Juho Lee

Edwin Fong, Lancelot F. James, Juho Lee

Modeling sparse count data, which arise across numerous scientific fields, presents significant statistical challenges. This chapter addresses these challenges in the context of infectious disease prediction, with a focus on predicting outbreaks in geographic regions that have historically reported zero cases. To this end, we present the detailed computational framework and experimental application of the Poisson Hierarchical Indian Buffet Process (PHIBP), with demonstrated success in handling sparse count data in microbiome and ecological studies. The PHIBP's architecture, grounded in the concept of absolute abundance, systematically borrows statistical strength from related regions and circumvents the known sensitivities of relative-rate methods to zero counts. Through a series of experiments on infectious disease data, we show that this principled approach provides a robust foundation for generating coherent predictive distributions and for the effective use of comparative measures such as alpha and beta diversity. The chapter's emphasis on algorithmic implementation and experimental results confirms that this unified framework delivers both accurate outbreak predictions and meaningful epidemiological insights in data-sparse settings.

Jungwon Choi, Seongho Keum, EungGu Yun et al.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model naïvely trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Young-Jin Park, Donghyun Kim, Frédéric Odermatt et al.

Time series forecasting is one of the most essential and ubiquitous tasks in many business problems, including demand forecasting and logistics optimization. Traditional time series forecasting methods, however, have resulted in small models with limited expressive power because they have difficulty in scaling their model size up while maintaining high accuracy. In this paper, we propose Forecasting orchestra (Forchestra), a simple but powerful framework capable of accurately predicting future demand for a diverse range of items. We empirically demonstrate that the model size is scalable to up to 0.8 billion parameters. The proposed method not only outperforms existing forecasting models with a significant margin, but it could generalize well to unseen data points when evaluated in a zero-shot fashion on downstream datasets. Last but not least, we present extensive qualitative and quantitative studies to analyze how the proposed model outperforms baseline models and differs from conventional approaches. The original paper was presented as a full paper at ICDM 2022 and is available at: https://ieeexplore.ieee.org/document/10027662.

Jungwon Choi, Hyungi Lee, Byung-Hoon Kim et al.

Graph Neural Networks (GNNs) have shown promise in learning dynamic functional connectivity for distinguishing phenotypes from human brain networks. However, obtaining extensive labeled clinical data for training is often resource-intensive, making practical application difficult. Leveraging unlabeled data thus becomes crucial for representation learning in a label-scarce setting. Although generative self-supervised learning techniques, especially masked autoencoders, have shown promising results in representation learning in various domains, their application to dynamic graphs for dynamic functional connectivity remains underexplored, facing challenges in capturing high-level semantic representations. Here, we introduce the Spatio-Temporal Joint Embedding Masked Autoencoder (ST-JEMA), drawing inspiration from the Joint Embedding Predictive Architecture (JEPA) in computer vision. ST-JEMA employs a JEPA-inspired strategy for reconstructing dynamic graphs, which enables the learning of higher-level semantic representations considering temporal perspectives, addressing the challenges in fMRI data representation learning. Utilizing the large-scale UK Biobank dataset for self-supervised learning, ST-JEMA shows exceptional representation learning performance on dynamic functional connectivity demonstrating superiority over previous methods in predicting phenotypes and psychiatric diagnoses across eight benchmark fMRI datasets even with limited samples and effectiveness of temporal reconstruction on missing data scenarios. These findings highlight the potential of our approach as a robust representation learning method for leveraging label-scarce fMRI data.

Lancelot F. James, Juho Lee, Abhinav Pandey

We introduce the Poisson Hierarchical Indian Buffet Process (PHIBP), a new class of species sampling models designed to address the challenges of complex, sparse count data by facilitating information sharing across and within groups. Our theoretical developments enable a tractable Bayesian nonparametric framework with machine learning elements, accommodating a potentially infinite number of species (taxa) whose parameters are learned from data. Focusing on microbiome analysis, we address key gaps by providing a flexible multivariate count model that accounts for overdispersion and robustly handles diverse data types (OTUs, ASVs). We introduce novel parameters reflecting species abundance and diversity. The model borrows strength across groups while explicitly distinguishing between technical and biological zeros to interpret sparse co-occurrence patterns. This results in a framework with tractable posterior inference, exact generative sampling, and a principled solution to the unseen species problem. We describe extensions where domain experts can incorporate knowledge through covariates and structured priors, with potential for strain-level analysis. While motivated by ecology, our work provides a broadly applicable methodology for hierarchical count modeling in genetics, commerce, and text analysis, and has significant implications for the broader theory of species sampling models arising in probability and statistics.

Jongmin Yoon, Juho Lee

Straightening the probability flow of the continuous-time generative models, such as diffusion models or flow-based models, is the key to fast sampling through the numerical solvers, existing methods learn a linear path by directly generating the probability path the joint distribution between the noise and data distribution. One key reason for the slow sampling speed of the ODE-based solvers that simulate these generative models is the global truncation error of the ODE solver, caused by the high curvature of the ODE trajectory, which explodes the truncation error of the numerical solvers in the low-NFE regime. To address this challenge, We propose a novel method called SeqRF, a learning technique that straightens the probability flow to reduce the global truncation error and hence enable acceleration of sampling and improve the synthesis quality. In both theoretical and empirical studies, we first observe the straightening property of our SeqRF. Through empirical evaluations via SeqRF over flow-based generative models, We achieve surpassing results on CIFAR-10, CelebA-$64 \times 64$, and LSUN-Church datasets.

Giung Nam, Jongmin Yoon, Yoonho Lee et al.

Deep ensembles excel in large-scale image classification tasks both in terms of prediction accuracy and calibration. Despite being simple to train, the computation and memory cost of deep ensembles limits their practicability. While some recent works propose to distill an ensemble model into a single model to reduce such costs, there is still a performance gap between the ensemble and distilled models. We propose a simple approach for reducing this gap, i.e., making the distilled performance close to the full ensemble. Our key assumption is that a distilled model should absorb as much function diversity inside the ensemble as possible. We first empirically show that the typical distillation procedure does not effectively transfer such diversity, especially for complex models that achieve near-zero training error. To fix this, we propose a perturbation strategy for distillation that reveals diversity by seeking inputs for which ensemble member outputs disagree. We empirically show that a model distilled with such perturbed samples indeed exhibits enhanced diversity, leading to improved performance.

Jeffrey Willette, Hae Beom Lee, Juho Lee et al.

Numerous recent works utilize bi-Lipschitz regularization of neural network layers to preserve relative distances between data instances in the feature spaces of each layer. This distance sensitivity with respect to the data aids in tasks such as uncertainty calibration and out-of-distribution (OOD) detection. In previous works, features extracted with a distance sensitive model are used to construct feature covariance matrices which are used in deterministic uncertainty estimation or OOD detection. However, in cases where there is a distribution over tasks, these methods result in covariances which are sub-optimal, as they may not leverage all of the meta information which can be shared among tasks. With the use of an attentive set encoder, we propose to meta learn either diagonal or diagonal plus low-rank factors to efficiently construct task specific covariance matrices. Additionally, we propose an inference procedure which utilizes scaled energy to achieve a final predictive distribution which is well calibrated under a distributional dataset shift.

Hyungi Lee, Eunggu Yun, Hongseok Yang et al.

Recent works have revealed that infinitely-wide feed-forward or recurrent neural networks of any architecture correspond to Gaussian processes referred to as Neural Network Gaussian Processes (NNGPs). While these works have extended the class of neural networks converging to Gaussian processes significantly, however, there has been little focus on broadening the class of stochastic processes that such neural networks converge to. In this work, inspired by the scale mixture of Gaussian random variables, we propose the scale mixture of NNGPs for which we introduce a prior distribution on the scale of the last-layer parameters. We show that simply introducing a scale prior on the last-layer parameters can turn infinitely-wide neural networks of any architecture into a richer class of stochastic processes. With certain scale priors, we obtain heavy-tailed stochastic processes, and in the case of inverse gamma priors, we recover Student's $t$ processes. We further analyze the distributions of the neural networks initialized with our prior setting and trained with gradient descents and obtain similar results as for NNGPs. We present a practical posterior-inference algorithm for the scale mixture of NNGPs and empirically demonstrate its usefulness on regression and classification tasks. In particular, we show that in both tasks, the heavy-tailed stochastic processes obtained from our framework are robust to out-of-distribution data.

Jihoon Ko, Taehyung Kwon, Kijung Shin et al.

Graph neural networks (GNNs) are one of the most popular approaches to using deep learning on graph-structured data, and they have shown state-of-the-art performances on a variety of tasks. However, according to a recent study, a careful choice of pooling functions, which are used for the aggregation and readout operations in GNNs, is crucial for enabling GNNs to extrapolate. Without proper choices of pooling functions, which varies across tasks, GNNs completely fail to generalize to out-of-distribution data, while the number of possible choices grows exponentially with the number of layers. In this paper, we present GNP, a $L^p$ norm-like pooling function that is trainable end-to-end for any given task. Notably, GNP generalizes most of the widely-used pooling functions. We verify experimentally that simply using GNP for every aggregation and readout operation enables GNNs to extrapolate well on many node-level, graph-level, and set-related tasks; and GNP sometimes performs even better than the best-performing choices among existing pooling functions.

Saehoon Kim, Sungwoong Kim, Juho Lee

Unsupervised representation learning has recently received lots of interest due to its powerful generalizability through effectively leveraging large-scale unlabeled data. There are two prevalent approaches for this, contrastive learning and generative pre-training, where the former learns representations from instance-wise discrimination tasks and the latter learns them from estimating the likelihood. These seemingly orthogonal approaches have their own strengths and weaknesses. Contrastive learning tends to extract semantic information and discards details irrelevant for classifying objects, making the representations effective for discriminative tasks while degrading robustness to out-of-distribution data. On the other hand, the generative pre-training directly estimates the data distribution, so the representations tend to be robust but not optimal for discriminative tasks. In this paper, we show that we could achieve the best of both worlds by a hybrid training scheme. Specifically, we demonstrated that a transformer-based encoder-decoder architecture trained with both contrastive and generative losses can learn highly discriminative and robust representations without hurting the generative performance. We extensively validate our approach on various tasks.

Seanie Lee, Minki Kang, Juho Lee et al.

QA models based on pretrained language mod-els have achieved remarkable performance on various benchmark datasets.However, QA models do not generalize well to unseen data that falls outside the training distribution, due to distributional shifts.Data augmentation (DA) techniques which drop/replace words have shown to be effective in regularizing the model from overfitting to the training data.Yet, they may adversely affect the QA tasks since they incur semantic changes that may lead to wrong answers for the QA task. To tackle this problem, we propose a simple yet effective DA method based on a stochastic noise generator, which learns to perturb the word embedding of the input questions and context without changing their semantics. We validate the performance of the QA models trained with our word embedding perturbation on a single source dataset, on five different target domains.The results show that our method significantly outperforms the baselineDA methods. Notably, the model trained with ours outperforms the model trained with more than 240K artificially generated QA pairs.

Yueqi Wang, Yoonho Lee, Pallab Basu et al.

Learning community structures in graphs has broad applications across scientific domains. While graph neural networks (GNNs) have been successful in encoding graph structures, existing GNN-based methods for community detection are limited by requiring knowledge of the number of communities in advance, in addition to lacking a proper probabilistic formulation to handle uncertainty. We propose a simple framework for amortized community detection, which addresses both of these issues by combining the expressive power of GNNs with recent methods for amortized clustering. Our models consist of a graph representation backbone that extracts structural information and an amortized clustering network that naturally handles variable numbers of clusters. Both components combine into well-defined models of the posterior distribution of graph communities and are jointly optimized given labeled graphs. At inference time, the models yield parallel samples from the posterior of community labels, quantifying uncertainty in a principled way. We evaluate several models from our framework on synthetic and real datasets, and demonstrate improved performance compared to previous methods. As a separate contribution, we extend recent amortized probabilistic clustering architectures by adding attention modules, which yield further improvements on community detection tasks.

Juho Lee, Yoonho Lee, Jungtaek Kim et al.

Unlike in the traditional statistical modeling for which a user typically hand-specify a prior, Neural Processes (NPs) implicitly define a broad class of stochastic processes with neural networks. Given a data stream, NP learns a stochastic process that best describes the data. While this "data-driven" way of learning stochastic processes has proven to handle various types of data, NPs still rely on an assumption that uncertainty in stochastic processes is modeled by a single latent variable, which potentially limits the flexibility. To this end, we propose the Boostrapping Neural Process (BNP), a novel extension of the NP family using the bootstrap. The bootstrap is a classical data-driven technique for estimating uncertainty, which allows BNP to learn the stochasticity in NPs without assuming a particular form. We demonstrate the efficacy of BNP on various types of data and its robustness in the presence of model-data mismatch.

Yoonho Lee, Juho Lee, Sung Ju Hwang et al.

While various complexity measures for deep neural networks exist, specifying an appropriate measure capable of predicting and explaining generalization in deep networks has proven challenging. We propose Neural Complexity (NC), a meta-learning framework for predicting generalization. Our model learns a scalar complexity measure through interactions with many heterogeneous tasks in a data-driven way. The trained NC model can be added to the standard training loss to regularize any task learner in a standard supervised learning scenario. We contrast NC's approach against existing manually-designed complexity measures and other meta-learning models, and we validate NC's performance on multiple regression and classification tasks

Juho Lee, Lancelot F. James, Seungjin Choi et al.

We consider a non-projective class of inhomogeneous random graph models with interpretable parameters and a number of interesting asymptotic properties. Using the results of Bollobás et al. [2007], we show that i) the class of models is sparse and ii) depending on the choice of the parameters, the model is either scale-free, with power-law exponent greater than 2, or with an asymptotic degree distribution which is power-law with exponential cut-off. We propose an extension of the model that can accommodate an overlapping community structure. Scalable posterior inference can be performed due to the specific choice of the link probability. We present experiments on five different real-world networks with up to 100,000 nodes and edges, showing that the model can provide a good fit to the degree distribution and recovers well the latent community structure.

Ingyo Chung, Saehoon Kim, Juho Lee et al.

We present a personalized and reliable prediction model for healthcare, which can provide individually tailored medical services such as diagnosis, disease treatment, and prevention. Our proposed framework targets at making personalized and reliable predictions from time-series data, such as Electronic Health Records (EHR), by modeling two complementary components: i) a shared component that captures global trend across diverse patients and ii) a patient-specific component that models idiosyncratic variability for each patient. To this end, we propose a composite model of a deep neural network to learn complex global trends from the large number of patients, and Gaussian Processes (GP) to probabilistically model individual time-series given relatively small number of visits per patient. We evaluate our model on diverse and heterogeneous tasks from EHR datasets and show practical advantages over standard time-series deep models such as pure Recurrent Neural Network (RNN).