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Nick Duffield

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6 papers

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NeurIPS Conference 2025 Conference Paper

Spectral Convolutional Conditional Neural Processes

Peiman Mohseni
Nick Duffield

Neural Processes (NPs) are meta-learning models that learn to map sets of observations to approximations of the corresponding posterior predictive distributions. By accommodating variable-sized, unstructured collections of observations and enabling probabilistic predictions at arbitrary query points, NPs provide a flexible framework for modeling functions over continuous domains. Since their introduction, numerous variants have emerged; however, early formulations shared a fundamental limitation: they compressed the observed data into finite-dimensional global representations via aggregation operations such as mean pooling. This strategy induces an intrinsic mismatch with the infinite-dimensional nature of the stochastic processes that NPs intend to model. Convolutional conditional neural processes (ConvCNPs) address this limitation by constructing infinite-dimensional functional embeddings processed through convolutional neural networks (CNNs) to enforce translation equivariance. Yet CNNs with local spatial kernels struggle to capture long-range dependencies without resorting to large kernels, which impose significant computational costs. To overcome this limitation, we propose spectral ConvCNPs (SConvCNPs), which perform global convolution in the frequency domain. Inspired by Fourier neural operators (FNOs) for learning solution operators of partial differential equations (PDEs), our approach directly parameterizes convolution kernels in the frequency domain, leveraging the relatively compact yet global Fourier representation of many natural signals. We validate the effectiveness of SConvCNPs on both synthetic and real-world datasets, demonstrating how ideas from operator learning can advance the capabilities of NPs.

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NeurIPS Conference 2020 Conference Paper

Adaptive Shrinkage Estimation for Streaming Graphs

Nesreen Ahmed
Nick Duffield

Networks are a natural representation of complex systems across the sciences, and higher-order dependencies are central to the understanding and modeling of these systems. However, in many practical applications such as online social networks, networks are massive, dynamic, and naturally streaming, where pairwise interactions among vertices become available one at a time in some arbitrary order. The massive size and streaming nature of these networks allow only partial observation, since it is infeasible to analyze the entire network. Under such scenarios, it is challenging to study the higher-order structural and connectivity patterns of streaming networks. In this work, we consider the fundamental problem of estimating the higher-order dependencies using adaptive sampling. We propose a novel adaptive, single-pass sampling framework and unbiased estimators for higher-order network analysis of large streaming networks. Our algorithms exploit adaptive techniques to identify edges that are highly informative for efficiently estimating the higher-order structure of streaming networks from small sample data. We also introduce a novel James-Stein shrinkage estimator to reduce the estimation error. Our approach is fully analytic, computationally efficient, and can be incrementally updated in a streaming setting. Numerical experiments on large networks show that our approach is superior to baseline methods.

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NeurIPS Conference 2020 Conference Paper

BayReL: Bayesian Relational Learning for Multi-omics Data Integration

Ehsan Hajiramezanali
Arman Hasanzadeh
Nick Duffield
Krishna Narayanan
Xiaoning Qian

High-throughput molecular profiling technologies have produced high-dimensional multi-omics data, enabling systematic understanding of living systems at the genome scale. Studying molecular interactions across different data types helps reveal signal transduction mechanisms across different classes of molecules. In this paper, we develop a novel Bayesian representation learning method that infers the relational interactions across multi-omics data types. Our method, Bayesian Relational Learning (BayReL) for multi-omics data integration, takes advantage of a priori known relationships among the same class of molecules, modeled as a graph at each corresponding view, to learn view-specific latent variables as well as a multi-partite graph that encodes the interactions across views. Our experiments on several real-world datasets demonstrate enhanced performance of BayReL in inferring meaningful interactions compared to existing baselines.

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NeurIPS Conference 2019 Conference Paper

Semi-Implicit Graph Variational Auto-Encoders

Arman Hasanzadeh
Ehsan Hajiramezanali
Krishna Narayanan
Nick Duffield
Mingyuan Zhou
Xiaoning Qian

Semi-implicit graph variational auto-encoder (SIG-VAE) is proposed to expand the flexibility of variational graph auto-encoders (VGAE) to model graph data. SIG-VAE employs a hierarchical variational framework to enable neighboring node sharing for better generative modeling of graph dependency structure, together with a Bernoulli-Poisson link decoder. Not only does this hierarchical construction provide a more flexible generative graph model to better capture real-world graph properties, but also does SIG-VAE naturally lead to semi-implicit hierarchical variational inference that allows faithful modeling of implicit posteriors of given graph data, which may exhibit heavy tails, multiple modes, skewness, and rich dependency structures. SIG-VAE integrates a carefully designed generative model, well suited to model real-world sparse graphs, and a sophisticated variational inference network, which propagates the graph structural information and distribution uncertainty to capture complex posteriors. SIG-VAE clearly outperforms a simple combination of VGAE with variational inference, including semi-implicit variational inference~(SIVI) or normalizing flow (NF), which does not propagate uncertainty in its inference network, and provides more interpretable latent representations than VGAE does. Extensive experiments with a variety of graph data show that SIG-VAE significantly outperforms state-of-the-art methods on several different graph analytic tasks.

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NeurIPS Conference 2019 Conference Paper

Variational Graph Recurrent Neural Networks

Ehsan Hajiramezanali
Arman Hasanzadeh
Krishna Narayanan
Nick Duffield
Mingyuan Zhou
Xiaoning Qian

Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction.

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IJCAI Conference 2018 Conference Paper

Sampling for Approximate Bipartite Network Projection

Nesreen Ahmed
Nick Duffield
Liangzhen Xia

Bipartite graphs manifest as a stream of edges that represent transactions, e. g. , purchases by retail customers. Recommender systems employ neighborhood-based measures of node similarity, such as the pairwise number of common neighbors (CN) and related metrics. While the number of node pairs that share neighbors is potentially enormous, only a relatively small proportion of them have many common neighbors. This motivates finding a weighted sampling approach to preferentially sample these node pairs. This paper presents a new sampling algorithm that provides a fixed size unbiased estimate of the similarity matrix resulting from a bipartite edge stream projection. The algorithm has two components. First, it maintains a reservoir of sampled bipartite edges with sampling weights that favor selection of high similarity nodes. Second, arriving edges generate a stream of similarity updates, based on their adjacency with the current sample. These updates are aggregated in a second reservoir sample-based stream aggregator to yield the final unbiased estimate. Experiments on real world graphs show that a 10% sample at each stage yields estimates of high similarity edges with weighted relative errors of about 1%.

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