, and a charger unaware formulation that accounts for degradation but ignores shared charger capacity limits.

Hongkai Ye, Xin Zhou, Zhepei Wang et al.

In this paper, we propose a lightweight yet effective Topology Guided Kinodynamic planner (TGK-Planner) for quadrotor aggressive flights with limited onboard computing resources. The proposed system follows the traditional hierarchical planning workflow, with novel designs to improve the robustness and efficiency in both the pathfinding and trajectory optimization sub-modules. Firstly, we propose the topology guided graph, which roughly captures the topological structure of the environment and guides the state sampling of a sampling-based kinodynamic planner. In this way, we significantly improve the efficiency of finding a safe and dynamically feasible trajectory. Then, we refine the smoothness and continuity of the trajectory in an optimization framework, which incorporates the homotopy constraint to guarantee the safety of the trajectory. The optimization program is formulated as a sequence of quadratic programmings (QPs) and can be iteratively solved in a few milliseconds. Finally, the proposed system is integrated into a fully autonomous quadrotor and validated in various simulated and real-world scenarios. Benchmark comparisons show that our method outperforms state-of-the-art methods with regard to efficiency and trajectory quality. Moreover, we will release our code as an open-source package.

Zhepei Wang, Xin Zhou, Chao Xu et al.

With much research has been conducted into trajectory planning for quadrotors, planning with spatial and temporal optimal trajectories in real-time is still challenging. In this paper, we propose a framework for generating large-scale piecewise polynomial trajectories for aggressive autonomous flights, with highlights on its superior computational efficiency and simultaneous spatial-temporal optimality. Exploiting the implicitly decoupled structure of the planning problem, we conduct alternating minimization between boundary conditions and time durations of trajectory pieces. In each minimization phase, we leverage the algebraic convenience of the sub-problem to escape poor local minima and achieve the lowest time consumption. Theoretical analysis for the global/local convergence rate of our proposed method is provided. Moreover, based on polynomial theory, an extremely fast feasibility check method is designed for various kinds of constraints. By incorporating the method into our alternating structure, a constrained minimization algorithm is constructed to optimize trajectories on the premise of feasibility. Benchmark evaluation shows that our algorithm outperforms state-of-the-art methods regarding efficiency, optimality, and scalability. Aggressive flight experiments in a limited space with dense obstacles are presented to demonstrate the performance of the proposed algorithm. We release our implementation as an open-source ros-package.

Jiachen Li, Shihao Li, Jian Chu et al.

Data Enabled Predictive Control (DeePC) is an established model free approach to predictive control, but it faces two open challenges: computational complexity that scales cubically with dataset size and performance degradation when data are corrupted. This paper introduces Robust Data Selection DeePC (RDS DeePC), a framework that addresses both obstacles through influence function analysis. We derive a sensitivity score quantifying the leverage each trajectory segment exerts on the optimization solution and prove that high sensitivity segments correspond to outliers while low sensitivity segments represent consistent data. Selecting low sensitivity segments thus yields both computational efficiency and automatic outlier filtering without requiring data quality labels. For nonlinear systems, we extend the framework via a two stage online selection approach accelerated by the LiSSA algorithm. Experiments on four systems of increasing complexity including a DC motor, an inverted pendulum, a planar quadrotor UAV tracking a figure 8 trajectory, and a kinematic bicycle vehicle following a figure 8 path demonstrate that RDS DeePC achieves 94 to 97 percent clean data selection and comparable or better tracking performance under 20 percent data corruption.

Xinxing Yang, Genke Yang, Jian Chu

Computational drug repositioning technology is an effective tool to accelerate drug development. Although this technique has been widely used and successful in recent decades, many existing models still suffer from multiple drawbacks such as the massive number of unvalidated drug-disease associations and the inner product. The limitations of these works are mainly due to the following two reasons: firstly, previous works used negative sampling techniques to treat unvalidated drug-disease associations as negative samples, which is invalid in real-world settings; secondly, the inner product cannot fully take into account the feature information contained in the latent factor of drug and disease. In this paper, we propose a novel PUON framework for addressing the above deficiencies, which models the risk estimator of computational drug repositioning only using validated (Positive) and unvalidated (Unlabelled) drug-disease associations without employing negative sampling techniques. The PUON also proposed an Outer Neighborhood-based classifier for modeling the cross-feature information of the latent facotor. For a comprehensive comparison, we considered 8 popular baselines. Extensive experiments in four real-world datasets showed that PUON model achieved the best performance based on 6 evaluation metrics.

Chunlin Chen, Daoyi Dong, Han-Xiong Li et al.

The balance between exploration and exploitation is a key problem for reinforcement learning methods, especially for Q-learning. In this paper, a fidelity-based probabilistic Q-learning (FPQL) approach is presented to naturally solve this problem and applied for learning control of quantum systems. In this approach, fidelity is adopted to help direct the learning process and the probability of each action to be selected at a certain state is updated iteratively along with the learning process, which leads to a natural exploration strategy instead of a pointed one with configured parameters. A probabilistic Q-learning (PQL) algorithm is first presented to demonstrate the basic idea of probabilistic action selection. Then the FPQL algorithm is presented for learning control of quantum systems. Two examples (a spin- 1/2 system and a lamda-type atomic system) are demonstrated to test the performance of the FPQL algorithm. The results show that FPQL algorithms attain a better balance between exploration and exploitation, and can also avoid local optimal policies and accelerate the learning process.