Jana Doppa

AAAI Conference 2026 Conference Paper

Nanoporous Materials Discovery via Search Bias-Guided Surrogate Modeling

• Azza Fadhel
• Yassine Chemingui
• Minh Hoang
• Aryan Deshwal
• Trong Nghia Hoang
• Jana Doppa

Nanoporous materials (NPMs) are suitable for solving some of the society's biggest challenges including carbon capture and conversion, storing hydrogen and methane, and sensing gases. The key challenge in discovering high-performing NPMs for a target application is that making and evaluating candidate NPMs requires performing resource-expensive wet-lab experiments. We consider the problem of discovering NPMs using existing experimental data of NPM evaluations. The overall goal is to find better NPMs than the best NPMs from the past experimental data. A simple approach is to create a surrogate model to match the objective values on the given dataset and employ it to score candidate NPMs to discover optimized NPMs. However, this surrogate model will fail because it does not have the appropriate search bias for the goal of optimization. To address this challenge, we propose a novel surrogate modeling approach that combines value matching loss with an optimization bias as regularizer. The key idea is to algorithmically realize search bias is to mimic the search behavior of monotonically increasing sequences of NPMs from the given dataset. Experiments on multiple real-world NPM discovery tasks demonstrate that our proposed surrogate model discovers significantly better NPMs than baselines including value matching surrogate model and one-step Bayesian optimization.

UAI Conference 2025 Conference Paper

Conformal Prediction Sets for Deep Generative Models via Reduction to Conformal Regression

• Hooman Shahrokhi
• Devjeet Raj Roy
• Yan Yan 0006
• Venera Arnaoudova
• Jana Doppa

We consider the problem of generating valid and small prediction sets by sampling outputs (e. g. , software code and natural language text) from a black-box deep generative model for a given input (e. g. , textual prompt). The validity of a prediction set is determined by a user-defined binary admissibility function depending on the target application. For example, requiring at least one program in the set to pass all test cases in code generation application. To address this problem, we develop a simple and effective conformal inference algorithm referred to as {\em Generative Prediction Sets (GPS)}. Given a set of calibration examples and black-box access to a deep generative model, GPS can generate prediction sets with provable guarantees. The key insight behind GPS is to exploit the inherent structure within the distribution over the minimum number of samples needed to obtain an admissible output to develop a simple conformal regression approach over the minimum number of samples. Unlike prior work, the sets generated by GPS do not require iterative sampling at test time, while maintaining strict marginal coverage guarantees. Experiments on multiple datasets for code and math word problems using different large language models demonstrate the efficacy of GPS over state-of-the-art methods.

AAAI Conference 2025 Conference Paper

Constraint-Adaptive Policy Switching for Offline Safe Reinforcement Learning

• Yassine Chemingui
• Aryan Deshwal
• Honghao Wei
• Alan Fern
• Jana Doppa

Offline safe reinforcement learning (OSRL) involves learning a decision-making policy to maximize rewards from a fixed batch of training data to satisfy pre-defined safety constraints. However, adapting to varying safety constraints during deployment without retraining remains an under-explored challenge. To address this challenge, we introduce constraint-adaptive policy switching (CAPS), a wrapper framework around existing offline RL algorithms. During training, CAPS uses offline data to learn multiple policies with a shared representation that optimize different reward and cost trade-offs. During testing, CAPS switches between those policies by selecting at each state the policy that maximizes future rewards among those that satisfy the current cost constraint. Our experiments on 38 tasks from the DSRL benchmark demonstrate that CAPS consistently outperforms existing methods, establishing a strong wrapper-based baseline for OSRL.

ICML Conference 2025 Conference Paper

Direct Prediction Set Minimization via Bilevel Conformal Classifier Training

• Yuanjie Shi
• Hooman Shahrokhi
• Xuesong Jia
• Xiongzhi Chen
• Jana Doppa
• Yan Yan 0006

Conformal prediction (CP) is a promising uncertainty quantification framework which works as a wrapper around a black-box classifier to construct prediction sets (i. e. , subset of candidate classes) with provable guarantees. However, standard calibration methods for CP tend to produce large prediction sets which makes them less useful in practice. This paper considers the problem of integrating conformal principles into the training process of deep classifiers to directly minimize the size of prediction sets. We formulate conformal training as a bilevel optimization problem and propose the Direct Prediction Set Minimization (DPSM) algorithm to solve it. The key insight behind DPSM is to minimize a measure of the prediction set size (upper level) that is conditioned on the learned quantile of conformity scores (lower level). We analyze that DPSM has a learning bound of $O(1/\sqrt{n})$ (with $n$ training samples), while prior conformal training methods based on stochastic approximation for the quantile has a bound of $\Omega(1/s)$ (with batch size $s$ and typically $s \ll \sqrt{n}$). Experiments on various benchmark datasets and deep models show that DPSM significantly outperforms the best prior conformal training baseline with $20. 46\%\downarrow$ in the prediction set size and validates our theory.

TMLR Journal 2025 Journal Article

Non-Myopic Multi-Objective Bayesian Optimization

• Syrine Belakaria
• Alaleh Ahmadian
• Barbara E Engelhardt
• Stefano Ermon
• Jana Doppa

We consider the problem of finite-horizon sequential experimental design to solve multi-objective optimization (MOO) of expensive black-box objective functions. This problem arises in many real-world applications, including materials design, where we have a small resource budget to make and evaluate candidate materials in the lab. We solve this problem using the framework of Bayesian optimization (BO) and propose the first set of non-myopic methods for MOO problems. Prior work on non-myopic BO for single-objective problems relies on the Bellman optimality principle to handle the lookahead reasoning process. However, this principle does not hold for most MOO problems because the reward function needs to satisfy some conditions: scalar variable, monotonicity, and additivity. We address this challenge by using hypervolume improvement (HVI) as our scalarization approach, which allows us to use a lower-bound on the Bellman equation to approximate the finite-horizon using a batch expected hypervolume improvement (EHVI) acquisition function (AF) for MOO. Our formulation naturally allows us to use other improvement-based scalarizations and compare their efficacy to HVI. We derive three non-myopic AFs for MOBO: 1) the Nested AF, which is based on the exact computation of the lower bound, 2) the Joint AF, which is a lower bound on the nested AF, and 3) the BINOM AF, which is a fast and approximate variant based on batch multi-objective acquisition functions. Our experiments on multiple diverse real-world MO problems demonstrate that our non-myopic AFs substantially improve performance over the existing myopic AFs for MOBO.

NeurIPS Conference 2025 Conference Paper

Online Optimization for Offline Safe Reinforcement Learning

• Yassine Chemingui
• Aryan Deshwal
• Alan Fern
• Thanh Nguyen-Tang
• Jana Doppa

We study the problem of Offline Safe Reinforcement Learning (OSRL), where the goal is to learn a reward-maximizing policy from fixed data under a cumulative cost constraint. We propose a novel OSRL approach that frames the problem as a minimax objective and solves it by combining offline RL with online optimization algorithms. We prove the approximate optimality of this approach when integrated with an approximate offline RL oracle and no-regret online optimization. We also present a practical approximation that can be combined with any offline RL algorithm, eliminating the need for offline policy evaluation. Empirical results on the DSRL benchmark demonstrate that our method reliably enforces safety constraints under stringent cost budgets, while achieving high rewards. The code is available at https: //github. com/yassineCh/O3SRL.

ICML Conference 2024 Conference Paper

Learning Surrogates for Offline Black-Box Optimization via Gradient Matching

• Minh Hoang
• Azza Fadhel
• Aryan Deshwal
• Jana Doppa
• Trong Nghia Hoang

Offline design optimization problem arises in numerous science and engineering applications including material and chemical design, where expensive online experimentation necessitates the use of in silico surrogate functions to predict and maximize the target objective over candidate designs. Although these surrogates can be learned from offline data, their predictions are often inaccurate outside the offline data regime. This challenge raises a fundamental question about the impact of imperfect surrogate model on the performance gap between its optima and the true optima, and to what extent the performance loss can be mitigated. Although prior work developed methods to improve the robustness of surrogate models and their associated optimization processes, a provably quantifiable relationship between an imperfect surrogate and the corresponding performance gap, as well as whether prior methods directly address it, remain elusive. To shed light on this important question, we present a theoretical framework to understand offline black-box optimization, by explicitly bounding the optimization quality based on how well the surrogate matches the latent gradient field that underlines the offline data. Inspired by our theoretical analysis, we propose a principled black-box gradient matching algorithm to create effective surrogate models for offline optimization, improving over prior approaches on various real-world benchmarks.

UAI Conference 2023 Conference Paper

Probabilistically robust conformal prediction

• Subhankar Ghosh
• Yuanjie Shi
• Taha Belkhouja
• Yan Yan 0006
• Jana Doppa
• Brian Jones

Conformal prediction (CP) is a framework to quantify uncertainty of machine learning classifiers including deep neural networks. Given a testing example and a trained classifier, CP produces a prediction set of candidate labels with a user-specified coverage (i. e. , true class label is contained with high probability). Almost all the existing work on CP assumes clean testing data and there is not much known about the robustness of CP algorithms w. r. t natural/adversarial perturbations to testing examples. This paper studies the problem of probabilistically robust conformal prediction (PRCP) which ensures robustness to most perturbations around clean input examples. PRCP generalizes the standard CP (cannot handle perturbations) and adversarially robust CP (ensures robustness w. r. t worst-case perturbations) to achieve better trade-offs between nominal performance and robustness. We propose a novel adaptive PRCP (aPRCP) algorithm to achieve probabilistically robust coverage. The key idea behind aPRCP is to determine two parallel thresholds, one for data samples and another one for the perturbations on data (aka "quantile-of-quantile” design). We provide theoretical analysis to show that aPRCP algorithm achieves robust coverage. Our experiments on CIFAR-10, CIFAR-100, and ImageNet datasets using deep neural networks demonstrate that aPRCP achieves better trade-offs than state-of-the-art CP and adversarially robust CP algorithms.

ICML Conference 2021 Conference Paper

Bayesian Optimization over Hybrid Spaces

• Aryan Deshwal
• Syrine Belakaria
• Jana Doppa

We consider the problem of optimizing hybrid structures (mixture of discrete and continuous input variables) via expensive black-box function evaluations. This problem arises in many real-world applications. For example, in materials design optimization via lab experiments, discrete and continuous variables correspond to the presence/absence of primitive elements and their relative concentrations respectively. The key challenge is to accurately model the complex interactions between discrete and continuous variables. In this paper, we propose a novel approach referred as Hybrid Bayesian Optimization (HyBO) by utilizing diffusion kernels, which are naturally defined over continuous and discrete variables. We develop a principled approach for constructing diffusion kernels over hybrid spaces by utilizing the additive kernel formulation, which allows additive interactions of all orders in a tractable manner. We theoretically analyze the modeling strength of additive hybrid kernels and prove that it has the universal approximation property. Our experiments on synthetic and six diverse real-world benchmarks show that HyBO significantly outperforms the state-of-the-art methods.

NeurIPS Conference 2021 Conference Paper

Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spaces

• Aryan Deshwal
• Jana Doppa

We consider the problem of optimizing combinatorial spaces (e. g. , sequences, trees, and graphs) using expensive black-box function evaluations. For example, optimizing molecules for drug design using physical lab experiments. Bayesian optimization (BO) is an efficient framework for solving such problems by intelligently selecting the inputs with high utility guided by a learned surrogate model. A recent BO approach for combinatorial spaces is through a reduction to BO over continuous spaces by learning a latent representation of structures using deep generative models (DGMs). The selected input from the continuous space is decoded into a discrete structure for performing function evaluation. However, the surrogate model over the latent space only uses the information learned by the DGM, which may not have the desired inductive bias to approximate the target black-box function. To overcome this drawback, this paper proposes a principled approach referred as LADDER. The key idea is to define a novel structure-coupled kernel that explicitly integrates the structural information from decoded structures with the learned latent space representation for better surrogate modeling. Our experiments on real-world benchmarks show that LADDER significantly improves over the BO over latent space method, and performs better or similar to state-of-the-art methods.

ICAPS Conference 2017 Conference Paper

Learning to Speed Up Query Planning in Graph Databases

• Mohammad Hossein Namaki
• F. A. Rezaur Rahman Chowdhury
• Md. Rakibul Islam 0001
• Jana Doppa
• Yinghui Wu 0001

Querying graph structured data is a fundamental operation that enables important applications including knowledge graph search, social network analysis, and cyber-network security. However, the growing size of real-world data graphs poses severe challenges for graph databases to meet the response-time requirements of the applications. Planning the computational steps of query processing — Query Planning — is central to address these challenges. In this paper, we study the problem of learning to speedup query planning in graph databases towards the goal of improving the computational-efficiency of query processing via training queries. We present a Learning to Plan (L2P) framework that is applicable to a large class of query reasoners that follow the Threshold Algorithm (TA) approach. First, we define a generic search space over candidate query plans, and identify target search trajectories (query plans) corresponding to the training queries by performing an expensive search. Subsequently, we learn greedy search control knowledge to imitate the search behavior of the target query plans. We provide a concrete instantiation of our L2P framework for STAR, a state-of-the-art graph query reasoner. Our experiments on benchmark knowledge graphs including dbpedia, yago, and freebase show that using the query plans generated by the learned search control knowledge, we can significantly improve the speed of STAR with negligible loss in accuracy.

ICML Conference 2012 Conference Paper

Output Space Search for Structured Prediction

• Jana Doppa
• Alan Fern
• Prasad Tadepalli