Junier 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.

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.

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/}.

Shreyas Bhat Brahmavar, Qiyang Liu, Yang Li et al.

Open-world conditional modeling (OCM), requires a single model to answer arbitrary conditional queries across heterogeneous datasets, where observed variables and targets vary and arise from a vast open-ended task universe. Because any finite collection of real-world datasets covers only a small fraction of this space, we propose Task Expansion and Cross Refinement (TEXR), a semi-supervised framework that enlarges effective task coverage through structured synthesis and refinement of semantic data contexts. TEXR first generates diverse uninstantiated dataset schemas and weakly instantiates them via structured probabilistic generators guided by large language models. It then performs cross-model refinement by training on disjoint data partitions and revising synthetic values across splits to reduce confirmation bias and improve pseudo-value quality. The refined synthetic datasets are aggregated with real data to train a unified conditional model. Across heterogeneous tabular benchmarks, TEXR consistently improves zero-, few-, and many-shot performance for multiple OCM backbones, demonstrating that structured task expansion and cross refinement enhance open-world conditional modeling.

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.

Shreyas Bhat Brahmavar, Yang Li, Junier Oliva

Real-world data often appears in diverse, disjoint forms -- with varying schemas, inconsistent semantics, and no fixed feature ordering -- making it challenging to build general-purpose models that can leverage information across datasets. We introduce ASPIRE, Arbitrary Set-based Permutation-Invariant Reasoning Engine, a Universal Neural Inference model for semantic reasoning and prediction over heterogeneous structured data. ASPIRE combines a permutation-invariant, set-based Transformer with a semantic grounding module that incorporates natural language descriptions, dataset metadata, and in-context examples to learn cross-dataset feature dependencies. This architecture allows ASPIRE to ingest arbitrary sets of feature--value pairs and support examples, align semantics across disjoint tables, and make predictions for any specified target. Once trained, ASPIRE generalizes to new inference tasks without additional tuning. In addition to delivering strong results across diverse benchmarks, ASPIRE naturally supports cost-aware active feature acquisition in an open-world setting, selecting informative features under test-time budget constraints for an arbitrary unseen dataset. These capabilities position ASPIRE as a step toward truly universal, semantics-aware inference over structured data.

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.

Noah Frahm, Dongxu Zhao, Andrea Dunn Beltran et al.

Next Best View (NBV) algorithms aim to maximize 3D scene acquisition quality using minimal resources, e.g. number of acquisitions, time taken, or distance traversed. Prior methods often rely on coverage maximization as a proxy for reconstruction quality, but for complex scenes with occlusions and finer details, this is not always sufficient and leads to poor reconstructions. Our key insight is to train an acquisition policy that directly optimizes for reconstruction quality rather than just coverage. To achieve this, we introduce the View Introspection Network (VIN): a lightweight neural network that predicts the Relative Reconstruction Improvement (RRI) of a potential next viewpoint without making any new acquisitions. We use this network to power a simple, yet effective, sequential samplingbased greedy NBV policy. Our approach, VIN-NBV, generalizes to unseen object categories, operates without prior scene knowledge, is adaptable to resource constraints, and can handle occlusions. We show that our RRI fitness criterion leads to a ~30% gain in reconstruction quality over a coverage-based criterion using the same greedy strategy. Furthermore, VIN-NBV also outperforms deep reinforcement learning methods, Scan-RL and GenNBV, by ~40%.

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.

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.

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.

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.

Siyuan Shan, Yang Li, Junier Oliva

Making an adaptive prediction based on one's input is an important ability for general artificial intelligence. In this work, we step forward in this direction and propose a semi-parametric method, Meta-Neighborhoods, where predictions are made adaptively to the neighborhood of the input. We show that Meta-Neighborhoods is a generalization of $k$-nearest-neighbors. Due to the simpler manifold structure around a local neighborhood, Meta-Neighborhoods represent the predictive distribution $p(y \mid x)$ more accurately. To reduce memory and computation overhead, we propose induced neighborhoods that summarize the training data into a much smaller dictionary. A meta-learning based training mechanism is then exploited to jointly learn the induced neighborhoods and the model. Extensive studies demonstrate the superiority of our method.

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.

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.

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 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.