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Jeet Mohapatra

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5 papers

2 author rows

ICML Conference 2025 Conference Paper

Symmetry-Driven Discovery of Dynamical Variables in Molecular Simulations

Jeet Mohapatra
Nima Dehmamy
Csaba Both
Subhro Das
Tommi Jaakkola

We introduce a novel approach for discovering effective degrees of freedom (DOF) in molecular dynamics simulations by mapping the DOF to approximate symmetries of the energy landscape. Unlike most existing methods, we do not require trajectory data but instead rely on knowledge of the forcefield (energy function) around the initial state. We present a scalable symmetry loss function compatible with existing force-field frameworks and a Hessian-based method efficient for smaller systems. Our approach enables systematic exploration of conformational space by connecting structural dynamics to energy landscape symmetries. We apply our method to two systems, Alanine dipeptide and Chignolin, recovering their known important conformations. Our approach can prove useful for efficient exploration in molecular simulations with potential applications in protein folding and drug discovery.

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NeurIPS Conference 2024 Conference Paper

Neural Network Reparametrization for Accelerated Optimization in Molecular Simulations

Nima Dehmamy
Csaba Both
Jeet Mohapatra
Subhro Das
Tommi Jaakkola

We propose a novel approach to molecular simulations using neural network reparametrization, which offers a flexible alternative to traditional coarse-graining methods. Unlike conventional techniques that strictly reduce degrees of freedom, the complexity of the system can be adjusted in our model, sometimes increasing it to simplify the optimization process. Our approach also maintains continuous access to fine-grained modes and eliminates the need for force-matching, enhancing both the efficiency and accuracy of energy minimization. Importantly, our framework allows for the use of potentially arbitrary neural networks (e. g. , Graph Neural Networks (GNN)) to perform the reparametrization, incorporating CG modes as needed. In fact, our experiments using very weak molecular forces (Lennard-Jones potential) the GNN-based model is the sole model to find the correct configuration. Similarly, in protein-folding scenarios, our GNN-based CG method consistently outperforms traditional optimization methods. It not only recovers the target structures more accurately but also achieves faster convergence to the deepest energy states. This work demonstrates significant advancements in molecular simulations by optimizing energy minimization and convergence speeds, offering a new, efficient framework for simulating complex molecular systems.

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ICML Conference 2024 Conference Paper

What Would Gauss Say About Representations? Probing Pretrained Image Models using Synthetic Gaussian Benchmarks

Ching-Yun Ko
Pin-Yu Chen
Payel Das
Jeet Mohapatra
Luca Daniel

Recent years have witnessed a paradigm shift in deep learning from task-centric model design to task-agnostic representation learning and task-specific fine-tuning. Pretrained model representations are commonly evaluated extensively across various real-world tasks and used as a foundation for different downstream tasks. This paper proposes a solution for assessing the quality of representations in a task-agnostic way. To circumvent the need for real-world data in evaluation, we explore the use of synthetic binary classification tasks with Gaussian mixtures to probe pretrained models and compare the robustness-accuracy performance on pretrained representations with an idealized reference. Our approach offers a holistic evaluation, revealing intrinsic model capabilities and reducing the dependency on real-life data for model evaluation. Evaluated with various pretrained image models, the experimental results confirm that our task-agnostic evaluation correlates with actual linear probing performance on downstream tasks and can also guide parameter choice in robust linear probing to achieve a better robustness-accuracy trade-off.

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ICML Conference 2022 Conference Paper

Revisiting Contrastive Learning through the Lens of Neighborhood Component Analysis: an Integrated Framework

Ching-Yun Ko
Jeet Mohapatra
Sijia Liu 0001
Pin-Yu Chen
Luca Daniel
Lily Weng

As a seminal tool in self-supervised representation learning, contrastive learning has gained unprecedented attention in recent years. In essence, contrastive learning aims to leverage pairs of positive and negative samples for representation learning, which relates to exploiting neighborhood information in a feature space. By investigating the connection between contrastive learning and neighborhood component analysis (NCA), we provide a novel stochastic nearest neighbor viewpoint of contrastive learning and subsequently propose a series of contrastive losses that outperform the existing ones. Under our proposed framework, we show a new methodology to design integrated contrastive losses that could simultaneously achieve good accuracy and robustness on downstream tasks. With the integrated framework, we achieve up to 6% improvement on the standard accuracy and 17% improvement on the robust accuracy.

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NeurIPS Conference 2020 Conference Paper

Higher-Order Certification For Randomized Smoothing

Jeet Mohapatra
Ching-Yun Ko
Tsui-Wei Weng
Pin-Yu Chen
Sijia Liu
Luca Daniel

Randomized smoothing is a recently proposed defense against adversarial attacks that has achieved state-of-the-art provable robustness against $\ell_2$ perturbations. A number of works have extended the guarantees to other metrics, such as $\ell_1$ or $\ell_\infty$, by using different smoothing measures. Although the current framework has been shown to yield near-optimal $\ell_p$ radii, the total safety region certified by the current framework can be arbitrarily small compared to the optimal. In this work, we propose a framework to improve the certified safety region for these smoothed classifiers without changing the underlying smoothing scheme. The theoretical contributions are as follows: 1) We generalize the certification for randomized smoothing by reformulating certified radius calculation as a nested optimization problem over a class of functions. 2) We provide a method to calculate the certified safety region using zeroth-order and first-order information for Gaussian-smoothed classifiers. We also provide a framework that generalizes the calculation for certification using higher-order information. 3) We design efficient, high-confidence estimators for the relevant statistics of the first-order information. Combining the theoretical contribution 2) and 3) allows us to certify safety region that are significantly larger than ones provided by the current methods. On CIFAR and Imagenet, the new regions achieve significant improvements on general $\ell_1$ certified radii and on the $\ell_2$ certified radii for color-space attacks ($\ell_2$ perturbation restricted to only one color/channel) while also achieving smaller improvements on the general $\ell_2$ certified radii. As discussed in the future works section, our framework can also provide a way to circumvent the current impossibility results on achieving higher magnitudes of certified radii without requiring the use of data-dependent smoothing techniques.

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