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Bani K. Mallick

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9 papers

2 author rows

ICML Conference 2025 Conference Paper

Global-Local Dirichlet Processes for Clustering Grouped Data in the Presence of Group-Specific Idiosyncratic Variables

Arhit Chakrabarti
Yang Ni
Debdeep Pati
Bani K. Mallick

We consider the problem of clustering grouped data for which the observations may include group-specific variables in addition to the variables that are shared across groups. This type of data is quite common; for example, in cancer genomic studies, molecular information is available for all cancers whereas cancer-specific clinical information may only be available for certain cancers. Existing grouped clustering methods only consider the shared variables but ignore valuable information from the group-specific variables. To allow for these group-specific variables to aid in the clustering, we propose a novel Bayesian nonparametric approach, termed global-local (GLocal) Dirichlet process, that models the "global-local" structure of the observations across groups. We characterize the GLocal Dirichlet process using the stick-breaking representation and the representation as a limit of a finite mixture model. We theoretically quantify the approximation errors of the truncated prior, the corresponding finite mixture model, and the associated posterior distribution. We develop a fast variational Bayes algorithm for scalable posterior inference, which we illustrate with extensive simulations and a TCGA pan-gastrointestinal cancer dataset.

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JMLR Journal 2024 Journal Article

Graphical Dirichlet Process for Clustering Non-Exchangeable Grouped Data

Arhit Chakrabarti
Yang Ni
Ellen Ruth A. Morris
Michael L. Salinas
Robert S. Chapkin
Bani K. Mallick

We consider the problem of clustering grouped data with possibly non-exchangeable groups whose dependencies can be characterized by a known directed acyclic graph. To allow the sharing of clusters among the non-exchangeable groups, we propose a Bayesian nonparametric approach, termed graphical Dirichlet process, that jointly models the dependent group-specific random measures by assuming each random measure to be distributed as a Dirichlet process whose concentration parameter and base probability measure depend on those of its parent groups. The resulting joint stochastic process respects the Markov property of the directed acyclic graph that links the groups. We characterize the graphical Dirichlet process using a novel hypergraph representation as well as the stick-breaking representation, the restaurant-type representation, and the representation as a limit of a finite mixture model. We develop an efficient posterior inference algorithm and illustrate our model with simulations and a real grouped single-cell data set. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2024. ( edit, beta )

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JMLR Journal 2024 Journal Article

Structured Optimal Variational Inference for Dynamic Latent Space Models

Peng Zhao
Anirban Bhattacharya
Debdeep Pati
Bani K. Mallick

We consider a latent space model for dynamic networks, where our objective is to estimate the pairwise inner products plus the intercept of the latent positions. To balance posterior inference and computational scalability, we consider a structured mean-field variational inference framework, where the time-dependent properties of the dynamic networks are exploited to facilitate computation and inference. Additionally, an easy-to-implement block coordinate ascent algorithm is developed with message-passing type updates in each block, whereas the complexity per iteration is linear with the number of nodes and time points. To certify the optimality, we demonstrate that the variational risk of the proposed variational inference approach attains the minimax optimal rate with only a logarithm factor under certain conditions. To this end, we first derive the minimax lower bound, which might be of independent interest. In addition, we show that the posterior under commonly adopted Gaussian random walk priors can achieve the minimax lower bound with only a logarithm factor. To the best of our knowledge, this is the first such a throughout theoretical analysis of Bayesian dynamic latent space models. Simulations and real data analysis demonstrate the efficacy of our methodology and the efficiency of our algorithm. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2024. ( edit, beta )

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UAI Conference 2023 Conference Paper

Adaptive Conditional Quantile Neural Processes

Peiman Mohseni
Nick G. Duffield
Bani K. Mallick
Arman Hasanzadeh

Neural processes are a family of probabilistic models that inherit the flexibility of neural networks to parameterize stochastic processes. Despite providing well-calibrated predictions, especially in regression problems, and quick adaptation to new tasks, the Gaussian assumption that is commonly used to represent the predictive likelihood fails to capture more complicated distributions such as multimodal ones. To overcome this limitation, we propose Conditional Quantile Neural Processes (CQNPs), a new member of the neural processes family, which exploits the attractive properties of quantile regression in modeling the distributions irrespective of their form. By introducing an extension of quantile regression where the model learns to focus on estimating informative quantiles, we show that the sampling efficiency and prediction accuracy can be further enhanced. Our experiments with real and synthetic datasets demonstrate substantial improvements in predictive performance compared to the baselines, and better modeling of heterogeneous distributions’ characteristics such as multimodality.

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ICLR Conference 2023 Conference Paper

Calibrating the Rigged Lottery: Making All Tickets Reliable

Bowen Lei
Ruqi Zhang
Dongkuan Xu
Bani K. Mallick

Although sparse training has been successfully used in various deep learning tasks to save memory and reduce inference time, the reliability of the produced sparse models remains unexplored. Previous research has shown that deep neural networks tend to be over-confident, and we find that sparse training exacerbates this problem. Therefore, calibrating the sparse models is crucial for reliable prediction and decision making. In this paper, we propose a new sparse training method to produce sparse models with improved confidence calibration. In contrast to previous research that uses only one mask to control the sparse topology, our method utilizes two masks, including a deterministic mask and a random mask. The former efficiently searches and activates important weights by exploiting the magnitude of weights and gradients. While the latter brings better exploration and finds more appropriate weight values by random updates. Theoretically, we prove our method can be viewed as a hierarchical variational approximation of a probabilistic deep Gaussian process. Extensive experiments on multiple datasets, model architectures, and sparsities show that our method can reduce ECE values by up to 47.8\% and simultaneously maintain or even improve accuracy with only a slight increase in computational and storage burden.

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ICML Conference 2022 Conference Paper

BAMDT: Bayesian Additive Semi-Multivariate Decision Trees for Nonparametric Regression

Zhao Tang Luo
Huiyan Sang
Bani K. Mallick

Bayesian additive regression trees (BART; Chipman et al. , 2010) have gained great popularity as a flexible nonparametric function estimation and modeling tool. Nearly all existing BART models rely on decision tree weak learners with axis-parallel univariate split rules to partition the Euclidean feature space into rectangular regions. In practice, however, many regression problems involve features with multivariate structures (e. g. , spatial locations) possibly lying in a manifold, where rectangular partitions may fail to respect irregular intrinsic geometry and boundary constraints of the structured feature space. In this paper, we develop a new class of Bayesian additive multivariate decision tree models that combine univariate split rules for handling possibly high dimensional features without known multivariate structures and novel multivariate split rules for features with multivariate structures in each weak learner. The proposed multivariate split rules are built upon stochastic predictive spanning tree bipartition models on reference knots, which are capable of achieving highly flexible nonlinear decision boundaries on manifold feature spaces while enabling efficient dimension reduction computations. We demonstrate the superior performance of the proposed method using simulation data and a Sacramento housing price data set.

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UAI Conference 2022 Conference Paper

Ordinal causal discovery

Yang Ni
Bani K. Mallick

Causal discovery for purely observational, categorical data is a long-standing challenging problem. Unlike continuous data, the vast majority of existing methods for categorical data focus on inferring the Markov equivalence class only, which leaves the direction of some causal relationships undetermined. This paper proposes an identifiable ordinal causal discovery method that exploits the ordinal information contained in many real-world applications to uniquely identify the causal structure. The proposed method is applicable beyond ordinal data via data discretization. Through real-world and synthetic experiments, we demonstrate that the proposed ordinal causal discovery method combined with simple score-and-search algorithms has favorable and robust performance compared to state-of-the-art alternative methods in both ordinal categorical and non-categorical data. An accompanied R package OCD is freely available at the first author’s website.

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JMLR Journal 2020 Journal Article

Quantile Graphical Models: a Bayesian Approach

Nilabja Guha
Veera Baladandayuthapani
Bani K. Mallick

Graphical models are ubiquitous tools to describe the interdependence between variables measured simultaneously such as large-scale gene or protein expression data. Gaussian graphical models (GGMs) are well-established tools for probabilistic exploration of dependence structures using precision matrices and they are generated under a multivariate normal joint distribution. However, they suffer from several shortcomings since they are based on Gaussian distribution assumptions. In this article, we propose a Bayesian quantile based approach for sparse estimation of graphs. We demonstrate that the resulting graph estimation is robust to outliers and applicable under general distributional assumptions. Furthermore, we develop efficient variational Bayes approximations to scale the methods for large data sets. Our methods are applied to a novel cancer proteomics data dataset where-in multiple proteomic antibodies are simultaneously assessed on tumor samples using reverse-phase protein arrays (RPPA) technology. [abs] [ pdf ][ bib ] &copy JMLR 2020. ( edit, beta )

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JMLR Journal 2015 Journal Article

Absent Data Generating Classifier for Imbalanced Class Sizes

Arash Pourhabib
Bani K. Mallick
Yu Ding

We propose an algorithm for two-class classification problems when the training data are imbalanced. This means the number of training instances in one of the classes is so low that the conventional classification algorithms become ineffective in detecting the minority class. We present a modification of the kernel Fisher discriminant analysis such that the imbalanced nature of the problem is explicitly addressed in the new algorithm formulation. The new algorithm exploits the properties of the existing minority points to learn the effects of other minority data points, had they actually existed. The algorithm proceeds iteratively by employing the learned properties and conditional sampling in such a way that it generates sufficient artificial data points for the minority set, thus enhancing the detection probability of the minority class. Implementing the proposed method on a number of simulated and real data sets, we show that our proposed method performs competitively compared to a set of alternative state-of-the-art imbalanced classification algorithms. [abs] [ pdf ][ bib ] &copy JMLR 2015. ( edit, beta )

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