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Register a new userTri-graph Information Propagation for Polypharmacy Side Effect Prediction
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The use of drug combinations often leads to polypharmacy side effects (POSE). A recent method formulates POSE prediction as a link prediction problem on a graph of drugs and proteins, and solves it with Graph Convolutional Networks (GCNs). However, due to the complex relationships in POSE, this method has high computational cost and memory demand. This paper proposes a flexible Tri-graph Information Propagation (TIP) model that operates on three subgraphs to learn representations progressively by propagation from protein-protein graph to drug-drug graph via protein-drug graph. Experiments show that TIP improves accuracy by 7%+, time efficiency by 83$times$, and space efficiency by 3$times$.
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Supervised, semi-supervised, and unsupervised learning estimate a function given input/output samples. Generalization of the learned function to unseen data can be improved by incorporating side information into learning. Side information are data that are neither from the input space nor from the output space of the function, but include useful information for learning it. In this paper we show that learning with side information subsumes a variety of related approaches, e.g. multi-task learning, multi-view learning and learning using privileged information. Our main contributions are (i) a new perspective that connects these previously isolated approaches, (ii) insights about how these methods incorporate different types of prior knowledge, and hence implement different patterns, (iii) facilitating the application of these methods in novel tasks, as well as (iv) a systematic experimental evaluation of these patterns in two supervised learning tasks.
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can prioritize disease-causing mutations have, therefore, enormous applications. It is well-known that genes function through a complex regulatory network. However, existing variant effect prediction models only consider a variant in isolation. In contrast, we propose VEGN, which models variant effect prediction using a graph neural network (GNN) that operates on a heterogeneous graph with genes and variants. The graph is created by assigning variants to genes and connecting genes with an gene-gene interaction network. In this context, we explore an approach where a gene-gene graph is given and another where VEGN learns the gene-gene graph and therefore operates both on given and learnt edges. The graph neural network is trained to aggregate information between genes, and between genes and variants. Variants can exchange information via the genes they connect to. This approach improves the performance of existing state-of-the-art models.
Graph neural networks (GNNs) have been popularly used in analyzing graph-structured data, showing promising results in various applications such as node classification, link prediction and network recommendation. In this paper, we present a new graph attention neural network, namely GIPA, for attributed graph data learning. GIPA consists of three key components: attention, feature propagation and aggregation. Specifically, the attention component introduces a new multi-layer perceptron based multi-head to generate better non-linear feature mapping and representation than conventional implementations such as dot-product. The propagation component considers not only node features but also edge features, which differs from existing GNNs that merely consider node features. The aggregation component uses a residual connection to generate the final embedding. We evaluate the performance of GIPA using the Open Graph Benchmark proteins (ogbn-proteins for short) dataset. The experimental results reveal that GIPA can beat the state-of-the-art models in terms of prediction accuracy, e.g., GIPA achieves an average test ROC-AUC of $0.8700pm 0.0010$ and outperforms all the previous methods listed in the ogbn-proteins leaderboard.
We give an online algorithm and prove novel mistake and regret bounds for online binary matrix completion with side information. The mistake bounds we prove are of the form $tilde{O}(D/gamma^2)$. The term $1/gamma^2$ is analogous to the usual margin term in SVM (perceptron) bounds. More specifically, if we assume that there is some factorization of the underlying $m times n$ matrix into $P Q^intercal$ where the rows of $P$ are interpreted as classifiers in $mathcal{R}^d$ and the rows of $Q$ as instances in $mathcal{R}^d$, then $gamma$ is the maximum (normalized) margin over all factorizations $P Q^intercal$ consistent with the observed matrix. The quasi-dimension term $D$ measures the quality of side information. In the presence of vacuous side information, $D= m+n$. However, if the side information is predictive of the underlying factorization of the matrix, then in an ideal case, $D in O(k + ell)$ where $k$ is the number of distinct row factors and $ell$ is the number of distinct column factors. We additionally provide a generalization of our algorithm to the inductive setting. In this setting, we provide an example where the side information is not directly specified in advance. For this example, the quasi-dimension $D$ is now bounded by $O(k^2 + ell^2)$.
Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is aligning model design with strategies adopted by chemists. Building on this viewpoint, this paper introduces a graph-based approach that capitalizes on the idea that the graph topology of precursor molecules is largely unaltered during a chemical reaction. The model first predicts the set of graph edits transforming the target into incomplete molecules called synthons. Next, the model learns to expand synthons into complete molecules by attaching relevant leaving groups. This decomposition simplifies the architecture, making its predictions more interpretable, and also amenable to manual correction. Our model achieves a top-1 accuracy of $53.7%$, outperforming previous template-free and semi-template-based methods.
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