Xia Ning

Junning Lyu, Qizhi Guo, Xia Ning et al.

LiDAR-inertial odometry (LIO) is a key component of autonomous navigation, but high-dynamic driving exposes two coupled challenges: intra-scan motion distortion and vibration-contaminated inertial measurements. Most real-time LiDAR-inertial pipelines propagate the system state by integrating raw IMU measurements and then use the propagated trajectory for point cloud de-distortion, thereby propagating inertial noise into both the corrected scan and the subsequent scan-to-map registration. This paper presents WNOJ-LIO, a LiDAR-IMU fusion framework based on a White-Noise-on-Jerk (WNOJ) Extended Kalman Filter (EKF). WNOJ-LIO employs a decoupled WNOJ prior on $\R^3 \times \SO(3)$ for state prediction and treats the IMU as a high-frequency measurement source rather than the driver of state propagation. The resulting posterior state history is then used for LiDAR scan de-distortion and subsequent point-to-plane LiDAR updates. The decoupled process model enables closed-form covariance propagation, thereby bridging the gap between batch WNOJ Gaussian process (GP) trajectory priors and recursive filtering. Simulation results demonstrate improvements in acceleration and angular-velocity denoising, scan de-distortion, and localization accuracy over a FAST-LIO-style baseline. Real-world experiments were conducted using an autonomous racing car on four driving segments with maximum speeds ranging from 53 to 208~km/h, covering a wide range of vehicle vibration levels. The experiments further validate the proposed method and provide a comprehensive evaluation of its performance in estimating acceleration, angular velocity, body-frame linear velocity, attitude, and position under highly dynamic driving. The source code of WNOJ-LIO is publicly available at https://github.com/LvJohny/wnoj-ekf-lio.git.

Ziqi Chen, Martin Renqiang Min, Hongyu Guo et al.

T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is known as TCR recognition and constitutes a key step for immune response. Optimizing TCR sequences for TCR recognition represents a fundamental step towards the development of personalized treatments to trigger immune responses killing cancerous or virus-infected cells. In this paper, we formulated the search for these optimized TCRs as a reinforcement learning (RL) problem, and presented a framework TCRPPO with a mutation policy using proximal policy optimization. TCRPPO mutates TCRs into effective ones that can recognize given peptides. TCRPPO leverages a reward function that combines the likelihoods of mutated sequences being valid TCRs measured by a new scoring function based on deep autoencoders, with the probabilities of mutated sequences recognizing peptides from a peptide-TCR interaction predictor. We compared TCRPPO with multiple baseline methods and demonstrated that TCRPPO significantly outperforms all the baseline methods to generate positive binding and valid TCRs. These results demonstrate the potential of TCRPPO for both precision immunotherapy and peptide-recognizing TCR motif discovery.

Ziqi Chen, Oluwatosin R. Ayinde, James R. Fuchs et al.

Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches have been developed to accelerate the design of synthesis routes. In this paper, we develop a generative framework $\mathsf{G^2Retro}$ for one-step retrosynthesis prediction. $\mathsf{G^2Retro}$ imitates the reversed logic of synthetic reactions. It first predicts the reaction centers in the target molecules (products), identifies the synthons needed to assemble the products, and transforms these synthons into reactants. $\mathsf{G^2Retro}$ defines a comprehensive set of reaction center types, and learns from the molecular graphs of the products to predict potential reaction centers. To complete synthons into reactants, $\mathsf{G^2Retro}$ considers all the involved synthon structures and the product structures to identify the optimal completion paths, and accordingly attaches small substructures sequentially to the synthons. Here we show that $\mathsf{G^2Retro}$ is able to better predict the reactants for given products in the benchmark dataset than the state-of-the-art methods.

Athanasios N. Nikolakopoulos, Xia Ning, Christian Desrosiers et al.

Collaborative recommendation approaches based on nearest-neighbors are still highly popular today due to their simplicity, their efficiency, and their ability to produce accurate and personalized recommendations. This chapter offers a comprehensive survey of neighborhood-based methods for the item recommendation problem. It presents the main characteristics and benefits of such methods, describes key design choices for implementing a neighborhood-based recommender system, and gives practical information on how to make these choices. A broad range of methods is covered in the chapter, including traditional algorithms like k-nearest neighbors as well as advanced approaches based on matrix factorization, sparse coding and random walks.

Wen-Hao Chiang, Li Shen, Lang Li et al.

Background: The problem of predicting whether a drug combination of arbitrary orders is likely to induce adverse drug reactions is considered in this manuscript. Methods: Novel kernels over drug combinations of arbitrary orders are developed within support vector machines for the prediction. Graph matching methods are used in the novel kernels to measure the similarities among drug combinations, in which drug co-medication patterns are leveraged to measure single drug similarities. Results: The experimental results on a real-world dataset demonstrated that the new kernels achieve an area under the curve (AUC) value 0.912 for the prediction problem. Conclusions: The new methods with drug co-medication based single drug similarities can accurately predict whether a drug combination is likely to induce adverse drug reactions of interest. Keywords: drug-drug interaction prediction; drug combination similarity; co-medication; graph matching