Accurate prediction of the binding affinity between drugs and target proteins is a core task in computer-aided drug design. Existing deep learning methods tend to ignore the information of internal sub-structural features of drug molecules and drug-target interactions, resulting in limited prediction performance. In this paper, we propose a drug-target association prediction model HCAF-DTA based on cross-attention fusion hypergraph neural network. The model innovatively introduces hypergraph representation in the feature extraction stage: drug molecule hypergraphs are constructed based on the tree decomposition algorithm, and the sub-structural and global features extracted by fusing the hypergraph neural network with the graphical neural network through hopping connections, in which the hyper edges can efficiently characterise the functional functional groups and other key chemical features; for the protein feature extraction, a weighted graph is constructed based on the residues predicted by the ESM model contact maps to construct weighted graphs, and multilayer graph neural networks were used to capture spatial dependencies. In the prediction stage, a bidirectional multi-head cross-attention mechanism is designed to model intermolecular interactions from the dual viewpoints of atoms and amino acids, and cross-modal features with correlated information are fused by attention. Experiments on benchmark datasets such as Davis and KIBA show that HCAF-DTA outperforms state of the arts in all three performance evaluation metrics, with the MSE metrics reaching 0.198 and 0.122, respectively, with an improvement of up to 4% from the optimal baseline.
The goal of graph inference is to design algorithms for learning properties of a hidden graph using queries to an oracle that returns information about the graph. Graph reconstruction, verification, and property testing are all types of graph inference. In this work, we study graph inference using an oracle that returns the effective resistance (ER) between a pair of vertices. Effective resistance is a distance originating from the study of electrical circuits with many applications. However, ER has received little attention from a graph inference perspective. Indeed, although it is known that an $n$-vertex graph can be uniquely reconstructed from all $\binom{n}{2}$ possible ER queries, little else is known. We address this gap with several new results, including: 1. $O(n)$-query algorithms for testing whether a graph is a tree; deciding whether two graphs are equal assuming one is a subgraph of the other; and testing whether a given vertex (or edge) is a cut vertex (or cut edge). 2. Property testing algorithms, including for testing whether a graph is vertex- or edge-biconnected. We also give a reduction to adapt property testing results from the bounded-degree model to our ER query model. This yields ER-query-based algorithms for testing $k$-connectivity, bipartiteness, planarity, and containment of a fixed subgraph. 3. Graph reconstruction algorithms, including an algorithm for reconstructing a graph from a low-width tree decomposition; a $\Theta(k^2)$-query, polynomial-time algorithm for recovering the adjacency matrix $A$ of a hidden graph, given $A$ with $k$ of its entries deleted; and a $k$-query, exponential-time algorithm for the same task. We also compare the power of ER queries and shortest path queries, which are closely related but better studied. Interestingly, we show that the two query models are incomparable in power.
Over the past decade, several image-processing methods and algorithms have been proposed for identifying plant diseases based on visual data. DNN (Deep Neural Networks) have recently become popular for this task. Both traditional image processing and DNN-based methods encounter significant performance issues in real-time detection owing to computational limitations and a broad spectrum of plant disease features. This article proposes a novel technique for identifying and localising plant disease based on the Quad-Tree decomposition of an image and feature learning simultaneously. The proposed algorithm significantly improves accuracy and faster convergence in high-resolution images with relatively low computational load. Hence it is ideal for deploying the algorithm in a standalone processor in a remotely operated image acquisition and disease detection system, ideally mounted on drones and robots working on large agricultural fields. The technique proposed in this article is hybrid as it exploits the advantages of traditional image processing methods and DNN-based models at different scales, resulting in faster inference. The F1 score is approximately 0.80 for four disease classes corresponding to potato and tomato crops.
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination, reassortment, hybridization, or horizontal gene transfer. Typically, the complexity of a phylogenetic network is expressed in terms of its level, i.e., the maximum number of edges that are required to be removed from each biconnected component of the phylogenetic network to turn it into a tree. Here, we study the relationship between the level of a phylogenetic network and another popular graph complexity parameter - treewidth. We show a $\frac{k+3}{2}$ upper bound on the treewidth of level-$k$ phylogenetic networks and an improved $(1/3 + \delta) k$ upper bound for large $k$. These bounds imply that many computational problems on phylogenetic networks, such as the small parsimony problem or some variants of phylogenetic diversity maximization, are polynomial-time solvable on level-$k$ networks with constant $k$. Our first bound is applicable to any $k$, and it allows us to construct an explicit tree decomposition of width $\frac{k+3}{2}$ that can be used to analyze phylogenetic networks generated by tools like SNAQ that guarantee bounded network level. Finally, we show a $k/13$ lower bound on the maximum treewidth among level-$k$ phylogenetic networks for large enough $k$ based on expander graphs.
Answering complex queries over incomplete knowledge graphs (KGs) is a challenging job. Most previous works have focused on learning entity/relation embeddings and simulating first-order logic operators with various neural networks. However, they are bottlenecked by the inability to share world knowledge to improve logical reasoning, thus resulting in suboptimal performance. In this paper, we propose a complex reasoning schema over KG upon large language models (LLMs), containing a curriculum-based logical-aware instruction tuning framework, named LACT. Specifically, we augment the arbitrary first-order logical queries via binary tree decomposition, to stimulate the reasoning capability of LLMs. To address the difficulty gap among different types of complex queries, we design a simple and flexible logic-aware curriculum learning framework. Experiments across widely used datasets demonstrate that LACT has substantial improvements~(brings an average +5.5% MRR score) over advanced methods, achieving the new state-of-the-art. Our code and model will be released at GitHub and huggingface soon.
We show how any PAC learning algorithm that works under the uniform distribution can be transformed, in a blackbox fashion, into one that works under an arbitrary and unknown distribution $\mathcal{D}$. The efficiency of our transformation scales with the inherent complexity of $\mathcal{D}$, running in $\mathrm{poly}(n, (md)^d)$ time for distributions over $\{\pm 1\}^n$ whose pmfs are computed by depth-$d$ decision trees, where $m$ is the sample complexity of the original algorithm. For monotone distributions our transformation uses only samples from $\mathcal{D}$, and for general ones it uses subcube conditioning samples. A key technical ingredient is an algorithm which, given the aforementioned access to $\mathcal{D}$, produces an optimal decision tree decomposition of $\mathcal{D}$: an approximation of $\mathcal{D}$ as a mixture of uniform distributions over disjoint subcubes. With this decomposition in hand, we run the uniform-distribution learner on each subcube and combine the hypotheses using the decision tree. This algorithmic decomposition lemma also yields new algorithms for learning decision tree distributions with runtimes that exponentially improve on the prior state of the art -- results of independent interest in distribution learning.
We propose a new approach, the calibrated nonparametric scan statistic (CNSS), for more accurate detection of anomalous patterns in large-scale, real-world graphs. Scan statistics identify connected subgraphs that are interesting or unexpected through maximization of a likelihood ratio statistic; in particular, nonparametric scan statistics (NPSSs) identify subgraphs with a higher than expected proportion of individually significant nodes. However, we show that recently proposed NPSS methods are miscalibrated, failing to account for the maximization of the statistic over the multiplicity of subgraphs. This results in both reduced detection power for subtle signals, and low precision of the detected subgraph even for stronger signals. Thus we develop a new statistical approach to recalibrate NPSSs, correctly adjusting for multiple hypothesis testing and taking the underlying graph structure into account. While the recalibration, based on randomization testing, is computationally expensive, we propose both an efficient (approximate) algorithm and new, closed-form lower bounds (on the expected maximum proportion of significant nodes for subgraphs of a given size, under the null hypothesis of no anomalous patterns). These advances, along with the integration of recent core-tree decomposition methods, enable CNSS to scale to large real-world graphs, with substantial improvement in the accuracy of detected subgraphs. Extensive experiments on both semi-synthetic and real-world datasets are demonstrated to validate the effectiveness of our proposed methods, in comparison with state-of-the-art counterparts.
Active Directory is the default security management system for Windows domain networks. We study the shortest path edge interdiction problem for defending Active Directory style attack graphs. The problem is formulated as a Stackelberg game between one defender and one attacker. The attack graph contains one destination node and multiple entry nodes. The attacker's entry node is chosen by nature. The defender chooses to block a set of edges limited by his budget. The attacker then picks the shortest unblocked attack path. The defender aims to maximize the expected shortest path length for the attacker, where the expectation is taken over entry nodes. We observe that practical Active Directory attack graphs have small maximum attack path lengths and are structurally close to trees. We first show that even if the maximum attack path length is a constant, the problem is still $W[1]$-hard with respect to the defender's budget. Having a small maximum attack path length and a small budget is not enough to design fixed-parameter algorithms. If we further assume that the number of entry nodes is small, then we derive a fixed-parameter tractable algorithm. We then propose two other fixed-parameter algorithms by exploiting the tree-like features. One is based on tree decomposition and requires a small tree width. The other assumes a small number of splitting nodes (nodes with multiple out-going edges). Finally, the last algorithm is converted into a graph convolutional neural network based heuristic, which scales to larger graphs with more splitting nodes.
Graph encoders in AMR-to-text generation models often rely on neighborhood convolutions or global vertex attention. While these approaches apply to general graphs, AMRs may be amenable to encoders that target their tree-like structure. By clustering edges into a hierarchy, a tree decomposition summarizes graph structure. Our model encodes a derivation forest of tree decompositions and extracts an expected tree. From tree node embeddings, it builds graph edge features used in vertex attention of the graph encoder. Encoding TD forests instead of shortest-pairwise paths in a self-attentive baseline raises BLEU by 0.7 and chrF++ by 0.3. The forest encoder also surpasses a convolutional baseline for molecular property prediction by 1.92% ROC-AUC.
Graph Neural Networks (GNNs) have achieved significant success in learning better representations by performing feature propagation and transformation iteratively to leverage neighborhood information. Nevertheless, iterative propagation restricts the information of higher-layer neighborhoods to be transported through and fused with the lower-layer neighborhoods', which unavoidably results in feature smoothing between neighborhoods in different layers and can thus compromise the performance, especially on heterophily networks. Furthermore, most deep GNNs only recognize the importance of higher-layer neighborhoods while yet to fully explore the importance of multi-hop dependency within the context of different layer neighborhoods in learning better representations. In this work, we first theoretically analyze the feature smoothing between neighborhoods in different layers and empirically demonstrate the variance of the homophily level across neighborhoods at different layers. Motivated by these analyses, we further propose a tree decomposition method to disentangle neighborhoods in different layers to alleviate feature smoothing among these layers. Moreover, we characterize the multi-hop dependency via graph diffusion within our tree decomposition formulation to construct Tree Decomposed Graph Neural Network (TDGNN), which can flexibly incorporate information from large receptive fields and aggregate this information utilizing the multi-hop dependency. Comprehensive experiments demonstrate the superior performance of TDGNN on both homophily and heterophily networks under a variety of node classification settings. Extensive parameter analysis highlights the ability of TDGNN to prevent over-smoothing and incorporate features from shallow layers with deeper multi-hop dependencies, which provides new insights towards deeper graph neural networks. Code of TDGNN: http://github.com/YuWVandy/TDGNN
Computing the Newton-step of a generic function with $N$ decision variables takes $O(N^3)$ flops. In this paper, we show that given the computational graph of the function, this bound can be reduced to $O(m\tau^3)$, where $\tau, m$ are the width and size of a tree-decomposition of the graph. The proposed algorithm generalizes nonlinear optimal-control methods based on LQR to general optimization problems and provides non-trivial gains in iteration-complexity even in cases where the Hessian is dense.
We propose TD-GEN, a graph generation framework based on tree decomposition, and introduce a reduced upper bound on the maximum number of decisions needed for graph generation. The framework includes a permutation invariant tree generation model which forms the backbone of graph generation. Tree nodes are supernodes, each representing a cluster of nodes in the graph. Graph nodes and edges are incrementally generated inside the clusters by traversing the tree supernodes, respecting the structure of the tree decomposition, and following node sharing decisions between the clusters. Finally, we discuss the shortcomings of standard evaluation criteria based on statistical properties of the generated graphs as performance measures. We propose to compare the performance of models based on likelihood. Empirical results on a variety of standard graph generation datasets demonstrate the superior performance of our method.
Protein side-chain packing is a critical component in obtaining the 3D coordinates of a structure and drug discovery. Single-domain protein side-chain packing has been thoroughly studied. A major challenge in generalizing these methods to protein complexes is that they, unlike monomers, often have very large treewidth, and thus algorithms such as TreePack cannot be directly applied. To address this issue, SCWRL4 treats the complex effectively as a monomer, heuristically excluding weak interactions to decrease treewidth; as a result, SCWRL4 generates poor packings on protein interfaces. To date, few side-chain packing methods exist that are specifically designed for protein complexes. In this paper, we introduce a method, iTreePack, which solves the side-chain packing problem for complexes by using a novel combination of dual decomposition and tree decomposition. In particular, iTreePack overcomes the problem of large treewidth by decomposing a protein complex into smaller subgraphs and novelly reformulating the complex side-chain packing problem as a dual relaxation problem; this allows us to solve the side-chain packing of each small subgraph separately using tree-decomposition. A projected subgradient algorithm is applied to enforcing the consistency among the side-chain packings of all the small subgraphs. Computational results demonstrate that our iTreePack program outperforms SCWRL4 on protein complexes. In particular, iTreePack places side-chain atoms much more accurately on very large complexes, which constitute a significant portion of protein-protein interactions. Moreover, the advantage of iTreePack over SCWRL4 increases with respect to the treewidth of a complex. Even for monomeric proteins, iTreePack is much more efficient than SCWRL and slightly more accurate.
A considerable amount of success has been achieved in developing monolingual OCR systems for Indic scripts. But in a country like India, where multi-script scenario is prevalent, identifying scripts beforehand becomes obligatory. In this paper, we present the significance of Gabor wavelets filters in extracting directional energy and entropy distributions for 11 official handwritten scripts namely, Bangla, Devanagari, Gujarati, Gurumukhi, Kannada, Malayalam, Oriya, Tamil, Telugu, Urdu and Roman. The experimentation is conducted at block level based on a quad-tree decomposition approach and evaluated using six different well-known classifiers. Finally, the best identification accuracy of 96.86% has been achieved by Multi Layer Perceptron (MLP) classifier for 3-fold cross validation at level-2 decomposition. The results serve to establish the efficacy of the present approach to the classification of handwritten Indic scripts
We propose a unifying dynamic-programming framework to compute exact literal-weighted model counts of formulas in conjunctive normal form. At the center of our framework are project-join trees, which specify efficient project-join orders to apply additive projections (variable eliminations) and joins (clause multiplications). In this framework, model counting is performed in two phases. First, the planning phase constructs a project-join tree from a formula. Second, the execution phase computes the model count of the formula, employing dynamic programming as guided by the project-join tree. We empirically evaluate various methods for the planning phase and compare constraint-satisfaction heuristics with tree-decomposition tools. We also investigate the performance of different data structures for the execution phase and compare algebraic decision diagrams with tensors. We show that our dynamic-programming model-counting framework DPMC is competitive with the state-of-the-art exact weighted model counters cachet, c2d, d4, and miniC2D.
We propose a Reinforcement Learning based approach to approximately solve the Tree Decomposition (TD) problem. TD is a combinatorial problem, which is central to the analysis of graph minor structure and computational complexity, as well as in the algorithms of probabilistic inference, register allocation, and other practical tasks. Recently, it has been shown that combinatorial problems can be successively solved by learned heuristics. However, the majority of existing works do not address the question of the generalization of learning-based solutions. Our model is based on the graph convolution neural network (GCN) for learning graph representations. We show that the agent builton GCN and trained on a single graph using an Actor-Critic method can efficiently generalize to real-world TD problem instances. We establish that our method successfully generalizes from small graphs, where TD can be found by exact algorithms, to large instances of practical interest, while still having very low time-to-solution. On the other hand, the agent-based approach surpasses all greedy heuristics by the quality of the solution.
Sparse residual tree (SRT) is an adaptive exploration method for multivariate scattered data approximation. It leads to sparse and stable approximations in areas where the data is sufficient or redundant, and points out the possible local regions where data refinement is needed. Sparse residual forest (SRF) is a combination of SRT predictors to further improve the approximation accuracy and stability according to the error characteristics of SRTs. The hierarchical parallel SRT algorithm is based on both tree decomposition and adaptive radial basis function (RBF) explorations, whereby for each child a sparse and proper RBF refinement is added to the approximation by minimizing the norm of the residual inherited from its parent. The convergence results are established for both SRTs and SRFs. The worst case time complexity of SRTs is $\mathcal{O}(N\log_2N)$ for the initial work and $\mathcal{O}(\log_2N)$ for each prediction, meanwhile, the worst case storage requirement is $\mathcal{O}(N\log_2N)$, where the $N$ data points can be arbitrary distributed. Numerical experiments are performed for several illustrative examples.
Answer Set Programming (ASP) is a purely declarative formalism developed in the field of logic programming and nonmonotonic reasoning: computational problems are encoded by logic programs whose answer sets, corresponding to solutions, are computed by an ASP system. Different, semantically equivalent, programs can be defined for the same problem; however, performance of systems evaluating them might significantly vary. We propose an approach for automatically transforming an input logic program into an equivalent one that can be evaluated more efficiently. One can make use of existing tree-decomposition techniques for rewriting selected rules into a set of multiple ones; the idea is to guide and adaptively apply them on the basis of proper new heuristics, to obtain a smart rewriting algorithm to be integrated into an ASP system. The method is rather general: it can be adapted to any system and implement different preference policies. Furthermore, we define a set of new heuristics tailored at optimizing grounding, one of the main phases of the ASP computation; we use them in order to implement the approach into the ASP system DLV, in particular into its grounding subsystem I-DLV, and carry out an extensive experimental activity for assessing the impact of the proposal. Under consideration in Theory and Practice of Logic Programming (TPLP).
In recent years, spectral clustering has become one of the most popular clustering algorithms for image segmentation. However, it has restricted applicability to large-scale images due to its high computational complexity. In this paper, we first propose a novel algorithm called Fast Spectral Clustering based on quad-tree decomposition. The algorithm focuses on the spectral clustering at superpixel level and its computational complexity is O(nlogn) + O(m) + O(m^(3/2)); its memory cost is O(m), where n and m are the numbers of pixels and the superpixels of a image. Then we propose Multiscale Fast Spectral Clustering by improving Fast Spectral Clustering, which is based on the hierarchical structure of the quad-tree. The computational complexity of Multiscale Fast Spectral Clustering is O(nlogn) and its memory cost is O(m). Extensive experiments on real large-scale images demonstrate that Multiscale Fast Spectral Clustering outperforms Normalized cut in terms of lower computational complexity and memory cost, with comparable clustering accuracy.
This paper describes a generalization of previous methods for constructing tree-structured belief network with hidden variables. The major new feature of the described method is the ability to produce a tree decomposition even when there are errors in the correlation data among the input variables. This is an important extension of existing methods since the correlational coefficients usually cannot be measured with precision. The technique involves using a greedy search algorithm that locally minimizes an error function.