FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are often slow and costly. The advent of deep learning-based approaches has shown significant promise, offering increases in both accuracy and efficiency. Building upon the foundational work of FABind, a model designed with a focus on speed and accuracy, we present FABind+, an enhanced iteration that largely boosts the performance of its predecessor. We identify pocket prediction as a critical bottleneck in molecular docking and propose a novel methodology that significantly refines pocket prediction, thereby streamlining the docking process. Furthermore, we introduce modifications to the docking module to enhance its pose generation capabilities. In an effort to bridge the gap with conventional sampling/generative methods, we incorporate a simple yet effective sampling technique coupled with a confidence model, requiring only minor adjustments to the regression framework of FABind. Experimental results and analysis reveal that FABind+ remarkably outperforms the original FABind, achieves competitive state-of-the-art performance, and delivers insightful modeling strategies. This demonstrates FABind+ represents a substantial step forward in molecular docking and drug discovery. Our code is in https://github.com/QizhiPei/FABind.

Benchmarks and Challenges in Pose Estimation for Egocentric Hand Interactions with Objects

We interact with the world with our hands and see it through our own (egocentric) perspective. A holistic 3D understanding of such interactions from egocentric views is important for tasks in robotics, AR/VR, action recognition and motion generation. Accurately reconstructing such interactions in 3D is challenging due to heavy occlusion, viewpoint bias, camera distortion, and motion blur from the head movement. To this end, we designed the HANDS23 challenge based on the AssemblyHands and ARCTIC datasets with carefully designed training and testing splits. Based on the results of the top submitted methods and more recent baselines on the leaderboards, we perform a thorough analysis on 3D hand(-object) reconstruction tasks. Our analysis demonstrates the effectiveness of addressing distortion specific to egocentric cameras, adopting high-capacity transformers to learn complex hand-object interactions, and fusing predictions from different views. Our study further reveals challenging scenarios intractable with state-of-the-art methods, such as fast hand motion, object reconstruction from narrow egocentric views, and close contact between two hands and objects. Our efforts will enrich the community's knowledge foundation and facilitate future hand studies on egocentric hand-object interactions.

Rolling bearing fault diagnosis method based on generative adversarial enhanced multi-scale convolutional neural network model

In order to solve the problem that current convolutional neural networks can not capture the correlation features between the time domain signals of rolling bearings effectively, and the model accuracy is limited by the number and quality of samples, a rolling bearing fault diagnosis method based on generative adversarial enhanced multi-scale convolutional neural network model is proposed. Firstly, Gram angular field coding technique is used to encode the time domain signal of the rolling bearing and generate the feature map to retain the complete information of the vibration signal. Then, the re-sulting data is divided into a training set, a validation set, and a test set. Among them, the training set is input into the gradient penalty Wasserstein distance generation adversarial network to complete the training, and a new sample with similar features to the training sample is obtained, and then the original training set is expanded. Next, multi-scale convolution is used to extract the fault features of the extended training set, and the feature graph is normalized by example to overcome the influence of the difference in feature distribution. Finally, the attention mechanism is applied to the adaptive weighting of normalized features and the extraction of deep features, and the fault diagnosis is completed by the softmax classifier. Compared with ResNet method, the experimental results show that the proposed method has better generalization performance and anti-noise performance.

Revisiting Edge Perturbation for Graph Neural Network in Graph Data Augmentation and Attack

Edge perturbation is a basic method to modify graph structures. It can be categorized into two veins based on their effects on the performance of graph neural networks (GNNs), i.e., graph data augmentation and attack. Surprisingly, both veins of edge perturbation methods employ the same operations, yet yield opposite effects on GNNs' accuracy. A distinct boundary between these methods in using edge perturbation has never been clearly defined. Consequently, inappropriate perturbations may lead to undesirable outcomes, necessitating precise adjustments to achieve desired effects. Therefore, questions of ``why edge perturbation has a two-faced effect?'' and ``what makes edge perturbation flexible and effective?'' still remain unanswered. In this paper, we will answer these questions by proposing a unified formulation and establishing a clear boundary between two categories of edge perturbation methods. Specifically, we conduct experiments to elucidate the differences and similarities between these methods and theoretically unify the workflow of these methods by casting it to one optimization problem. Then, we devise Edge Priority Detector (EPD) to generate a novel priority metric, bridging these methods up in the workflow. Experiments show that EPD can make augmentation or attack flexibly and achieve comparable or superior performance to other counterparts with less time overhead.

Boosting Meta-Training with Base Class Information for Few-Shot Learning

Few-shot learning, a challenging task in machine learning, aims to learn a classifier adaptable to recognize new, unseen classes with limited labeled examples. Meta-learning has emerged as a prominent framework for few-shot learning. Its training framework is originally a task-level learning method, such as Model-Agnostic Meta-Learning (MAML) and Prototypical Networks. And a recently proposed training paradigm called Meta-Baseline, which consists of sequential pre-training and meta-training stages, gains state-of-the-art performance. However, as a non-end-to-end training method, indicating the meta-training stage can only begin after the completion of pre-training, Meta-Baseline suffers from higher training cost and suboptimal performance due to the inherent conflicts of the two training stages. To address these limitations, we propose an end-to-end training paradigm consisting of two alternative loops. In the outer loop, we calculate cross entropy loss on the entire training set while updating only the final linear layer. In the inner loop, we employ the original meta-learning training mode to calculate the loss and incorporate gradients from the outer loss to guide the parameter updates. This training paradigm not only converges quickly but also outperforms existing baselines, indicating that information from the overall training set and the meta-learning training paradigm could mutually reinforce one another. Moreover, being model-agnostic, our framework achieves significant performance gains, surpassing the baseline systems by approximate 1%.

An Effective Branch-and-Bound Algorithm with New Bounding Methods for the Maximum $s$-Bundle Problem

The Maximum s-Bundle Problem (MBP) addresses the task of identifying a maximum s-bundle in a given graph. A graph G=(V, E) is called an s-bundle if its vertex connectivity is at least |V|-s, where the vertex connectivity equals the minimum number of vertices whose deletion yields a disconnected or trivial graph. MBP is NP-hard and holds relevance in numerous realworld scenarios emphasizing the vertex connectivity. Exact algorithms for MBP mainly follow the branch-and-bound (BnB) framework, whose performance heavily depends on the quality of the upper bound on the cardinality of a maximum s-bundle and the initial lower bound with graph reduction. In this work, we introduce a novel Partition-based Upper Bound (PUB) that leverages the graph partitioning technique to achieve a tighter upper bound compared to existing ones. To increase the lower bound, we propose to do short random walks on a clique to generate larger initial solutions. Then, we propose a new BnB algorithm that uses the initial lower bound and PUB in preprocessing for graph reduction, and uses PUB in the BnB search process for branch pruning. Extensive experiments with diverse s values demonstrate the significant progress of our algorithm over state-of-the-art BnB MBP algorithms. Moreover, our initial lower bound can also be generalized to other relaxation clique problems.

CORE: Mitigating Catastrophic Forgetting in Continual Learning through Cognitive Replay

This paper introduces a novel perspective to significantly mitigate catastrophic forgetting in continuous learning (CL), which emphasizes models' capacity to preserve existing knowledge and assimilate new information. Current replay-based methods treat every task and data sample equally and thus can not fully exploit the potential of the replay buffer. In response, we propose COgnitive REplay (CORE), which draws inspiration from human cognitive review processes. CORE includes two key strategies: Adaptive Quantity Allocation and Quality-Focused Data Selection. The former adaptively modulates the replay buffer allocation for each task based on its forgetting rate, while the latter guarantees the inclusion of representative data that best encapsulates the characteristics of each task within the buffer. Our approach achieves an average accuracy of 37.95% on split-CIFAR10, surpassing the best baseline method by 6.52%. Additionally, it significantly enhances the accuracy of the poorest-performing task by 6.30% compared to the top baseline.

Fast Adversarial Training against Textual Adversarial Attacks

Many adversarial defense methods have been proposed to enhance the adversarial robustness of natural language processing models. However, most of them introduce additional pre-set linguistic knowledge and assume that the synonym candidates used by attackers are accessible, which is an ideal assumption. We delve into adversarial training in the embedding space and propose a Fast Adversarial Training (FAT) method to improve the model robustness in the synonym-unaware scenario from the perspective of single-step perturbation generation and perturbation initialization. Based on the observation that the adversarial perturbations crafted by single-step and multi-step gradient ascent are similar, FAT uses single-step gradient ascent to craft adversarial examples in the embedding space to expedite the training process. Based on the observation that the perturbations generated on the identical training sample in successive epochs are similar, FAT fully utilizes historical information when initializing the perturbation. Extensive experiments demonstrate that FAT significantly boosts the robustness of BERT models in the synonym-unaware scenario, and outperforms the defense baselines under various attacks with character-level and word-level modifications.

Rethinking the Soft Conflict Pseudo Boolean Constraint on MaxSAT Local Search Solvers

MaxSAT is an optimization version of the famous NP-complete Satisfiability problem (SAT). Algorithms for MaxSAT mainly include complete solvers and local search incomplete solvers. In many complete solvers, once a better solution is found, a Soft conflict Pseudo Boolean (SPB) constraint will be generated to enforce the algorithm to find better solutions. In many local search algorithms, clause weighting is a key technique for effectively guiding the search directions. In this paper, we propose to transfer the SPB constraint into the clause weighting system of the local search method, leading the algorithm to better solutions. We further propose an adaptive clause weighting strategy that breaks the tradition of using constant values to adjust clause weights. Based on the above methods, we propose a new local search algorithm called SPB-MaxSAT that provides new perspectives for clause weighting on MaxSAT local search solvers. Extensive experiments demonstrate the excellent performance of the proposed methods.