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Register a new userA Novel Graph-based Approach for Determining Molecular Similarity
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In this paper, we tackle the problem of measuring similarity among graphs that represent real objects with noisy data. To account for noise, we relax the definition of similarity using the maximum weighted co-$k$-plex relaxation method, which allows dissimilarities among graphs up to a predetermined level. We then formulate the problem as a novel quadratic unconstrained binary optimization problem that can be solved by a quantum annealer. The context of our study is molecular similarity where the presence of noise might be due to regular errors in measuring molecular features. We develop a similarity measure and use it to predict the mutagenicity of a molecule. Our results indicate that the relaxed similarity measure, designed to accommodate the regular errors, yields a higher prediction accuracy than the measure that ignores the noise.
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Brain Electroencephalography (EEG) classification is widely applied to analyze cerebral diseases in recent years. Unfortunately, invalid/noisy EEGs degrade the diagnosis performance and most previously developed methods ignore the necessity of EEG selection for classification. To this end, this paper proposes a novel maximum weight clique-based EEG selection approach, named mwcEEGs, to map EEG selection to searching maximum similarity-weighted cliques from an improved Fr{e}chet distance-weighted undirected EEG graph simultaneously considering edge weights and vertex weights. Our mwcEEGs improves the classification performance by selecting intra-clique pairwise similar and inter-clique discriminative EEGs with similarity threshold $delta$. Experimental results demonstrate the algorithm effectiveness compared with the state-of-the-art time series selection algorithms on real-world EEG datasets.
The graph isomorphism problem is of practical importance, as well as being a theoretical curiosity in computational complexity theory in that it is not known whether it is $NP$-complete or $P$. However, for many graphs, the problem is tractable, and related to the problem of finding the automorphism group of the graph. Perhaps the most well known state-of-the art implementation for finding the automorphism group is Nauty. However, Nauty is particularly susceptible to poor performance on star configurations, where the spokes of the star are isomorphic with each other. In this work, I present an algorithm that explodes these star configurations, reducing the problem to a sequence of simpler automorphism group calculations.
Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular properties implicitly, existing works can hardly capture structural or property changes and complex structure, with much smaller atom vocabulary and highly frequent atoms. In this paper, we propose the Contrastive Knowledge-aware GNN (CKGNN) for self-supervised molecular representation learning to fuse domain knowledge into molecular graph representation. We explicitly encode domain knowledge via knowledge-aware molecular encoder under the contrastive learning framework, ensuring that the generated molecular embeddings equipped with chemical domain knowledge to distinguish molecules with similar chemical formula but dissimilar functions. Extensive experiments on 8 public datasets demonstrate the effectiveness of our model with a 6% absolute improvement on average against strong competitors. Ablation study and further investigation also verify the best of both worlds: incorporation of chemical domain knowledge into self-supervised learning.
Molecular graph generation is a fundamental but challenging task in various applications such as drug discovery and material science, which requires generating valid molecules with desired properties. Auto-regressive models, which usually construct graphs following sequential actions of adding nodes and edges at the atom-level, have made rapid progress in recent years. However, these atom-level models ignore high-frequency subgraphs that not only capture the regularities of atomic combination in molecules but also are often related to desired chemical properties. In this paper, we propose a method to automatically discover such common substructures, which we call {em graph pieces}, from given molecular graphs. Based on graph pieces, we leverage a variational autoencoder to generate molecules in two phases: piece-level graph generation followed by bond completion. Experiments show that our graph piece variational autoencoder achieves better performance over state-of-the-art baselines on property optimization and constrained property optimization tasks with higher computational efficiency.
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.
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