arXiv subjects

Kun He

Publications and source records attributed to Kun He.

At least 127 records · Page 7Linked to original sources

arXiv2022

Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design

Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the antibody patterns from data that could be complementary to human experiences. However, the computational methods heavily rely on high-quality antibody structure data, which is quite limited. Besides, the complementarity-determining region (CDR), which is the key component of an antibody that determines the specificity and binding affinity, is highly variable and hard to predict. Therefore, the data limitation issue further raises the difficulty of CDR generation for antibodies. Fortunately, there exists a large amount of sequence data of antibodies that can help model the CDR and alleviate the reliance on structure data. By witnessing the success of pre-training models for protein modeling, in this paper, we develop the antibody pre-training language model and incorporate it into the (antigen-specific) antibody design model in a systemic way. Specifically, we first pre-train an antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to avoid the heavy cost and error propagation from an autoregressive manner, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules. Through various experiments, we show that our method achieves superior performances over previous baselines on different tasks, such as sequence and structure generation and antigen-binding CDR-H3 design.

q-bio.BM↗

arXiv2022

Neighborhood Convolutional Network: A New Paradigm of Graph Neural Networks for Node Classification

The decoupled Graph Convolutional Network (GCN), a recent development of GCN that decouples the neighborhood aggregation and feature transformation in each convolutional layer, has shown promising performance for graph representation learning. Existing decoupled GCNs first utilize a simple neural network (e.g., MLP) to learn the hidden features of the nodes, then propagate the learned features on the graph with fixed steps to aggregate the information of multi-hop neighborhoods. Despite effectiveness, the aggregation operation, which requires the whole adjacency matrix as the input, is involved in the model training, causing high training cost that hinders its potential on larger graphs. On the other hand, due to the independence of node attributes as the input, the neural networks used in decoupled GCNs are very simple, and advanced techniques cannot be applied to the modeling. To this end, we further liberate the aggregation operation from the decoupled GCN and propose a new paradigm of GCN, termed Neighborhood Convolutional Network (NCN), that utilizes the neighborhood aggregation result as the input, followed by a special convolutional neural network tailored for extracting expressive node representations from the aggregation input. In this way, the model could inherit the merit of decoupled GCN for aggregating neighborhood information, at the same time, develop much more powerful feature learning modules. A training strategy called mask training is incorporated to further boost the model performance. Extensive results demonstrate the effectiveness of our model for the node classification task on diverse homophilic graphs and heterophilic graphs.

cs.LG↗

arXiv2022

Local Magnification for Data and Feature Augmentation

In recent years, many data augmentation techniques have been proposed to increase the diversity of input data and reduce the risk of overfitting on deep neural networks. In this work, we propose an easy-to-implement and model-free data augmentation method called Local Magnification (LOMA). Different from other geometric data augmentation methods that perform global transformations on images, LOMA generates additional training data by randomly magnifying a local area of the image. This local magnification results in geometric changes that significantly broaden the range of augmentations while maintaining the recognizability of objects. Moreover, we extend the idea of LOMA and random cropping to the feature space to augment the feature map, which further boosts the classification accuracy considerably. Experiments show that our proposed LOMA, though straightforward, can be combined with standard data augmentation to significantly improve the performance on image classification and object detection. And further combination with our feature augmentation techniques, termed LOMA_IF&FO, can continue to strengthen the model and outperform advanced intensity transformation methods for data augmentation.

cs.CV↗

arXiv2022

Adaptive Multi-Neighborhood Attention based Transformer for Graph Representation Learning

By incorporating the graph structural information into Transformers, graph Transformers have exhibited promising performance for graph representation learning in recent years. Existing graph Transformers leverage specific strategies, such as Laplacian eigenvectors and shortest paths of the node pairs, to preserve the structural features of nodes and feed them into the vanilla Transformer to learn the representations of nodes. It is hard for such predefined rules to extract informative graph structural features for arbitrary graphs whose topology structure varies greatly, limiting the learning capacity of the models. To this end, we propose an adaptive graph Transformer, termed Multi-Neighborhood Attention based Graph Transformer (MNA-GT), which captures the graph structural information for each node from the multi-neighborhood attention mechanism adaptively. By defining the input to perform scaled-dot product as an attention kernel, MNA-GT constructs multiple attention kernels based on different hops of neighborhoods such that each attention kernel can capture specific graph structural information of the corresponding neighborhood for each node pair. In this way, MNA-GT can preserve the graph structural information efficiently by incorporating node representations learned by different attention kernels. MNA-GT further employs an attention layer to learn the importance of different attention kernels to enable the model to adaptively capture the graph structural information for different nodes. Extensive experiments are conducted on a variety of graph benchmarks, and the empirical results show that MNA-GT outperforms many strong baselines.

cs.LG↗

arXiv2022

TextHacker: Learning based Hybrid Local Search Algorithm for Text Hard-label Adversarial Attack

Existing textual adversarial attacks usually utilize the gradient or prediction confidence to generate adversarial examples, making it hard to be deployed in real-world applications. To this end, we consider a rarely investigated but more rigorous setting, namely hard-label attack, in which the attacker can only access the prediction label. In particular, we find we can learn the importance of different words via the change on prediction label caused by word substitutions on the adversarial examples. Based on this observation, we propose a novel adversarial attack, termed Text Hard-label attacker (TextHacker). TextHacker randomly perturbs lots of words to craft an adversarial example. Then, TextHacker adopts a hybrid local search algorithm with the estimation of word importance from the attack history to minimize the adversarial perturbation. Extensive evaluations for text classification and textual entailment show that TextHacker significantly outperforms existing hard-label attacks regarding the attack performance as well as adversary quality.

cs.CL↗

arXiv2022

Hybrid Learning with New Value Function for the Maximum Common Subgraph Problem

Maximum Common induced Subgraph (MCS) is an important NP-hard problem with wide real-world applications. Branch-and-Bound (BnB) is the basis of a class of efficient algorithms for MCS, consisting in successively selecting vertices to match and pruning when it is discovered that a solution better than the best solution found so far does not exist. The method of selecting the vertices to match is essential for the performance of BnB. In this paper, we propose a new value function and a hybrid selection strategy used in reinforcement learning to define a new vertex selection method, and propose a new BnB algorithm, called McSplitDAL, for MCS. Extensive experiments show that McSplitDAL significantly improves the current best BnB algorithms, McSplit+LL and McSplit+RL. An empirical analysis is also performed to illustrate why the new value function and the hybrid selection strategy are effective.

cs.AI↗

arXiv2022

Robust Textual Embedding against Word-level Adversarial Attacks

We attribute the vulnerability of natural language processing models to the fact that similar inputs are converted to dissimilar representations in the embedding space, leading to inconsistent outputs, and we propose a novel robust training method, termed Fast Triplet Metric Learning (FTML). Specifically, we argue that the original sample should have similar representation with its adversarial counterparts and distinguish its representation from other samples for better robustness. To this end, we adopt the triplet metric learning into the standard training to pull words closer to their positive samples (i.e., synonyms) and push away their negative samples (i.e., non-synonyms) in the embedding space. Extensive experiments demonstrate that FTML can significantly promote the model robustness against various advanced adversarial attacks while keeping competitive classification accuracy on original samples. Besides, our method is efficient as it only needs to adjust the embedding and introduces very little overhead on the standard training. Our work shows great potential of improving the textual robustness through robust word embedding.

cs.CL↗

arXiv2022

Triangle Attack: A Query-efficient Decision-based Adversarial Attack

Decision-based attack poses a severe threat to real-world applications since it regards the target model as a black box and only accesses the hard prediction label. Great efforts have been made recently to decrease the number of queries; however, existing decision-based attacks still require thousands of queries in order to generate good quality adversarial examples. In this work, we find that a benign sample, the current and the next adversarial examples can naturally construct a triangle in a subspace for any iterative attacks. Based on the law of sines, we propose a novel Triangle Attack (TA) to optimize the perturbation by utilizing the geometric information that the longer side is always opposite the larger angle in any triangle. However, directly applying such information on the input image is ineffective because it cannot thoroughly explore the neighborhood of the input sample in the high dimensional space. To address this issue, TA optimizes the perturbation in the low frequency space for effective dimensionality reduction owing to the generality of such geometric property. Extensive evaluations on ImageNet dataset show that TA achieves a much higher attack success rate within 1,000 queries and needs a much less number of queries to achieve the same attack success rate under various perturbation budgets than existing decision-based attacks. With such high efficiency, we further validate the applicability of TA on real-world API, i.e., Tencent Cloud API.

cs.CV↗

arXiv2022

Detecting Textual Adversarial Examples through Randomized Substitution and Vote

A line of work has shown that natural text processing models are vulnerable to adversarial examples. Correspondingly, various defense methods are proposed to mitigate the threat of textual adversarial examples, eg, adversarial training, input transformations, detection, etc. In this work, we treat the optimization process for synonym substitution based textual adversarial attacks as a specific sequence of word replacement, in which each word mutually influences other words. We identify that we could destroy such mutual interaction and eliminate the adversarial perturbation by randomly substituting a word with its synonyms. Based on this observation, we propose a novel textual adversarial example detection method, termed Randomized Substitution and Vote (RS&V), which votes the prediction label by accumulating the logits of k samples generated by randomly substituting the words in the input text with synonyms. The proposed RS&V is generally applicable to any existing neural networks without modification on the architecture or extra training, and it is orthogonal to prior work on making the classification network itself more robust. Empirical evaluations on three benchmark datasets demonstrate that our RS&V could detect the textual adversarial examples more successfully than the existing detection methods while maintaining the high classification accuracy on benign samples.

cs.CL↗

arXiv2022

Reinforced Lin-Kernighan-Helsgaun Algorithms for the Traveling Salesman Problems

TSP is a classical NP-hard combinatorial optimization problem with many practical variants. LKH is one of the state-of-the-art local search algorithms for the TSP. LKH-3 is a powerful extension of LKH that can solve many TSP variants. Both LKH and LKH-3 associate a candidate set to each city to improve the efficiency, and have two different methods, $α$-measure and POPMUSIC, to decide the candidate sets. In this work, we first propose a Variable Strategy Reinforced LKH (VSR-LKH) algorithm, which incorporates three reinforcement learning methods (Q-learning, Sarsa, Monte Carlo) with LKH, for the TSP. We further propose a new algorithm called VSR-LKH-3 that combines the variable strategy reinforcement learning method with LKH-3 for typical TSP variants, including the TSP with time windows (TSPTW) and Colored TSP (CTSP). The proposed algorithms replace the inflexible traversal operations in LKH and LKH-3 and let the algorithms learn to make a choice at each search step by reinforcement learning. Both LKH and LKH-3, with either $α$-measure or POPMUSIC, can be significantly improved by our methods. Extensive experiments on 236 widely-used TSP benchmarks with up to 85,900 cities demonstrate the excellent performance of VSR-LKH. VSR-LKH-3 also significantly outperforms the state-of-the-art heuristics for TSPTW and CTSP.

cs.AI↗

arXiv2022

Generating Pseudo-labels Adaptively for Few-shot Model-Agnostic Meta-Learning

Model-Agnostic Meta-Learning (MAML) is a famous few-shot learning method that has inspired many follow-up efforts, such as ANIL and BOIL. However, as an inductive method, MAML is unable to fully utilize the information of query set, limiting its potential of gaining higher generality. To address this issue, we propose a simple yet effective method that generates psuedo-labels adaptively and could boost the performance of the MAML family. The proposed methods, dubbed Generative Pseudo-label based MAML (GP-MAML), GP-ANIL and GP-BOIL, leverage statistics of the query set to improve the performance on new tasks. Specifically, we adaptively add pseudo labels and pick samples from the query set, then re-train the model using the picked query samples together with the support set. The GP series can also use information from the pseudo query set to re-train the network during the meta-testing. While some transductive methods, such as Transductive Propagation Network (TPN), struggle to achieve this goal.

cs.LG↗

arXiv2022

Reinforced Hybrid Genetic Algorithm for the Traveling Salesman Problem

In this paper, we propose a new method called the Reinforced Hybrid Genetic Algorithm (RHGA) for solving the famous NP-hard Traveling Salesman Problem (TSP). Specifically, we combine reinforcement learning with the well-known Edge Assembly Crossover genetic algorithm (EAX-GA) and the Lin-Kernighan-Helsgaun (LKH) local search heuristic. In the hybrid algorithm, LKH can help EAX-GA improve the population by its effective local search, and EAX-GA can help LKH escape from local optima by providing high-quality and diverse initial solutions. We restrict that there is only one special individual among the population in EAX-GA that can be improved by LKH. Such a mechanism can prevent the population diversity, efficiency, and algorithm performance from declining due to the redundant calling of LKH upon the population. As a result, our proposed hybrid mechanism can help EAX-GA and LKH boost each other's performance without reducing the convergence rate of the population. The reinforcement learning technique based on Q-learning further promotes the hybrid genetic algorithm. Experimental results on 138 well-known and widely used TSP benchmarks with the number of cities ranging from 1,000 to 85,900 demonstrate the excellent performance of RHGA.

cs.NE↗

arXiv2022

Propagation with Adaptive Mask then Training for Node Classification on Attributed Networks

Node classification on attributed networks is a semi-supervised task that is crucial for network analysis. By decoupling two critical operations in Graph Convolutional Networks (GCNs), namely feature transformation and neighborhood aggregation, some recent works of decoupled GCNs could support the information to propagate deeper and achieve advanced performance. However, they follow the traditional structure-aware propagation strategy of GCNs, making it hard to capture the attribute correlation of nodes and sensitive to the structure noise described by edges whose two endpoints belong to different categories. To address these issues, we propose a new method called the itshape Propagation with Adaptive Mask then Training (PAMT). The key idea is to integrate the attribute similarity mask into the structure-aware propagation process. In this way, PAMT could preserve the attribute correlation of adjacent nodes during the propagation and effectively reduce the influence of structure noise. Moreover, we develop an iterative refinement mechanism to update the similarity mask during the training process for improving the training performance. Extensive experiments on four real-world datasets demonstrate the superior performance and robustness of PAMT.

cs.LG↗

arXiv2022

Tight Lower Complexity Bounds for Strongly Convex Finite-Sum Optimization

Finite-sum optimization plays an important role in the area of machine learning, and hence has triggered a surge of interest in recent years. To address this optimization problem, various randomized incremental gradient methods have been proposed with guaranteed upper and lower complexity bounds for their convergence. Nonetheless, these lower bounds rely on certain conditions: deterministic optimization algorithm, or fixed probability distribution for the selection of component functions. Meanwhile, some lower bounds even do not match the upper bounds of the best known methods in certain cases. To break these limitations, we derive tight lower complexity bounds of randomized incremental gradient methods, including SAG, SAGA, SVRG, and SARAH, for two typical cases of finite-sum optimization. Specifically, our results tightly match the upper complexity of Katyusha or VRADA when each component function is strongly convex and smooth, and tightly match the upper complexity of SDCA without duality and of KatyushaX when the finite-sum function is strongly convex and the component functions are average smooth.

cs.LG↗

arXiv2022

BandMaxSAT: A Local Search MaxSAT Solver with Multi-armed Bandit

We address Partial MaxSAT (PMS) and Weighted PMS (WPMS), two practical generalizations of the MaxSAT problem, and propose a local search algorithm for these problems, called BandMaxSAT, that applies a multi-armed bandit model to guide the search direction. The bandit in our method is associated with all the soft clauses in the input (W)PMS instance. Each arm corresponds to a soft clause. The bandit model can help BandMaxSAT to select a good direction to escape from local optima by selecting a soft clause to be satisfied in the current step, that is, selecting an arm to be pulled. We further propose an initialization method for (W)PMS that prioritizes both unit and binary clauses when producing the initial solutions. Extensive experiments demonstrate that BandMaxSAT significantly outperforms the state-of-the-art (W)PMS local search algorithm SATLike3.0. Specifically, the number of instances in which BandMaxSAT obtains better results is about twice that obtained by SATLike3.0. Moreover, we combine BandMaxSAT with the complete solver TT-Open-WBO-Inc. The resulting solver BandMaxSAT-c also outperforms some of the best state-of-the-art complete (W)PMS solvers, including SATLike-c, Loandra and TT-Open-WBO-Inc.

cs.AI↗

arXiv2022

Effective Variable Depth Local Search for the Budgeted Maximum Coverage Problem

We address the Budgeted Maximum Coverage Problem (BMCP), which is a natural and more practical extension of the standard 0-1 knapsack problem and the set cover problem. Given m elements with nonnegative weights, n subsets of elements with nonnegative costs, and a total budget, BMCP aims to select some subsets such that the total cost of selected subsets does not exceed the budget, and the total weight of associated elements is maximized. In this paper, we propose a variable depth local search algorithm (VDLS) for the BMCP. VDLS first generates an initial solution by a greedy algorithm, then iteratively improves the solution through a partial depth-first search method, that can improve the solution by simultaneously changing the states (selected or not) of multiple subsets. Such method allows VDLS to explore the solution space widely and deeply, and to yield high-quality solutions. We further propose a neighbour structure to boost the algorithm performance, that is, both subsets have a neighbour relation if they have at least one common associated element. By applying the neighbour structure, VDLS can adjust the selected subsets while losing as few covered elements as possible. Since the existing BMCP benchmarks only have simple structures and small scales, we design 60 new instances with relatively large scales and complex structures to enrich the diversity of the BMCP instances. Experimental results on 30 public instances and 60 new instances we designed demonstrate that VDLS significantly outperforms the existing heuristic and the general CPLEX exact solver, for the BMCP.

cs.DS↗

arXiv2022

An efficient thermal lattice Boltzmann method for simulating three-dimensional liquid-vapor phase change

In this paper, a multiple-relaxation-time lattice Boltzmann (LB) approach is developed for the simulation of three-dimensional (3D) liquid-vapor phase change based on the pseudopotential model. In contrast to some existing 3D thermal LB models for liquid-vapor phase change, the present approach has two advantages: for one thing, the current approach does not require calculating the gradient of volumetric heat capacity [i.e., $\nabla \left( {ρ{c_v}} \right)$], and for another, the current approach is constructed based on the seven discrete velocities in three dimensions (D3Q7), making the current thermal LB model more efficient and easy to implement. Also, based on the scheme proposed by Zhou and He [Phys Fluids 9:1591-1598, 1997], a pressure boundary condition for the D3Q19 lattice is proposed to model the multiphase flow in open systems. The current method is then validated by considering the temperature distribution in a 3D saturated liquid-vapor system, the $d^2$ law and the droplet evaporation on a heated surface. It is observed that the numerical results fit well with the analytical solutions, the results of the finite difference method and the experimental data. Our numerical results indicate that the present approach is reliable and efficient in dealing with the 3D liquid-vapor phase change.

math.NA↗

arXiv2022

HoSIM: Higher-order Structural Importance based Method for Multiple Local Community Detection

Local community detection has attracted much research attention recently, and many methods have been proposed for the single local community detection that finds a community containing the given set of query nodes. However, nodes may belong to several communities in the network, and detecting all the communities for the query node set, termed as the multiple local community detection (MLCD), is more important as it could uncover more potential information. MLCD is also more challenging because when a query node belongs to multiple communities, it always locates in the complicated overlapping region and the marginal region of communities. Accordingly, detecting multiple communities for such nodes by applying seed expansion methods is insufficient. In this work, we address the MLCD based on higher-order structural importance (HoSI). First, to effectively estimate the influence of higher-order structures, we propose a new variant of random walk called Active Random Walk to measure the HoSI score between nodes. Then, we propose two new metrics to evaluate the HoSI score of a subgraph to a node and the HoSI score of a node, respectively. Based on the proposed metrics, we present a novel algorithm called HoSIM to detect multiple local communities for a single query node. HoSIM enforces a three-stage processing, namely subgraph sampling, core member identification, and local community detection. The key idea is utilizing HoSI to find and identify the core members of communities relevant to the query node and optimize the generated communities. Extensive experiments illustrate the effectiveness of HoSIM.

cs.SI↗