Junier B. Oliva

Ahsan Mahmood, Junier Oliva, Martin Styner

We propose Gumbel Noise Score Matching (GNSM), a novel unsupervised method to detect anomalies in categorical data. GNSM accomplishes this by estimating the scores, i.e. the gradients of log likelihoods w.r.t.~inputs, of continuously relaxed categorical distributions. We test our method on a suite of anomaly detection tabular datasets. GNSM achieves a consistently high performance across all experiments. We further demonstrate the flexibility of GNSM by applying it to image data where the model is tasked to detect poor segmentation predictions. Images ranked anomalous by GNSM show clear segmentation failures, with the outputs of GNSM strongly correlating with segmentation metrics computed on ground-truth. We outline the score matching training objective utilized by GNSM and provide an open-source implementation of our work.

Vishal Athreya Baskaran, Jolene Ranek, Siyuan Shan et al.

Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells in a multi-patient cohort. While bioinformatics approaches can be used to link immune cell heterogeneity to external variables of interest, such as, clinical outcome or experimental label, they often struggle to accommodate such a large number of profiled cells. To ease this computational burden, a limited number of cells are typically \emph{sketched} or subsampled from each patient. However, existing sketching approaches fail to adequately subsample rare cells from rare cell-populations, or fail to preserve the true frequencies of particular immune cell-types. Here, we propose a novel sketching approach based on Kernel Herding that selects a limited subsample of all cells while preserving the underlying frequencies of immune cell-types. We tested our approach on three flow and mass cytometry datasets and on one single-cell RNA sequencing dataset and demonstrate that the sketched cells (1) more accurately represent the overall cellular landscape and (2) facilitate increased performance in downstream analysis tasks, such as classifying patients according to their clinical outcome. An implementation of sketching with Kernel Herding is publicly available at \url{https://github.com/vishalathreya/Set-Summarization}.

David K Lim, Naim U Rashid, Junier B Oliva et al.

Deep Learning (DL) methods have dramatically increased in popularity in recent years, with significant growth in their application to supervised learning problems in the biomedical sciences. However, the greater prevalence and complexity of missing data in modern biomedical datasets present significant challenges for DL methods. Here, we provide a formal treatment of missing data in the context of deeply learned generalized linear models, a supervised DL architecture for regression and classification problems. We propose a new architecture, \textit{dlglm}, that is one of the first to be able to flexibly account for both ignorable and non-ignorable patterns of missingness in input features and response at training time. We demonstrate through statistical simulation that our method outperforms existing approaches for supervised learning tasks in the presence of missing not at random (MNAR) missingness. We conclude with a case study of a Bank Marketing dataset from the UCI Machine Learning Repository, in which we predict whether clients subscribed to a product based on phone survey data. Supplementary materials for this article are available online.

Avinash Madasu, Junier Oliva, Gedas Bertasius

The majority of traditional text-to-video retrieval systems operate in static environments, i.e., there is no interaction between the user and the agent beyond the initial textual query provided by the user. This can be sub-optimal if the initial query has ambiguities, which would lead to many falsely retrieved videos. To overcome this limitation, we propose a novel framework for Video Retrieval using Dialog (ViReD), which enables the user to interact with an AI agent via multiple rounds of dialog, where the user refines retrieved results by answering questions generated by an AI agent. Our novel multimodal question generator learns to ask questions that maximize the subsequent video retrieval performance using (i) the video candidates retrieved during the last round of interaction with the user and (ii) the text-based dialog history documenting all previous interactions, to generate questions that incorporate both visual and linguistic cues relevant to video retrieval. Furthermore, to generate maximally informative questions, we propose an Information-Guided Supervision (IGS), which guides the question generator to ask questions that would boost subsequent video retrieval accuracy. We validate the effectiveness of our interactive ViReD framework on the AVSD dataset, showing that our interactive method performs significantly better than traditional non-interactive video retrieval systems. We also demonstrate that our proposed approach generalizes to the real-world settings that involve interactions with real humans, thus, demonstrating the robustness and generality of our framework

Yunni Qu, Dzung Dinh, Grant King et al.

In many biomedical applications, measurements are not freely available at inference time: each laboratory test, imaging modality, or assessment incurs financial cost, time burden, or patient risk. Longitudinal active feature acquisition (LAFA) seeks to optimize predictive performance under such constraints by adaptively selecting measurements over time, yet the problem remains inherently challenging due to temporally coupled decisions (missed early measurements cannot be revisited, and acquisition choices influence all downstream predictions). Moreover, real-world clinical workflows typically begin with an initial onboarding phase, during which relatively stable contextual descriptors (e.g., demographics or baseline characteristics) are collected once and subsequently condition longitudinal decision-making. Despite its practical importance, the efficient selection of onboarding context has not been studied jointly with temporally adaptive acquisition. We therefore propose REACT (Relaxed Efficient Acquisition of Context and Temporal features), an end-to-end differentiable framework that simultaneously optimizes (i) selection of onboarding contextual descriptors and (ii) adaptive feature--time acquisition plans for longitudinal measurements under cost constraints. REACT employs a Gumbel--Sigmoid relaxation with straight-through estimation to enable gradient-based optimization over discrete acquisition masks, allowing direct backpropagation from prediction loss and acquisition cost. Across real-world longitudinal health and behavioral datasets, REACT achieves improved predictive performance at lower acquisition costs compared to existing longitudinal acquisition baselines, demonstrating the benefit of modeling onboarding and temporally coupled acquisition within a unified optimization framework.

Siyuan Shan, Yang Li, Amartya Banerjee et al.

Voice conversion (VC) aims at altering a person's voice to make it sound similar to the voice of another person while preserving linguistic content. Existing methods suffer from a dilemma between content intelligibility and speaker similarity; i.e., methods with higher intelligibility usually have a lower speaker similarity, while methods with higher speaker similarity usually require plenty of target speaker voice data to achieve high intelligibility. In this work, we propose a novel method \textit{Phoneme Hallucinator} that achieves the best of both worlds. Phoneme Hallucinator is a one-shot VC model; it adopts a novel model to hallucinate diversified and high-fidelity target speaker phonemes based just on a short target speaker voice (e.g. 3 seconds). The hallucinated phonemes are then exploited to perform neighbor-based voice conversion. Our model is a text-free, any-to-any VC model that requires no text annotations and supports conversion to any unseen speaker. Objective and subjective evaluations show that \textit{Phoneme Hallucinator} outperforms existing VC methods for both intelligibility and speaker similarity.

Michael Valancius, Max Lennon, Junier Oliva

We develop novel methodology for active feature acquisition (AFA), the study of how to sequentially acquire a dynamic (on a per instance basis) subset of features that minimizes acquisition costs whilst still yielding accurate predictions. The AFA framework can be useful in a myriad of domains, including health care applications where the cost of acquiring additional features for a patient (in terms of time, money, risk, etc.) can be weighed against the expected improvement to diagnostic performance. Previous approaches for AFA have employed either: deep learning RL techniques, which have difficulty training policies in the AFA MDP due to sparse rewards and a complicated action space; deep learning surrogate generative models, which require modeling complicated multidimensional conditional distributions; or greedy policies, which fail to account for how joint feature acquisitions can be informative together for better predictions. In this work we show that we can bypass many of these challenges with a novel, nonparametric oracle based approach, which we coin the acquisition conditioned oracle (ACO). Extensive experiments show the superiority of the ACO to state-of-the-art AFA methods when acquiring features for both predictions and general decision-making.

Ahsan Mahmood, Junier Oliva, Martin Styner

Anomaly detection and localization in medical imaging remain critical challenges in healthcare. This paper introduces Spatial-MSMA (Multiscale Score Matching Analysis), a novel unsupervised method for anomaly localization in volumetric brain MRIs. Building upon the MSMA framework, our approach incorporates spatial information and conditional likelihoods to enhance anomaly detection capabilities. We employ a flexible normalizing flow model conditioned on patch positions and global image features to estimate patch-wise anomaly scores. The method is evaluated on a dataset of 1,650 T1- and T2-weighted brain MRIs from typically developing children, with simulated lesions added to the test set. Spatial-MSMA significantly outperforms existing methods, including reconstruction-based, generative-based, and interpretation-based approaches, in lesion detection and segmentation tasks. Our model achieves superior performance in both distance-based metrics (99th percentile Hausdorff Distance: $7.05 \pm 0.61$, Mean Surface Distance: $2.10 \pm 0.43$) and component-wise metrics (True Positive Rate: $0.83 \pm 0.01$, Positive Predictive Value: $0.96 \pm 0.01$). These results demonstrate Spatial-MSMA's potential for accurate and interpretable anomaly localization in medical imaging, with implications for improved diagnosis and treatment planning in clinical settings. Our code is available at~\url{https://github.com/ahsanMah/sade/}.

Yang Li, Shoaib Akbar, Junier B. Oliva

Understanding the dependencies among features of a dataset is at the core of most unsupervised learning tasks. However, a majority of generative modeling approaches are focused solely on the joint distribution $p(x)$ and utilize models where it is intractable to obtain the conditional distribution of some arbitrary subset of features $x_u$ given the rest of the observed covariates $x_o$: $p(x_u \mid x_o)$. Traditional conditional approaches provide a model for a fixed set of covariates conditioned on another fixed set of observed covariates. Instead, in this work we develop a model that is capable of yielding all conditional distributions $p(x_u \mid x_o)$ (for arbitrary $x_u$) via tractable conditional likelihoods. We propose a novel extension of (change of variables based) flow generative models, arbitrary conditioning flow models (AC-Flow), that can be conditioned on arbitrary subsets of observed covariates, which was previously infeasible. We apply AC-Flow to the imputation of features, and also develop a unified platform for both multiple and single imputation by introducing an auxiliary objective that provides a principled single "best guess" for flow models. Extensive empirical evaluations show that our models achieve state-of-the-art performance in both single and multiple imputation across image inpainting and feature imputation in synthetic and real-world datasets. Code is available at https://github.com/lupalab/ACFlow.

Ke Lin, Yilin Lu, Shreyas Bhat et al.

Automated scientific discovery with large language models is transforming the research lifecycle from ideation to experimentation, yet existing agents struggle to autonomously process raw data collected from scientific experiments. We introduce SciDER, a data-centric end-to-end system that automates the research lifecycle. Unlike traditional frameworks, our specialized agents collaboratively parse and analyze raw scientific data, generate hypotheses and experimental designs grounded in specific data characteristics, and write and execute corresponding code. Evaluation on three benchmarks shows SciDER excels in specialized data-driven scientific discovery and outperforms general-purpose agents and state-of-the-art models through its self-evolving memory and critic-led feedback loop. Distributed as a modular Python package, we also provide easy-to-use PyPI packages with a lightweight web interface to accelerate autonomous, data-driven research and aim to be accessible to all researchers and developers.

Boqi Chen, Junier Oliva, Marc Niethammer

Medical records often consist of different modalities, such as images, text, and tabular information. Integrating all modalities offers a holistic view of a patient's condition, while analyzing them longitudinally provides a better understanding of disease progression. However, real-world longitudinal medical records present challenges: 1) patients may lack some or all of the data for a specific timepoint, and 2) certain modalities or views might be absent for all patients during a particular period. In this work, we introduce a unified model for longitudinal multi-modal multi-view prediction with missingness. Our method allows as many timepoints as desired for input, and aims to leverage all available data, regardless of their availability. We conduct extensive experiments on the knee osteoarthritis dataset from the Osteoarthritis Initiative for pain and Kellgren-Lawrence grade prediction at a future timepoint. We demonstrate the effectiveness of our method by comparing results from our unified model to specific models that use the same modality and view combinations during training and evaluation. We also show the benefit of having extended temporal data and provide post-hoc analysis for a deeper understanding of each modality/view's importance for different tasks.

Hung-Tien Huang, Maxwell Lennon, Shreyas Bhat Brahmavar et al.

We introduce Dynamic Information Sub-Selection (DISS), a novel framework of AI assistance designed to enhance the performance of black-box decision-makers by tailoring their information processing on a per-instance basis. Blackbox decision-makers (e.g., humans or real-time systems) often face challenges in processing all possible information at hand (e.g., due to cognitive biases or resource constraints), which can degrade decision efficacy. DISS addresses these challenges through policies that dynamically select the most effective features and options to forward to the black-box decision-maker for prediction. We develop a scalable frequentist data acquisition strategy and a decision-maker mimicking technique for enhanced budget efficiency. We explore several impactful applications of DISS, including biased decision-maker support, expert assignment optimization, large language model decision support, and interpretability. Empirical validation of our proposed DISS methodology shows superior performance to state-of-the-art methods across various applications.

Dzung Dinh, Boqi Chen, Marc Niethammer et al.

In many critical applications, resource constraints limit the amount of information that can be gathered to make predictions. For example, in healthcare, patient data often spans diverse features ranging from lab tests to imaging studies. Each feature may carry different information and must be acquired at a respective cost of time, money, or risk to the patient. Moreover, temporal prediction tasks, where both instance features and labels evolve over time, introduce additional complexity in deciding when or what information is important. In this work, we propose NOCTA, a Non-Greedy Objective Cost-Tradeoff Acquisition method that sequentially acquires the most informative features at inference time while accounting for both temporal dynamics and acquisition cost. We first introduce a cohesive estimation target for our NOCTA setting, and then develop two complementary estimators: 1) a non-parametric method based on nearest neighbors to guide the acquisition (NOCTA-NP), and 2) a parametric method that directly predicts the utility of potential acquisitions (NOCTA-P). Experiments on synthetic and real-world medical datasets demonstrate that both NOCTA variants outperform existing baselines.

Yunni Qu, James Wellnitz, Dzung Dinh et al.

EXPLOR is a novel framework that utilizes support-expanding, extrapolatory pseudo-labeling to improve prediction and uncertainty-based rejection on out-of-distribution (OOD) points. EXPLOR utilizes a diverse set of base models as pseudo-labelers on the expansive augmented data to improve OOD performance through multiple MLP heads (one per base model) with shared embedding trained with a novel per-head matching loss. Unlike prior methods that rely on modality-specific augmentations or assume access to OOD data, EXPLOR introduces extrapolatory pseudo-labeling on latent-space augmentations, enabling robust OOD generalization with any real-valued vector data. In contrast to prior modality-agnostic methods with neural backbones, EXPLOR is model-agnostic, working effectively with methods from simple tree-based models to complex OOD generalization models. We demonstrate that EXPLOR achieves superior performance compared to state-of-the-art methods on diverse datasets in single-source domain generalization settings.

Ryan R. Strauss, Junier B. Oliva

Arbitrary conditioning is an important problem in unsupervised learning, where we seek to model the conditional densities $p(\mathbf{x}_u \mid \mathbf{x}_o)$ that underly some data, for all possible non-intersecting subsets $o, u \subset \{1, \dots , d\}$. However, the vast majority of density estimation only focuses on modeling the joint distribution $p(\mathbf{x})$, in which important conditional dependencies between features are opaque. We propose a simple and general framework, coined Posterior Matching, that enables Variational Autoencoders (VAEs) to perform arbitrary conditioning, without modification to the VAE itself. Posterior Matching applies to the numerous existing VAE-based approaches to joint density estimation, thereby circumventing the specialized models required by previous approaches to arbitrary conditioning. We find that Posterior Matching is comparable or superior to current state-of-the-art methods for a variety of tasks with an assortment of VAEs (e.g.~discrete, hierarchical, VaDE).

Siyuan Shan, Vishal Baskaran, Haidong Yi et al.

Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of thousands of multidimensional cell feature vectors, which incurs a high computational cost to predict each biological sample's associated phenotype with machine learning models. Such a large set cardinality also limits the interpretability of machine learning models due to the difficulty in tracking how each individual cell influences the ultimate prediction. We propose using Kernel Mean Embedding to encode the cellular landscape of each profiled biological sample. Although our foremost goal is to make a more transparent model, we find that our method achieves comparable or better accuracies than the state-of-the-art gating-free methods through a simple linear classifier. As a result, our model contains few parameters but still performs similarly to deep learning models with millions of parameters. In contrast with deep learning approaches, the linearity and sub-selection step of our model makes it easy to interpret classification results. Analysis further shows that our method admits rich biological interpretability for linking cellular heterogeneity to clinical phenotype.

Somnath Basu Roy Chowdhury, Sayan Ghosh, Yiyuan Li et al.

Contextual representations learned by language models can often encode undesirable attributes, like demographic associations of the users, while being trained for an unrelated target task. We aim to scrub such undesirable attributes and learn fair representations while maintaining performance on the target task. In this paper, we present an adversarial learning framework "Adversarial Scrubber" (ADS), to debias contextual representations. We perform theoretical analysis to show that our framework converges without leaking demographic information under certain conditions. We extend previous evaluation techniques by evaluating debiasing performance using Minimum Description Length (MDL) probing. Experimental evaluations on 8 datasets show that ADS generates representations with minimal information about demographic attributes while being maximally informative about the target task.

Yang Li, Siyuan Shan, Qin Liu et al.

Truly intelligent systems are expected to make critical decisions with incomplete and uncertain data. Active feature acquisition (AFA), where features are sequentially acquired to improve the prediction, is a step towards this goal. However, current AFA models all deal with a small set of candidate features and have difficulty scaling to a large feature space. Moreover, they are ignorant about the valid domains where they can predict confidently, thus they can be vulnerable to out-of-distribution (OOD) inputs. In order to remedy these deficiencies and bring AFA models closer to practical use, we propose several techniques to advance the current AFA approaches. Our framework can easily handle a large number of features using a hierarchical acquisition policy and is more robust to OOD inputs with the help of an OOD detector for partially observed data. Extensive experiments demonstrate the efficacy of our framework over strong baselines.

Yang Li, Junier B. Oliva

Modeling dependencies among features is fundamental for many machine learning tasks. Although there are often multiple related instances that may be leveraged to inform conditional dependencies, typical approaches only model conditional dependencies over individual instances. In this work, we propose a novel framework, partially observed exchangeable modeling (POEx) that takes in a set of related partially observed instances and infers the conditional distribution for the unobserved dimensions over multiple elements. Our approach jointly models the intra-instance (among features in a point) and inter-instance (among multiple points in a set) dependencies in data. POEx is a general framework that encompasses many existing tasks such as point cloud expansion and few-shot generation, as well as new tasks like few-shot imputation. Despite its generality, extensive empirical evaluations show that our model achieves state-of-the-art performance across a range of applications.

Ryan R. Strauss, Junier B. Oliva

Modeling distributions of covariates, or density estimation, is a core challenge in unsupervised learning. However, the majority of work only considers the joint distribution, which has limited utility in practical situations. A more general and useful problem is arbitrary conditional density estimation, which aims to model any possible conditional distribution over a set of covariates, reflecting the more realistic setting of inference based on prior knowledge. We propose a novel method, Arbitrary Conditioning with Energy (ACE), that can simultaneously estimate the distribution $p(\mathbf{x}_u \mid \mathbf{x}_o)$ for all possible subsets of unobserved features $\mathbf{x}_u$ and observed features $\mathbf{x}_o$. ACE is designed to avoid unnecessary bias and complexity -- we specify densities with a highly expressive energy function and reduce the problem to only learning one-dimensional conditionals (from which more complex distributions can be recovered during inference). This results in an approach that is both simpler and higher-performing than prior methods. We show that ACE achieves state-of-the-art for arbitrary conditional likelihood estimation and data imputation on standard benchmarks.

Siyuan Shan, Yang Li, Junier B. Oliva

Time series imputation is a fundamental task for understanding time series with missing data. Existing methods either do not directly handle irregularly-sampled data or degrade severely with sparsely observed data. In this work, we reformulate time series as permutation-equivariant sets and propose a novel imputation model NRTSI that does not impose any recurrent structures. Taking advantage of the permutation equivariant formulation, we design a principled and efficient hierarchical imputation procedure. In addition, NRTSI can directly handle irregularly-sampled time series, perform multiple-mode stochastic imputation, and handle data with partially observed dimensions. Empirically, we show that NRTSI achieves state-of-the-art performance across a wide range of time series imputation benchmarks.

David K. Lim, Naim U. Rashid, Junier B. Oliva et al.

Deep Learning (DL) methods have dramatically increased in popularity in recent years. While its initial success was demonstrated in the classification and manipulation of image data, there has been significant growth in the application of DL methods to problems in the biomedical sciences. However, the greater prevalence and complexity of missing data in biomedical datasets present significant challenges for DL methods. Here, we provide a formal treatment of missing data in the context of Variational Autoencoders (VAEs), a popular unsupervised DL architecture commonly utilized for dimension reduction, imputation, and learning latent representations of complex data. We propose a new VAE architecture, NIMIWAE, that is one of the first to flexibly account for both ignorable and non-ignorable patterns of missingness in input features at training time. Following training, samples can be drawn from the approximate posterior distribution of the missing data can be used for multiple imputation, facilitating downstream analyses on high dimensional incomplete datasets. We demonstrate through statistical simulation that our method outperforms existing approaches for unsupervised learning tasks and imputation accuracy. We conclude with a case study of an EHR dataset pertaining to 12,000 ICU patients containing a large number of diagnostic measurements and clinical outcomes, where many features are only partially observed.

Ahsan Mahmood, Junier Oliva, Martin Styner

We present a new methodology for detecting out-of-distribution (OOD) images by utilizing norms of the score estimates at multiple noise scales. A score is defined to be the gradient of the log density with respect to the input data. Our methodology is completely unsupervised and follows a straight forward training scheme. First, we train a deep network to estimate scores for levels of noise. Once trained, we calculate the noisy score estimates for N in-distribution samples and take the L2-norms across the input dimensions (resulting in an NxL matrix). Then we train an auxiliary model (such as a Gaussian Mixture Model) to learn the in-distribution spatial regions in this L-dimensional space. This auxiliary model can now be used to identify points that reside outside the learned space. Despite its simplicity, our experiments show that this methodology significantly outperforms the state-of-the-art in detecting out-of-distribution images. For example, our method can effectively separate CIFAR-10 (inlier) and SVHN (OOD) images, a setting which has been previously shown to be difficult for deep likelihood models.

Yang Li, Junier B. Oliva

Many real-world situations allow for the acquisition of additional relevant information when making an assessment with limited or uncertain data. However, traditional ML approaches either require all features to be acquired beforehand or regard part of them as missing data that cannot be acquired. In this work, we consider models that perform active feature acquisition (AFA) and query the environment for unobserved features to improve the prediction assessments at evaluation time. Our work reformulates the Markov decision process (MDP) that underlies the AFA problem as a generative modeling task and optimizes a policy via a novel model-based approach. We propose learning a generative surrogate model (GSM) that captures the dependencies among input features to assess potential information gain from acquisitions. The GSM is leveraged to provide intermediate rewards and auxiliary information to aid the agent navigate a complicated high-dimensional action space and sparse rewards. Furthermore, we extend AFA in a task we coin active instance recognition (AIR) for the unsupervised case where the target variables are the unobserved features themselves and the goal is to collect information for a particular instance in a cost-efficient way. Empirical results demonstrate that our approach achieves considerably better performance than previous state of the art methods on both supervised and unsupervised tasks.

Yang Li, Haidong Yi, Christopher M. Bender et al.

Reasoning over an instance composed of a set of vectors, like a point cloud, requires that one accounts for intra-set dependent features among elements. However, since such instances are unordered, the elements' features should remain unchanged when the input's order is permuted. This property, permutation equivariance, is a challenging constraint for most neural architectures. While recent work has proposed global pooling and attention-based solutions, these may be limited in the way that intradependencies are captured in practice. In this work we propose a more general formulation to achieve permutation equivariance through ordinary differential equations (ODE). Our proposed module, Exchangeable Neural ODE (ExNODE), can be seamlessly applied for both discriminative and generative tasks. We also extend set modeling in the temporal dimension and propose a VAE based model for temporal set modeling. Extensive experiments demonstrate the efficacy of our method over strong baselines.

Yang Li, Junier B. Oliva

Many real-world situations allow for the acquisition of additional relevant information when making an assessment with limited or uncertain data. However, traditional ML approaches either require all features to be acquired beforehand or regard part of them as missing data that cannot be acquired. In this work, we propose models that dynamically acquire new features to further improve the prediction assessment. To trade off the improvement with the cost of acquisition, we leverage an information theoretic metric, conditional mutual information, to select the most informative feature to acquire. We leverage a generative model, arbitrary conditional flow (ACFlow), to learn the arbitrary conditional distributions required for estimating the information metric. We also learn a Bayesian network to accelerate the acquisition process. Our model demonstrates superior performance over baselines evaluated in multiple settings.

Yifeng Shi, Christopher M. Bender, Junier B. Oliva et al.

Clustering and prediction are two primary tasks in the fields of unsupervised and supervised learning, respectively. Although much of the recent advances in machine learning have been centered around those two tasks, the interdependent, mutually beneficial relationship between them is rarely explored. One could reasonably expect appropriately clustering the data would aid the downstream prediction task and, conversely, a better prediction performance for the downstream task could potentially inform a more appropriate clustering strategy. In this work, we focus on the latter part of this mutually beneficial relationship. To this end, we introduce Deep Goal-Oriented Clustering (DGC), a probabilistic framework that clusters the data by jointly using supervision via side-information and unsupervised modeling of the inherent data structure in an end-to-end fashion. We show the effectiveness of our model on a range of datasets by achieving prediction accuracies comparable to the state-of-the-art, while, more importantly in our setting, simultaneously learning congruent clustering strategies.

Christopher M. Bender, Yang Li, Yifeng Shi et al.

In this work we develop a novel Bayesian neural network methodology to achieve strong adversarial robustness without the need for online adversarial training. Unlike previous efforts in this direction, we do not rely solely on the stochasticity of network weights by minimizing the divergence between the learned parameter distribution and a prior. Instead, we additionally require that the model maintain some expected uncertainty with respect to all input covariates. We demonstrate that by encouraging the network to distribute evenly across inputs, the network becomes less susceptible to localized, brittle features which imparts a natural robustness to targeted perturbations. We show empirical robustness on several benchmark datasets.

Yifeng Shi, Junier Oliva, Marc Niethammer

Modern methods for learning over graph input data have shown the fruitfulness of accounting for relationships among elements in a collection. However, most methods that learn over set input data use only rudimentary approaches to exploit intra-collection relationships. In this work we introduce Deep Message Passing on Sets (DMPS), a novel method that incorporates relational learning for sets. DMPS not only connects learning on graphs with learning on sets via deep kernel learning, but it also bridges message passing on sets and traditional diffusion dynamics commonly used in denoising models. Based on these connections, we develop two new blocks for relational learning on sets: the set-denoising block and the set-residual block. The former is motivated by the connection between message passing on general graphs and diffusion-based denoising models, whereas the latter is inspired by the well-known residual network. In addition to demonstrating the interpretability of our model by learning the true underlying relational structure experimentally, we also show the effectiveness of our approach on both synthetic and real-world datasets by achieving results that are competitive with or outperform the state-of-the-art.

Mariya Popova, Mykhailo Shvets, Junier Oliva et al.

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph recurrent generative model for molecular structures. Our model generates diverse realistic molecular graphs after likelihood pretraining on a big database of molecules. We perform an analysis of our pretrained models on large-scale generated datasets of 1 million samples. Further, the model is tuned with policy gradient algorithm, provided a critic that estimates the reward for the property of interest. We show a significant distribution shift to the desired range for lipophilicity, drug-likeness, and melting point outperforming state-of-the-art works. With the use of rejection sampling based on valency constraints, our model yields 100% validity. Moreover, we show that invalid molecules provide a rich signal to the model through the use of structure penalty in our reinforcement learning pipeline.

Eunbyung Park, Junier B. Oliva

We propose meta-curvature (MC), a framework to learn curvature information for better generalization and fast model adaptation. MC expands on the model-agnostic meta-learner (MAML) by learning to transform the gradients in the inner optimization such that the transformed gradients achieve better generalization performance to a new task. For training large scale neural networks, we decompose the curvature matrix into smaller matrices in a novel scheme where we capture the dependencies of the model's parameters with a series of tensor products. We demonstrate the effects of our proposed method on several few-shot learning tasks and datasets. Without any task specific techniques and architectures, the proposed method achieves substantial improvement upon previous MAML variants and outperforms the recent state-of-the-art methods. Furthermore, we observe faster convergence rates of the meta-training process. Finally, we present an analysis that explains better generalization performance with the meta-trained curvature.

Christopher Bender, Kevin O'Connor, Yang Li et al.

In this work, we develop a new approach to generative density estimation for exchangeable, non-i.i.d. data. The proposed framework, FlowScan, combines invertible flow transformations with a sorted scan to flexibly model the data while preserving exchangeability. Unlike most existing methods, FlowScan exploits the intradependencies within sets to learn both global and local structure. FlowScan represents the first approach that is able to apply sequential methods to exchangeable density estimation without resorting to averaging over all possible permutations. We achieve new state-of-the-art performance on point cloud and image set modeling.

Yang Li, Tianxiang Gao, Junier B. Oliva

In this work, we propose to learn a generative model using both learned features (through a latent space) and memories (through neighbors). Although human learning makes seamless use of both learned perceptual features and instance recall, current generative learning paradigms only make use of one of these two components. Take, for instance, flow models, which learn a latent space of invertible features that follow a simple distribution. Conversely, kernel density techniques use instances to shift a simple distribution into an aggregate mixture model. Here we propose multiple methods to enhance the latent space of a flow model with neighborhood information. Not only does our proposed framework represent a more human-like approach by leveraging both learned features and memories, but it may also be viewed as a step forward in non-parametric methods. The efficacy of our model is shown empirically with standard image datasets. We observe compelling results and a significant improvement over baselines.

Junier B. Oliva, Avinava Dubey, Manzil Zaheer et al.

The fundamental task of general density estimation $p(x)$ has been of keen interest to machine learning. In this work, we attempt to systematically characterize methods for density estimation. Broadly speaking, most of the existing methods can be categorized into either using: \textit{a}) autoregressive models to estimate the conditional factors of the chain rule, $p(x_{i}\, |\, x_{i-1}, \ldots)$; or \textit{b}) non-linear transformations of variables of a simple base distribution. Based on the study of the characteristics of these categories, we propose multiple novel methods for each category. For example we proposed RNN based transformations to model non-Markovian dependencies. Further, through a comprehensive study over both real world and synthetic data, we show for that jointly leveraging transformations of variables and autoregressive conditional models, results in a considerable improvement in performance. We illustrate the use of our models in outlier detection and image modeling. Finally we introduce a novel data driven framework for learning a family of distributions.

Siamak Ravanbakhsh, Junier Oliva, Sebastien Fromenteau et al.

A grand challenge of the 21st century cosmology is to accurately estimate the cosmological parameters of our Universe. A major approach to estimating the cosmological parameters is to use the large-scale matter distribution of the Universe. Galaxy surveys provide the means to map out cosmic large-scale structure in three dimensions. Information about galaxy locations is typically summarized in a "single" function of scale, such as the galaxy correlation function or power-spectrum. We show that it is possible to estimate these cosmological parameters directly from the distribution of matter. This paper presents the application of deep 3D convolutional networks to volumetric representation of dark-matter simulations as well as the results obtained using a recently proposed distribution regression framework, showing that machine learning techniques are comparable to, and can sometimes outperform, maximum-likelihood point estimates using "cosmological models". This opens the way to estimating the parameters of our Universe with higher accuracy.

Junier B. Oliva, Kumar Avinava Dubey, Barnabas Poczos et al.

This paper presents the recurrent estimation of distributions (RED) for modeling real-valued data in a semiparametric fashion. RED models make two novel uses of recurrent neural networks (RNNs) for density estimation of general real-valued data. First, RNNs are used to transform input covariates into a latent space to better capture conditional dependencies in inputs. After, an RNN is used to compute the conditional distributions of the latent covariates. The resulting model is efficient to train, compute, and sample from, whilst producing normalized pdfs. The effectiveness of RED is shown via several real-world data experiments. Our results show that RED models achieve a lower held-out negative log-likelihood than other neural network approaches across multiple dataset sizes and dimensionalities. Further context of the efficacy of RED is provided by considering anomaly detection tasks, where we also observe better performance over alternative models.

Junier B. Oliva, Barnabas Poczos, Jeff Schneider

Sophisticated gated recurrent neural network architectures like LSTMs and GRUs have been shown to be highly effective in a myriad of applications. We develop an un-gated unit, the statistical recurrent unit (SRU), that is able to learn long term dependencies in data by only keeping moving averages of statistics. The SRU's architecture is simple, un-gated, and contains a comparable number of parameters to LSTMs; yet, SRUs perform favorably to more sophisticated LSTM and GRU alternatives, often outperforming one or both in various tasks. We show the efficacy of SRUs as compared to LSTMs and GRUs in an unbiased manner by optimizing respective architectures' hyperparameters in a Bayesian optimization scheme for both synthetic and real-world tasks.

Kirthevasan Kandasamy, Gautam Dasarathy, Junier B. Oliva et al.

In many scientific and engineering applications, we are tasked with the maximisation of an expensive to evaluate black box function $f$. Traditional settings for this problem assume just the availability of this single function. However, in many cases, cheap approximations to $f$ may be obtainable. For example, the expensive real world behaviour of a robot can be approximated by a cheap computer simulation. We can use these approximations to eliminate low function value regions cheaply and use the expensive evaluations of $f$ in a small but promising region and speedily identify the optimum. We formalise this task as a \emph{multi-fidelity} bandit problem where the target function and its approximations are sampled from a Gaussian process. We develop MF-GP-UCB, a novel method based on upper confidence bound techniques. In our theoretical analysis we demonstrate that it exhibits precisely the above behaviour, and achieves better regret than strategies which ignore multi-fidelity information. Empirically, MF-GP-UCB outperforms such naive strategies and other multi-fidelity methods on several synthetic and real experiments.

Junier B. Oliva, Danica J. Sutherland, Barnabás Póczos et al.

The use of distributions and high-level features from deep architecture has become commonplace in modern computer vision. Both of these methodologies have separately achieved a great deal of success in many computer vision tasks. However, there has been little work attempting to leverage the power of these to methodologies jointly. To this end, this paper presents the Deep Mean Maps (DMMs) framework, a novel family of methods to non-parametrically represent distributions of features in convolutional neural network models. DMMs are able to both classify images using the distribution of top-level features, and to tune the top-level features for performing this task. We show how to implement DMMs using a special mean map layer composed of typical CNN operations, making both forward and backward propagation simple. We illustrate the efficacy of DMMs at analyzing distributional patterns in image data in a synthetic data experiment. We also show that we extending existing deep architectures with DMMs improves the performance of existing CNNs on several challenging real-world datasets.

Danica J. Sutherland, Junier B. Oliva, Barnabás Póczos et al.

Many interesting machine learning problems are best posed by considering instances that are distributions, or sample sets drawn from distributions. Previous work devoted to machine learning tasks with distributional inputs has done so through pairwise kernel evaluations between pdfs (or sample sets). While such an approach is fine for smaller datasets, the computation of an $N \times N$ Gram matrix is prohibitive in large datasets. Recent scalable estimators that work over pdfs have done so only with kernels that use Euclidean metrics, like the $L_2$ distance. However, there are a myriad of other useful metrics available, such as total variation, Hellinger distance, and the Jensen-Shannon divergence. This work develops the first random features for pdfs whose dot product approximates kernels using these non-Euclidean metrics, allowing estimators using such kernels to scale to large datasets by working in a primal space, without computing large Gram matrices. We provide an analysis of the approximation error in using our proposed random features and show empirically the quality of our approximation both in estimating a Gram matrix and in solving learning tasks in real-world and synthetic data.

Junier Oliva, Avinava Dubey, Andrew G. Wilson et al.

Kernel methods are ubiquitous tools in machine learning. However, there is often little reason for the common practice of selecting a kernel a priori. Even if a universal approximating kernel is selected, the quality of the finite sample estimator may be greatly affected by the choice of kernel. Furthermore, when directly applying kernel methods, one typically needs to compute a $N \times N$ Gram matrix of pairwise kernel evaluations to work with a dataset of $N$ instances. The computation of this Gram matrix precludes the direct application of kernel methods on large datasets, and makes kernel learning especially difficult. In this paper we introduce Bayesian nonparmetric kernel-learning (BaNK), a generic, data-driven framework for scalable learning of kernels. BaNK places a nonparametric prior on the spectral distribution of random frequencies allowing it to both learn kernels and scale to large datasets. We show that this framework can be used for large scale regression and classification tasks. Furthermore, we show that BaNK outperforms several other scalable approaches for kernel learning on a variety of real world datasets.

Junier Oliva, Willie Neiswanger, Barnabas Poczos et al.

We analyze the problem of regression when both input covariates and output responses are functions from a nonparametric function class. Function to function regression (FFR) covers a large range of interesting applications including time-series prediction problems, and also more general tasks like studying a mapping between two separate types of distributions. However, previous nonparametric estimators for FFR type problems scale badly computationally with the number of input/output pairs in a data-set. Given the complexity of a mapping between general functions it may be necessary to consider large data-sets in order to achieve a low estimation risk. To address this issue, we develop a novel scalable nonparametric estimator, the Triple-Basis Estimator (3BE), which is capable of operating over datasets with many instances. To the best of our knowledge, the 3BE is the first nonparametric FFR estimator that can scale to massive datasets. We analyze the 3BE's risk and derive an upperbound rate. Furthermore, we show an improvement of several orders of magnitude in terms of prediction speed and a reduction in error over previous estimators in various real-world data-sets.

Junier B. Oliva, Willie Neiswanger, Barnabas Poczos et al.

We study the problem of distribution to real-value regression, where one aims to regress a mapping $f$ that takes in a distribution input covariate $P\in \mathcal{I}$ (for a non-parametric family of distributions $\mathcal{I}$) and outputs a real-valued response $Y=f(P) + ε$. This setting was recently studied, and a "Kernel-Kernel" estimator was introduced and shown to have a polynomial rate of convergence. However, evaluating a new prediction with the Kernel-Kernel estimator scales as $Ω(N)$. This causes the difficult situation where a large amount of data may be necessary for a low estimation risk, but the computation cost of estimation becomes infeasible when the data-set is too large. To this end, we propose the Double-Basis estimator, which looks to alleviate this big data problem in two ways: first, the Double-Basis estimator is shown to have a computation complexity that is independent of the number of of instances $N$ when evaluating new predictions after training; secondly, the Double-Basis estimator is shown to have a fast rate of convergence for a general class of mappings $f\in\mathcal{F}$.

Junier B. Oliva, Barnabas Poczos, Timothy Verstynen et al.

We present the FuSSO, a functional analogue to the LASSO, that efficiently finds a sparse set of functional input covariates to regress a real-valued response against. The FuSSO does so in a semi-parametric fashion, making no parametric assumptions about the nature of input functional covariates and assuming a linear form to the mapping of functional covariates to the response. We provide a statistical backing for use of the FuSSO via proof of asymptotic sparsistency under various conditions. Furthermore, we observe good results on both synthetic and real-world data.