arXiv subjects

Li-Ping Liu

Publications and source records attributed to Li-Ping Liu.

28 records · Page 2Linked to original sources

arXiv2022

Towards Accurate Subgraph Similarity Computation via Neural Graph Pruning

Subgraph similarity search, one of the core problems in graph search, concerns whether a target graph approximately contains a query graph. The problem is recently touched by neural methods. However, current neural methods do not consider pruning the target graph, though pruning is critically important in traditional calculations of subgraph similarities. One obstacle to applying pruning in neural methods is {the discrete property of pruning}. In this work, we convert graph pruning to a problem of node relabeling and then relax it to a differentiable problem. Based on this idea, we further design a novel neural network to approximate a type of subgraph distance: the subgraph edit distance (SED). {In particular, we construct the pruning component using a neural structure, and the entire model can be optimized end-to-end.} In the design of the model, we propose an attention mechanism to leverage the information about the query graph and guide the pruning of the target graph. Moreover, we develop a multi-head pruning strategy such that the model can better explore multiple ways of pruning the target graph. The proposed model establishes new state-of-the-art results across seven benchmark datasets. Extensive analysis of the model indicates that the proposed model can reasonably prune the target graph for SED computation. The implementation of our algorithm is released at our Github repo: https://github.com/tufts-ml/Prune4SED.

cs.LG↗

arXiv2022

Predicting Physics in Mesh-reduced Space with Temporal Attention

Graph-based next-step prediction models have recently been very successful in modeling complex high-dimensional physical systems on irregular meshes. However, due to their short temporal attention span, these models suffer from error accumulation and drift. In this paper, we propose a new method that captures long-term dependencies through a transformer-style temporal attention model. We introduce an encoder-decoder structure to summarize features and create a compact mesh representation of the system state, to allow the temporal model to operate on a low-dimensional mesh representations in a memory efficient manner. Our method outperforms a competitive GNN baseline on several complex fluid dynamics prediction tasks, from sonic shocks to vascular flow. We demonstrate stable rollouts without the need for training noise and show perfectly phase-stable predictions even for very long sequences. More broadly, we believe our approach paves the way to bringing the benefits of attention-based sequence models to solving high-dimensional complex physics tasks.

cs.LG↗

arXiv2021

Stochastic Iterative Graph Matching

Recent works leveraging Graph Neural Networks to approach graph matching tasks have shown promising results. Recent progress in learning discrete distributions poses new opportunities for learning graph matching models. In this work, we propose a new model, Stochastic Iterative Graph MAtching (SIGMA), to address the graph matching problem. Our model defines a distribution of matchings for a graph pair so the model can explore a wide range of possible matchings. We further introduce a novel multi-step matching procedure, which learns how to refine a graph pair's matching results incrementally. The model also includes dummy nodes so that the model does not have to find matchings for nodes without correspondence. We fit this model to data via scalable stochastic optimization. We conduct extensive experiments across synthetic graph datasets as well as biochemistry and computer vision applications. Across all tasks, our results show that SIGMA can produce significantly improved graph matching results compared to state-of-the-art models. Ablation studies verify that each of our components (stochastic training, iterative matching, and dummy nodes) offers noticeable improvement.

cs.LG↗

arXiv2021

Ladder Polynomial Neural Networks

Polynomial functions have plenty of useful analytical properties, but they are rarely used as learning models because their function class is considered to be restricted. This work shows that when trained properly polynomial functions can be strong learning models. Particularly this work constructs polynomial feedforward neural networks using the product activation, a new activation function constructed from multiplications. The new neural network is a polynomial function and provides accurate control of its polynomial order. It can be trained by standard training techniques such as batch normalization and dropout. This new feedforward network covers several previous polynomial models as special cases. Compared with common feedforward neural networks, the polynomial feedforward network has closed-form calculations of a few interesting quantities, which are very useful in Bayesian learning. In a series of regression and classification tasks in the empirical study, the proposed model outperforms previous polynomial models.

cs.LG↗

arXiv2021

Modeling Graph Node Correlations with Neighbor Mixture Models

We propose a new model, the Neighbor Mixture Model (NMM), for modeling node labels in a graph. This model aims to capture correlations between the labels of nodes in a local neighborhood. We carefully design the model so it could be an alternative to a Markov Random Field but with more affordable computations. In particular, drawing samples and evaluating marginal probabilities of single labels can be done in linear time. To scale computations to large graphs, we devise a variational approximation without introducing extra parameters. We further use graph neural networks (GNNs) to parameterize the NMM, which reduces the number of learnable parameters while allowing expressive representation learning. The proposed model can be either fit directly to large observed graphs or used to enable scalable inference that preserves correlations for other distributions such as deep generative graph models. Across a diverse set of node classification, image denoising, and link prediction tasks, we show our proposed NMM advances the state-of-the-art in modeling real-world labeled graphs.

cs.LG↗

arXiv2020

GAN Ensemble for Anomaly Detection

When formulated as an unsupervised learning problem, anomaly detection often requires a model to learn the distribution of normal data. Previous works apply Generative Adversarial Networks (GANs) to anomaly detection tasks and show good performances from these models. Motivated by the observation that GAN ensembles often outperform single GANs in generation tasks, we propose to construct GAN ensembles for anomaly detection. In the proposed method, a group of generators and a group of discriminators are trained together, so every generator gets feedback from multiple discriminators, and vice versa. Compared to a single GAN, a GAN ensemble can better model the distribution of normal data and thus better detect anomalies. Our theoretical analysis of GANs and GAN ensembles explains the role of a GAN discriminator in anomaly detection. In the empirical study, we evaluate ensembles constructed from four types of base models, and the results show that these ensembles clearly outperform single models in a series of tasks of anomaly detection.

cs.LG↗

arXiv2020

Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling

Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurements, we present an inference-based approach, termed Probabilistic modeling for Untargeted Metabolomics Analysis (PUMA). Our approach captures measurements and known information about the sample under study in a generative model and uses stochastic sampling to compute posterior probability distributions. PUMA predicts the likelihood of pathways being active, and then derives a probabilistic annotation, which assigns chemical identities to the measurements. PUMA is validated on synthetic datasets. When applied to test cases, the resulting pathway activities are biologically meaningful and distinctly different from those obtained using statistical pathway enrichment techniques. Annotation results are in agreement to those obtained using other tools that utilize additional information in the form of spectral signatures. Importantly, PUMA annotates many additional measurements.

q-bio.QM↗

arXiv2020

Learning graph representations of biochemical networks and its application to enzymatic link prediction

The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, Enzymatic Link Prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions catalogued in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity. We explore both transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding for predicting enzymatic links improves link prediction by 24% over fingerprint-similarity-based approaches. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can also guide visualization. The code and datasets are available through https://github.com/HassounLab/ELP.

q-bio.MN↗

arXiv2015

Transductive Optimization of Top k Precision

Consider a binary classification problem in which the learner is given a labeled training set, an unlabeled test set, and is restricted to choosing exactly $k$ test points to output as positive predictions. Problems of this kind---{\it transductive precision@$k$}---arise in information retrieval, digital advertising, and reserve design for endangered species. Previous methods separate the training of the model from its use in scoring the test points. This paper introduces a new approach, Transductive Top K (TTK), that seeks to minimize the hinge loss over all training instances under the constraint that exactly $k$ test instances are predicted as positive. The paper presents two optimization methods for this challenging problem. Experiments and analysis confirm the importance of incorporating the knowledge of $k$ into the learning process. Experimental evaluations of the TTK approach show that the performance of TTK matches or exceeds existing state-of-the-art methods on 7 UCI datasets and 3 reserve design problem instances.

cs.LG↗

arXiv2014

Gaussian Approximation of Collective Graphical Models

The Collective Graphical Model (CGM) models a population of independent and identically distributed individuals when only collective statistics (i.e., counts of individuals) are observed. Exact inference in CGMs is intractable, and previous work has explored Markov Chain Monte Carlo (MCMC) and MAP approximations for learning and inference. This paper studies Gaussian approximations to the CGM. As the population grows large, we show that the CGM distribution converges to a multivariate Gaussian distribution (GCGM) that maintains the conditional independence properties of the original CGM. If the observations are exact marginals of the CGM or marginals that are corrupted by Gaussian noise, inference in the GCGM approximation can be computed efficiently in closed form. If the observations follow a different noise model (e.g., Poisson), then expectation propagation provides efficient and accurate approximate inference. The accuracy and speed of GCGM inference is compared to the MCMC and MAP methods on a simulated bird migration problem. The GCGM matches or exceeds the accuracy of the MAP method while being significantly faster.

cs.LG↗