skip to main content

This content will become publicly available on July 20, 2022

Title: Multi-view spectral graph convolution with consistent edge attention for molecular modeling
Although graph convolutional networks (GCNs) that extend the convolution operation from images to graphs have led to competitive performance, the existing GCNs are still difficult to handle a variety of applications, especially cheminformatics problems. Recently multiple GCNs are applied to chemical compound structures which are represented by the hydrogen-depleted molecular graphs of different size. GCNs built for a binary adjacency matrix that reflects the connectivity among nodes in a graph do not account for the edge consistency in multiple molecular graphs, that is, chemical bonds (edges) in different molecular graphs can be similar due to the similar enthalpy and interatomic distance. In this paper, we propose a variant of GCN where a molecular graph is first decomposed into multiple views of the graph, each comprising a specific type of edges. In each view, an edge consistency constraint is enforced so that similar edges in different graphs can receive similar attention weights when passing information. Similarly to prior work, we prove that in each layer, our method corresponds to a spectral filter derived by the first order Chebyshev approximation of graph Laplacian. Extensive experiments demonstrate the substantial advantages of the proposed technique in quantitative structure-activity relationship prediction.
; ; ; ; ;
Award ID(s):
Publication Date:
Journal Name:
Page Range or eLocation-ID:
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract—Materials Genomics initiative has the goal of rapidly synthesizing materials with a given set of desired properties using data science techniques. An important step in this direction is the ability to predict the outcomes of complex chemical reactions. Some graph-based feature learning algorithms have been proposed recently. However, the comprehensive relationship between atoms or structures is not learned properly and not explainable, and multiple graphs cannot be handled. In this paper, chemical reaction processes are formulated as translation processes. Both atoms and edges are mapped to vectors represent- ing the structural information. We employ the graph convolution layers to learnmore »meaningful information of atom graphs, and further employ its variations, message passing networks (MPNN) and edge attention graph convolution network (EAGCN) to learn edge representations. Particularly, multi-view EAGCN groups and maps edges to a set of representations for the properties of the chemical bond between atoms from multiple views. Each bond is viewed from its atom type, bond type, distance and neighbor environment. The final node and edge representations are mapped to a sequence defined by the SMILES of the molecule and then fed to a decoder model with attention. To make full usage of multi-view information, we propose multi-view attention model to handle self correlation inside each atom or edge, and mutual correlation between edges and atoms, both of which are important in chemical reaction processes. We have evaluated our method on the standard benchmark datasets (that have been used by all the prior works), and the results show that edge embedding with multi-view attention achieves superior accuracy compared to existing techniques.« less
  2. Consider an algorithm performing a computation on a huge random object (for example a random graph or a "long" random walk). Is it necessary to generate the entire object prior to the computation, or is it possible to provide query access to the object and sample it incrementally "on-the-fly" (as requested by the algorithm)? Such an implementation should emulate the random object by answering queries in a manner consistent with an instance of the random object sampled from the true distribution (or close to it). This paradigm is useful when the algorithm is sub-linear and thus, sampling the entire objectmore »up front would ruin its efficiency. Our first set of results focus on undirected graphs with independent edge probabilities, i.e. each edge is chosen as an independent Bernoulli random variable. We provide a general implementation for this model under certain assumptions. Then, we use this to obtain the first efficient local implementations for the Erdös-Rényi G(n,p) model for all values of p, and the Stochastic Block model. As in previous local-access implementations for random graphs, we support Vertex-Pair and Next-Neighbor queries. In addition, we introduce a new Random-Neighbor query. Next, we give the first local-access implementation for All-Neighbors queries in the (sparse and directed) Kleinberg’s Small-World model. Our implementations require no pre-processing time, and answer each query using O(poly(log n)) time, random bits, and additional space. Next, we show how to implement random Catalan objects, specifically focusing on Dyck paths (balanced random walks on the integer line that are always non-negative). Here, we support Height queries to find the location of the walk, and First-Return queries to find the time when the walk returns to a specified location. This in turn can be used to implement Next-Neighbor queries on random rooted ordered trees, and Matching-Bracket queries on random well bracketed expressions (the Dyck language). Finally, we introduce two features to define a new model that: (1) allows multiple independent (and even simultaneous) instantiations of the same implementation, to be consistent with each other without the need for communication, (2) allows us to generate a richer class of random objects that do not have a succinct description. Specifically, we study uniformly random valid q-colorings of an input graph G with maximum degree Δ. This is in contrast to prior work in the area, where the relevant random objects are defined as a distribution with O(1) parameters (for example, n and p in the G(n,p) model). The distribution over valid colorings is instead specified via a "huge" input (the underlying graph G), that is far too large to be read by a sub-linear time algorithm. Instead, our implementation accesses G through local neighborhood probes, and is able to answer queries to the color of any given vertex in sub-linear time for q ≥ 9Δ, in a manner that is consistent with a specific random valid coloring of G. Furthermore, the implementation is memory-less, and can maintain consistency with non-communicating copies of itself.« less
  3. Abstract Gene co-expression networks (GCNs) provide multiple benefits to molecular research including hypothesis generation and biomarker discovery. Transcriptome profiles serve as input for GCN construction and are derived from increasingly larger studies with samples across multiple experimental conditions, treatments, time points, genotypes, etc. Such experiments with larger numbers of variables confound discovery of true network edges, exclude edges and inhibit discovery of context (or condition) specific network edges. To demonstrate this problem, a 475-sample dataset is used to show that up to 97% of GCN edges can be misleading because correlations are false or incorrect. False and incorrect correlations canmore »occur when tests are applied without ensuring assumptions are met, and pairwise gene expression may not meet test assumptions if the expression of at least one gene in the pairwise comparison is a function of multiple confounding variables. The ‘one-size-fits-all’ approach to GCN construction is therefore problematic for large, multivariable datasets. Recently, the Knowledge Independent Network Construction toolkit has been used in multiple studies to provide a dynamic approach to GCN construction that ensures statistical tests meet assumptions and confounding variables are addressed. Additionally, it can associate experimental context for each edge of the network resulting in context-specific GCNs (csGCNs). To help researchers recognize such challenges in GCN construction, and the creation of csGCNs, we provide a review of the workflow.« less
  4. Constructing a spanning tree of a graph is one of the most basic tasks in graph theory. We consider a relaxed version of this problem in the setting of local algorithms. The relaxation is that the constructed subgraph is a sparse spanning subgraph containing at most (1+ϵ)n edges (where n is the number of vertices and ϵ is a given approximation/sparsity parameter). In the local setting, the goal is to quickly determine whether a given edge e belongs to such a subgraph, without constructing the whole subgraph, but rather by inspecting (querying) the local neighborhood of e. The challenge ismore »to maintain consistency. That is, to provide answers concerning different edges according to the same spanning subgraph. We first show that for general bounded-degree graphs, the query complexity of any such algorithm must be Ω(n−−√). This lower bound holds for constant-degree graphs that have high expansion. Next we design an algorithm for (bounded-degree) graphs with high expansion, obtaining a result that roughly matches the lower bound. We then turn to study graphs that exclude a fixed minor (and are hence non-expanding). We design an algorithm for such graphs, which may have an unbounded maximum degree. The query complexity of this algorithm is poly(1/ϵ,h) (independent of n and the maximum degree), where h is the number of vertices in the excluded minor. Though our two algorithms are designed for very different types of graphs (and have very different complexities), on a high-level there are several similarities, and we highlight both the similarities and the differences.« less
  5. Given a directed acyclic graph (DAG) G=(V,E), we say that G is (e,d)-depth-robust (resp. (e,d)-edge-depth-robust) if for any set S⊆V (resp. S⊆E) of at most |S|≤e nodes (resp. edges) the graph G−S contains a directed path of length d. While edge-depth-robust graphs are potentially easier to construct, many applications in cryptography require node depth-robust graphs with small indegree. We create a graph reduction that transforms an (e,d)-edge-depth-robust graph with m edges into a (e/2,d)-depth-robust graph with O(m) nodes and constant indegree. One immediate consequence of this result is the first construction of a provably (nloglognlogn,nlogn(logn)loglogn)-depth-robust graph with constant indegree. Ourmore »reduction crucially relies on ST-robust graphs, a new graph property we introduce which may be of independent interest. We say that a directed, acyclic graph with n inputs and n outputs is (k1,k2)-ST-robust if we can remove any k1 nodes and there exists a subgraph containing at least k2 inputs and k2 outputs such that each of the k2 inputs is connected to all of the k2 outputs. If the graph if (k1,n−k1)-ST-robust for all k1≤n we say that the graph is maximally ST-robust. We show how to construct maximally ST-robust graphs with constant indegree and O(n) nodes. Given a family M of ST-robust graphs and an arbitrary (e,d)-edge-depth-robust graph G we construct a new constant-indegree graph Reduce(G,M) by replacing each node in G with an ST-robust graph from M. We also show that ST-robust graphs can be used to construct (tight) proofs-of-space and (asymptotically) improved wide-block labeling functions.« less