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Xiaoning Qian

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29 papers
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29

NeurIPS Conference 2025 Conference Paper

A Plug-and-Play Query Synthesis Active Learning Framework for Neural PDE Solvers

  • Zhiyuan Wang
  • Jinwoo Go
  • Byung-Jun Yoon
  • Nathan Urban
  • Xiaoning Qian

In recent developments in scientific machine learning (SciML), neural surrogate solvers for partial differential equations (PDEs) have become powerful tools for accelerating scientific computation for various science and engineering applications. However, training neural PDE solvers often demands a large amount of high-fidelity PDE simulation data, which are expensive to generate. Active learning (AL) offers a promising solution by adaptively selecting training data from the PDE settings--including parameters, initial and boundary conditions--that are expected to be most informative to help reduce this data burden. In this work, we introduce PaPQS, a Plug-and-Play Query Synthesis AL framework that synthesizes informative PDE settings directly in the continuous design space. PaPQS optimizes the Expected Information Gain (EIG) while encouraging batch diversity, enabling model-aware exploration of the design space via backpropagation through the neural PDE solution trajectories. The framework is applicable to general PDE systems and surrogate architectures, and can be seamlessly integrated with existing AL strategies. Extensive experiments across different PDE systems demonstrate that our AL framework, PaPQS, consistently improves sample efficiency over existing AL baselines.

NeurIPS Conference 2025 Conference Paper

C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models

  • Amir Hossein Rahmati
  • Sanket Jantre
  • Weifeng Zhang
  • Yucheng Wang
  • Byung-Jun Yoon
  • Nathan Urban
  • Xiaoning Qian

Low-Rank Adaptation (LoRA) offers a cost-effective solution for fine-tuning large language models (LLMs), but it often produces overconfident predictions in data-scarce few-shot settings. To address this issue, several classical statistical learning approaches have been repurposed for scalable uncertainty-aware LoRA fine-tuning. However, these approaches neglect how input characteristics affect the predictive uncertainty estimates. To address this limitation, we propose Contextual Low-Rank Adaptation ( C-LoRA ) as a novel uncertainty-aware and parameter efficient fine-tuning approach, by developing new lightweight LoRA modules contextualized to each input data sample to dynamically adapt uncertainty estimates. Incorporating data-driven contexts into the parameter posteriors, C-LoRA mitigates overfitting, achieves well-calibrated uncertainties, and yields robust predictions. Extensive experiments on LLaMA2-7B models demonstrate that C-LoRA consistently outperforms the state-of-the-art uncertainty-aware LoRA methods in both uncertainty quantification and model generalization. Ablation studies further confirm the critical role of our contextual modules in capturing sample-specific uncertainties. C-LoRA sets a new standard for robust, uncertainty-aware LLM fine-tuning in few-shot regimes. Although our experiments are limited to 7B models, our method is architecture-agnostic and, in principle, applies beyond this scale; studying its scaling to larger models remains an open problem. Our code is available at https: //github. com/ahra99/c_lora.

NeurIPS Conference 2025 Conference Paper

Graph-based Symbolic Regression with Invariance and Constraint Encoding

  • Ziyu Xiang
  • Kenna Ashen
  • Xiaofeng Qian
  • Xiaoning Qian

Symbolic regression (SR) seeks interpretable analytical expressions that uncover the governing relationships within data, providing mechanistic insight beyond 'black-box' models. However, existing SR methods often suffer from two key limitations: (1) *redundant representations* that fail to capture mathematical equivalences and higher-order operand relations, breaking permutation invariance and hindering efficient learning; and (2) *sparse rewards* caused by incomplete incorporation of constraints that can only be evaluated on full expressions, such as constant fitting or physical-law verification. To address these challenges, we propose a unified framework, **Graph-based Symbolic Regression (GSR)**, which compresses the search space through the permutation-invariant representations, expression graphs (EGs), that intrinsically encode expression equivalences via a term-rewriting system (TRS) and a directed acyclic graph (DAG) structure. GSR mitigates reward sparsity by employing a hybrid neural-guided Monte Carlo tree search (hnMCTS) on EGs, where constraint-informed neural guidance enables the direct incorporation of expression-level constraint priors, and an adaptive $\epsilon$-UCB policy balances exploration and exploitation. Theoretical analyses establish the uniqueness of our proposed EG representation and the convergence of the hnMCTS algorithm. Experiments on synthetic and real-world scientific datasets demonstrate the efficiency and accuracy of GSR in discovering underlying expressions and adhering to physical laws, offering practical solutions for scientific discovery.

ICLR Conference 2025 Conference Paper

Pareto Prompt Optimization

  • Guang Zhao
  • Byung-Jun Yoon
  • Gilchan Park
  • Shantenu Jha
  • Shinjae Yoo
  • Xiaoning Qian

Natural language prompt optimization, or prompt engineering, has emerged as a powerful technique to unlock the potential of Large Language Models (LLMs) for various tasks. While existing methods primarily focus on maximizing a single task-specific performance metric for LLM outputs, real-world applications often require considering trade-offs between multiple objectives. In this work, we address this limitation by proposing an effective technique for multi-objective prompt optimization for LLMs. Specifically, we propose **ParetoPrompt**, a reinforcement learning~(RL) method that leverages dominance relationships between prompts to derive a policy model for prompts optimization using preference-based loss functions. By leveraging multi-objective dominance relationships, ParetoPrompt enables efficient exploration of the entire Pareto front without the need for a predefined scalarization of multiple objectives. Our experimental results show that ParetoPrompt consistently outperforms existing algorithms that use specific objective values. ParetoPrompt also yields robust performances when the objective metrics differ between training and testing.

ICML Conference 2024 Conference Paper

A Space Group Symmetry Informed Network for O(3) Equivariant Crystal Tensor Prediction

  • Keqiang Yan
  • Alexandra Saxton
  • Xiaofeng Qian
  • Xiaoning Qian
  • Shuiwang Ji

We consider the prediction of general tensor properties of crystalline materials, including dielectric, piezoelectric, and elastic tensors. A key challenge here is how to make the predictions satisfy the unique tensor equivariance to both O(3) and crystal space groups. To this end, we propose a General Materials Tensor Network (GMTNet), which is carefully designed to satisfy the required symmetries. To evaluate our method, we curate a dataset and establish evaluation metrics that are tailored to the intricacies of crystal tensor predictions. Experimental results show that our GMTNet not only achieves promising performance on crystal tensors of various orders but also generates predictions fully consistent with the intrinsic crystal symmetries. Our code is publicly available as part of the AIRS library (https: //github. com/divelab/AIRS).

ICLR Conference 2024 Conference Paper

Complete and Efficient Graph Transformers for Crystal Material Property Prediction

  • Keqiang Yan
  • Cong Fu 0003
  • Xiaofeng Qian
  • Xiaoning Qian
  • Shuiwang Ji

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

ICML Conference 2024 Conference Paper

GFlowNet Training by Policy Gradients

  • Puhua Niu
  • Shili Wu
  • Mingzhou Fan
  • Xiaoning Qian

Generative Flow Networks (GFlowNets) have been shown effective to generate combinatorial objects with desired properties. We here propose a new GFlowNet training framework, with policy-dependent rewards, that bridges keeping flow balance of GFlowNets to optimizing the expected accumulated reward in traditional Reinforcement-Learning (RL). This enables the derivation of new policy-based GFlowNet training methods, in contrast to existing ones resembling value-based RL. It is known that the design of backward policies in GFlowNet training affects efficiency. We further develop a coupled training strategy that jointly solves GFlowNet forward policy training and backward policy design. Performance analysis is provided with a theoretical guarantee of our policy-based GFlowNet training. Experiments on both simulated and real-world datasets verify that our policy-based strategies provide advanced RL perspectives for robust gradient estimation to improve GFlowNet performance. Our code is available at: github. com/niupuhua1234/GFN-PG.

TMLR Journal 2024 Journal Article

Hashing with Uncertainty Quantification via Sampling-based Hypothesis Testing

  • Yucheng Wang
  • Mingyuan Zhou
  • Xiaoning Qian

To quantify different types of uncertainty when deriving hash-codes for image retrieval, we develop a probabilistic hashing model(ProbHash). Sampling-based hypothesis testing is then derived for hashing with uncertainty quantification(HashUQ) in ProbHash to improve the granularity of hashing-based retrieval by prioritizing the data with confident hash-codes. HashUQ can drastically improve the retrieval performance without sacrificing computational efficiency. For efficient deployment of HashUQ in real-world applications, we discretize the quantified uncertainty to reduce the potential storage overhead. Experimental results show that our HashUQ can achieve state-of-the-art retrieval performance on three image datasets. Ablation experiments on model hyperparameters, different model components, and effects of UQ are also provided with performance comparisons. Our code is available at https://github.com/QianLab/HashUQ.

ICML Conference 2024 Conference Paper

Hierarchical Neural Operator Transformer with Learnable Frequency-aware Loss Prior for Arbitrary-scale Super-resolution

  • Xihaier Luo
  • Xiaoning Qian
  • Byung-Jun Yoon

In this work, we present an arbitrary-scale super-resolution (SR) method to enhance the resolution of scientific data, which often involves complex challenges such as continuity, multi-scale physics, and the intricacies of high-frequency signals. Grounded in operator learning, the proposed method is resolution-invariant. The core of our model is a hierarchical neural operator that leverages a Galerkin-type self-attention mechanism, enabling efficient learning of mappings between function spaces. Sinc filters are used to facilitate the information transfer across different levels in the hierarchy, thereby ensuring representation equivalence in the proposed neural operator. Additionally, we introduce a learnable prior structure that is derived from the spectral resizing of the input data. This loss prior is model-agnostic and is designed to dynamically adjust the weighting of pixel contributions, thereby balancing gradients effectively across the model. We conduct extensive experiments on diverse datasets from different domains and demonstrate consistent improvements compared to strong baselines, which consist of various state-of-the-art SR methods.

NeurIPS Conference 2024 Conference Paper

Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation

  • Keqiang Yan
  • Xiner Li
  • Hongyi Ling
  • Kenna Ashen
  • Carl Edwards
  • Raymundo Arróyave
  • Marinka Zitnik
  • Heng Ji

We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.

UAI Conference 2024 Conference Paper

Multi-fidelity Bayesian Optimization with Multiple Information Sources of Input-dependent Fidelity

  • Mingzhou Fan
  • Byung-Jun Yoon
  • Edward R. Dougherty
  • Nathan M. Urban
  • Francis J. Alexander
  • Raymundo Arróyave
  • Xiaoning Qian

By querying approximate surrogate models of different fidelity as available information sources, Multi-Fidelity Bayesian Optimization (MFBO) aims at optimizing unknown functions that are costly if not infeasible to evaluate. Existing MFBO methods often assume that approximate surrogates have consistently high/low fidelity across the input domain. However, approximate evaluations from the same surrogate can have different fidelity at different input regions due to data availability and model constraints, especially when considering machine learning surrogates. In this work, we investigate MFBO when multi-fidelity approximations have input-dependent fidelity. By explicitly capturing input dependency for multi-fidelity queries in Gaussian Process (GP), our new input-dependent MFBO (iMFBO) with learnable noise models better captures the fidelity of each information source in an intuitive way. We further design a new acquisition function for iMFBO and prove that the queries selected by iMFBO have higher quality than those by naive MFBO methods, with the derived sub-linear regret bound. Experiments on both synthetic and real-world data demonstrate its superior empirical performance.

ICML Conference 2024 Conference Paper

Path-Guided Particle-based Sampling

  • Mingzhou Fan
  • Ruida Zhou
  • Chao Tian 0002
  • Xiaoning Qian

Particle-based Bayesian inference methods by sampling from a partition-free target (posterior) distribution, e. g. , Stein variational gradient descent (SVGD), have attracted significant attention. We propose a path-guided particle-based sampling (PGPS) method based on a novel Log-weighted Shrinkage (LwS) density path linking an initial distribution to the target distribution. We propose to utilize a Neural network to learn a vector field motivated by the Fokker-Planck equation of the designed density path. Particles, initiated from the initial distribution, evolve according to the ordinary differential equation defined by the vector field. The distribution of these particles is guided along a density path from the initial distribution to the target distribution. The proposed LwS density path allows for an efficient search of modes of the target distribution while canonical methods fail. We theoretically analyze the Wasserstein distance of the distribution of the PGPS-generated samples and the target distribution due to approximation and discretization errors. Practically, the proposed PGPS-LwS method demonstrates higher Bayesian inference accuracy and better calibration ability in experiments conducted on both synthetic and real-world Bayesian learning tasks, compared to baselines, such as SVGD and Langevin dynamics, etc.

ICML Conference 2023 Conference Paper

Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian

  • Haiyang Yu 0005
  • Zhao Xu 0005
  • Xiaofeng Qian
  • Xiaoning Qian
  • Shuiwang Ji

We consider the prediction of the Hamiltonian matrix, which finds use in quantum chemistry and condensed matter physics. Efficiency and equivariance are two important, but conflicting factors. In this work, we propose a SE(3)-equivariant network, named QHNet, that achieves efficiency and equivariance. Our key advance lies at the innovative design of QHNet architecture, which not only obeys the underlying symmetries, but also enables the reduction of number of tensor products by 92%. In addition, QHNet prevents the exponential growth of channel dimension when more atom types are involved. We perform experiments on MD17 datasets, including four molecular systems. Experimental results show that our QHNet can achieve comparable performance to the state of the art methods at a significantly faster speed. Besides, our QHNet consumes 50% less memory due to its streamlined architecture. Our code is publicly available as part of the AIRS library (https: //github. com/divelab/AIRS).

ICML Conference 2023 Conference Paper

Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction

  • Yuchao Lin
  • Keqiang Yan
  • Youzhi Luo
  • Yi Liu 0059
  • Xiaoning Qian
  • Shuiwang Ji

We study property prediction for crystal materials. A crystal structure consists of a minimal unit cell that is repeated infinitely in 3D space. How to accurately represent such repetitive structures in machine learning models remains unresolved. Current methods construct graphs by establishing edges only between nearby nodes, thereby failing to faithfully capture infinite repeating patterns and distant interatomic interactions. In this work, we propose several innovations to overcome these limitations. First, we propose to model physics-principled interatomic potentials directly instead of only using distances as in many existing methods. These potentials include the Coulomb potential, London dispersion potential, and Pauli repulsion potential. Second, we model the complete set of potentials among all atoms, instead of only between nearby atoms as in existing methods. This is enabled by our approximations of infinite potential summations with provable error bounds. We further develop efficient algorithms to compute the approximations. Finally, we propose to incorporate our computations of complete interatomic potentials into message passing neural networks for representation learning. We perform experiments on the JARVIS and Materials Project benchmarks for evaluation. Results show that the use of interatomic potentials and complete interatomic potentials leads to consistent performance improvements with reasonable computational costs. Our code is publicly available as part of the AIRS library (https: //github. com/divelab/AIRS).

NeurIPS Conference 2023 Conference Paper

QH9: A Quantum Hamiltonian Prediction Benchmark for QM9 Molecules

  • Haiyang Yu
  • Meng Liu
  • Youzhi Luo
  • Alex Strasser
  • Xiaofeng Qian
  • Xiaoning Qian
  • Shuiwang Ji

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 2, 399 molecular dynamics trajectories and 130, 831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at \url{https: //github. com/divelab/AIRS/tree/main/OpenDFT/QHBench}.

ICLR Conference 2022 Conference Paper

MoReL: Multi-omics Relational Learning

  • Arman Hasanzadeh
  • Ehsan Hajiramezanali
  • Nick G. Duffield
  • Xiaoning Qian

Multi-omics data analysis has the potential to discover hidden molecular interactions, revealing potential regulatory and/or signal transduction pathways for cellular processes of interest when studying life and disease systems. One of critical challenges when dealing with real-world multi-omics data is that they may manifest heterogeneous structures and data quality as often existing data may be collected from different subjects under different conditions for each type of omics data. We propose a novel deep Bayesian generative model to efficiently infer a multi-partite graph encoding molecular interactions across such heterogeneous views, using a fused Gromov-Wasserstein (FGW) regularization between latent representations of corresponding views for integrative analysis. With such an optimal transport regularization in the deep Bayesian generative model, it not only allows incorporating view-specific side information, either with graph-structured or unstructured data in different views, but also increases the model flexibility with the distribution-based regularization. This allows efficient alignment of heterogeneous latent variable distributions to derive reliable interaction predictions compared to the existing point-based graph embedding methods. Our experiments on several real-world datasets demonstrate enhanced performance of MoReL in inferring meaningful interactions compared to existing baselines.

ICML Conference 2022 Conference Paper

VariGrow: Variational Architecture Growing for Task-Agnostic Continual Learning based on Bayesian Novelty

  • Randy Ardywibowo
  • Zepeng Huo
  • Zhangyang Wang
  • Bobak J. Mortazavi
  • Shuai Huang 0001
  • Xiaoning Qian

Continual Learning (CL) is the problem of sequentially learning a set of tasks and preserving all the knowledge acquired. Many existing methods assume that the data stream is explicitly divided into a sequence of known contexts (tasks), and use this information to know when to transfer knowledge from one context to another. Unfortunately, many real-world CL scenarios have no clear task nor context boundaries, motivating the study of task-agnostic CL, where neither the specific tasks nor their switches are known both in training and testing. This paper proposes a variational architecture growing framework dubbed VariGrow. By interpreting dynamically growing neural networks as a Bayesian approximation, and defining flexible implicit variational distributions, VariGrow detects if a new task is arriving through an energy-based novelty score. If the novelty score is high and the sample is “detected" as a new task, VariGrow will grow a new expert module to be responsible for it. Otherwise, the sample will be assigned to one of the existing experts who is most “familiar" with it (i. e. , one with the lowest novelty score). We have tested VariGrow on several CIFAR and ImageNet-based benchmarks for the strict task-agnostic CL setting and demonstrate its consistent superior performance. Perhaps surprisingly, its performance can even be competitive compared to task-aware methods.

ICLR Conference 2021 Conference Paper

Contextual Dropout: An Efficient Sample-Dependent Dropout Module

  • Xinjie Fan
  • Shujian Zhang
  • Korawat Tanwisuth
  • Xiaoning Qian
  • Mingyuan Zhou

Dropout has been demonstrated as a simple and effective module to not only regularize the training process of deep neural networks, but also provide the uncertainty estimation for prediction. However, the quality of uncertainty estimation is highly dependent on the dropout probabilities. Most current models use the same dropout distributions across all data samples due to its simplicity. Despite the potential gains in the flexibility of modeling uncertainty, sample-dependent dropout, on the other hand, is less explored as it often encounters scalability issues or involves non-trivial model changes. In this paper, we propose contextual dropout with an efficient structural design as a simple and scalable sample-dependent dropout module, which can be applied to a wide range of models at the expense of only slightly increased memory and computational cost. We learn the dropout probabilities with a variational objective, compatible with both Bernoulli dropout and Gaussian dropout. We apply the contextual dropout module to various models with applications to image classification and visual question answering and demonstrate the scalability of the method with large-scale datasets, such as ImageNet and VQA 2.0. Our experimental results show that the proposed method outperforms baseline methods in terms of both accuracy and quality of uncertainty estimation.

NeurIPS Conference 2021 Conference Paper

Efficient Active Learning for Gaussian Process Classification by Error Reduction

  • Guang Zhao
  • Edward Dougherty
  • Byung-Jun Yoon
  • Francis Alexander
  • Xiaoning Qian

Active learning sequentially selects the best instance for labeling by optimizing an acquisition function to enhance data/label efficiency. The selection can be either from a discrete instance set (pool-based scenario) or a continuous instance space (query synthesis scenario). In this work, we study both active learning scenarios for Gaussian Process Classification (GPC). The existing active learning strategies that maximize the Estimated Error Reduction (EER) aim at reducing the classification error after training with the new acquired instance in a one-step-look-ahead manner. The computation of EER-based acquisition functions is typically prohibitive as it requires retraining the GPC with every new query. Moreover, as the EER is not smooth, it can not be combined with gradient-based optimization techniques to efficiently explore the continuous instance space for query synthesis. To overcome these critical limitations, we develop computationally efficient algorithms for EER-based active learning with GPC. We derive the joint predictive distribution of label pairs as a one-dimensional integral, as a result of which the computation of the acquisition function avoids retraining the GPC for each query, remarkably reducing the computational overhead. We also derive the gradient chain rule to efficiently calculate the gradient of the acquisition function, which leads to the first query synthesis active learning algorithm implementing EER-based strategies. Our experiments clearly demonstrate the computational efficiency of the proposed algorithms. We also benchmark our algorithms on both synthetic and real-world datasets, which show superior performance in terms of sampling efficiency compared to the existing state-of-the-art algorithms.

AAAI Conference 2021 Conference Paper

Physics-constrained Automatic Feature Engineering for Predictive Modeling in Materials Science

  • Ziyu Xiang
  • Mingzhou Fan
  • Guillermo Vázquez Tovar
  • William Trehern
  • Byung-Jun Yoon
  • Xiaofeng Qian
  • Raymundo Arroyave
  • Xiaoning Qian

Automatic Feature Engineering (AFE) aims to extract useful knowledge for interpretable predictions given data for the machine learning tasks. Here, we develop AFE to extract dependency relationships that can be interpreted with functional formulas to discover physics meaning or new hypotheses for the problems of interest. We focus on materials science applications, where interpretable predictive modeling may provide principled understanding of materials systems and guide new materials discovery. It is often computationally prohibitive to exhaust all the potential relationships to construct and search the whole feature space to identify interpretable and predictive features. We develop and evaluate new AFE strategies by exploring a feature generation tree (FGT) with deep Qnetwork (DQN) for scalable and efficient exploration policies. The developed DQN-based AFE strategies are benchmarked with the existing AFE methods on several materials science datasets.

ICLR Conference 2021 Conference Paper

Uncertainty-aware Active Learning for Optimal Bayesian Classifier

  • Guang Zhao
  • Edward R. Dougherty
  • Byung-Jun Yoon
  • Francis J. Alexander
  • Xiaoning Qian

For pool-based active learning, in each iteration a candidate training sample is chosen for labeling by optimizing an acquisition function. In Bayesian classification, expected Loss Reduction~(ELR) methods maximize the expected reduction in the classification error given a new labeled candidate based on a one-step-look-ahead strategy. ELR is the optimal strategy with a single query; however, since such myopic strategies cannot identify the long-term effect of a query on the classification error, ELR may get stuck before reaching the optimal classifier. In this paper, inspired by the mean objective cost of uncertainty (MOCU), a metric quantifying the uncertainty directly affecting the classification error, we propose an acquisition function based on a weighted form of MOCU. Similar to ELR, the proposed method focuses on the reduction of the uncertainty that pertains to the classification error. But unlike any other existing scheme, it provides the critical advantage that the resulting Bayesian active learning algorithm guarantees convergence to the optimal classifier of the true model. We demonstrate its performance with both synthetic and real-world datasets.

ICML Conference 2020 Conference Paper

Bayesian Graph Neural Networks with Adaptive Connection Sampling

  • Arman Hasanzadeh
  • Ehsan Hajiramezanali
  • Shahin Boluki
  • Mingyuan Zhou
  • Nick G. Duffield
  • Krishna Narayanan 0001
  • Xiaoning Qian

We propose a unified framework for adaptive connection sampling in graph neural networks (GNNs) that generalizes existing stochastic regularization methods for training GNNs. The proposed framework not only alleviates over-smoothing and over-fitting tendencies of deep GNNs, but also enables learning with uncertainty in graph analytic tasks with GNNs. Instead of using fixed sampling rates or hand-tuning themas model hyperparameters in existing stochastic regularization methods, our adaptive connection sampling can be trained jointly with GNN model parameters in both global and local fashions. GNN training with adaptive connection sampling is shown to be mathematically equivalent to an efficient approximation of training BayesianGNNs. Experimental results with ablation studies on benchmark datasets validate that adaptively learning the sampling rate given graph training data is the key to boost the performance of GNNs in semi-supervised node classification, less prone to over-smoothing and over-fitting with more robust prediction.

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.

ICML Conference 2020 Conference Paper

NADS: Neural Architecture Distribution Search for Uncertainty Awareness

  • Randy Ardywibowo
  • Shahin Boluki
  • Xinyu Gong
  • Zhangyang Wang
  • Xiaoning Qian

Machine learning (ML) systems often encounter Out-of-Distribution (OoD) errors when dealing with testing data coming from a distribution different from training data. It becomes important for ML systems in critical applications to accurately quantify its predictive uncertainty and screen out these anomalous inputs. However, existing OoD detection approaches are prone to errors and even sometimes assign higher likelihoods to OoD samples. Unlike standard learning tasks, there is currently no well established guiding principle for designing OoD detection architectures that can accurately quantify uncertainty. To address these problems, we first seek to identify guiding principles for designing uncertainty-aware architectures, by proposing Neural Architecture Distribution Search (NADS). NADS searches for a distribution of architectures that perform well on a given task, allowing us to identify common building blocks among all uncertainty-aware architectures. With this formulation, we are able to optimize a stochastic OoD detection objective and construct an ensemble of models to perform OoD detection. We perform multiple OoD detection experiments and observe that our NADS performs favorably, with up to 57% improvement in accuracy compared to state-of-the-art methods among 15 different testing configurations.

UAI Conference 2020 Conference Paper

Pairwise Supervised Hashing with Bernoulli Variational Auto-Encoder and Self-Control Gradient Estimator

  • Siamak Zamani Dadaneh
  • Shahin Boluki
  • Mingzhang Yin
  • Mingyuan Zhou
  • Xiaoning Qian

Semantic hashing has become a crucial component of fast similarity search in many large-scale information retrieval systems, in particular, for text data. Variational auto-encoders (VAEs) with binary latent variables as hashing codes provide state-of-the-art performance in terms of precision for document retrieval. We propose a pairwise loss function with discrete latent VAE to reward within-class similarity and between-class dissimilarity for supervised hashing. Instead of solving the optimization for training relying on existing biased gradient estimators, an unbiased, low-variance gradient estimator, which evaluates the non-differentiable loss function over two correlated sets of binary hashing codes to control the gradient variance, is adopted to optimize the hashing function to achieve superior performance compared to the state-of-the-arts, as demonstrated by our comprehensive experiments.

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.

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.

NeurIPS Conference 2018 Conference Paper

Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data

  • Ehsan Hajiramezanali
  • Siamak Zamani Dadaneh
  • Alireza Karbalayghareh
  • Mingyuan Zhou
  • Xiaoning Qian

Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Second, compared to the number of involved molecules and system complexity, the number of available samples for studying complex disease, such as cancer, is often limited, especially considering disease heterogeneity. The key question is whether we may integrate available data from all different sources or domains to achieve reproducible disease prognosis based on NGS count data. In this paper, we develop a Bayesian Multi-Domain Learning (BMDL) model that derives domain-dependent latent representations of overdispersed count data based on hierarchical negative binomial factorization for accurate cancer subtyping even if the number of samples for a specific cancer type is small. Experimental results from both our simulated and NGS datasets from The Cancer Genome Atlas (TCGA) demonstrate the promising potential of BMDL for effective multi-domain learning without ``negative transfer'' effects often seen in existing multi-task learning and transfer learning methods.

IROS Conference 2013 Conference Paper

Functional analysis of grasping motion

  • Wei Dai
  • Yu Sun 0004
  • Xiaoning Qian

This paper presents a novel grasping motion analysis technique based on functional principal component analysis (fPCA). The functional analysis of grasping motion provides an effective representation of grasping motion and emphasizes motion dynamic features that are omitted by classic PCA-based approaches. The proposed approach represents, processes, and compares grasping motion trajectories in a low-dimensional space. An experiment was conducted to record grasping motion trajectories of 15 different grasp types in Cutkosky grasp taxonomy. We implemented our method for the analysis of collected grasping motion in the PCA+fPCA space, which generated a new data-driven taxonomy of the grasp types, and naturally clustered grasping motion into 5 consistent groups across 5 different subjects. The robustness of the grouping was evaluated and confirmed using a tenfold cross validation approach.

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