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Preference Optimization for Molecule Synthesis with Conditional Residual Energy-based Models
Songtao Liu, Hanjun Dai, Yue Zhao, Peng Liu
Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner. Despite their effective performance, these strategies face limitations in the molecule synthetic route generation due to a greedy selection of the next molecule set without any lookahead. Furthermore, existing strategies cannot control the generation of synthetic routes based on possible criteria such as material costs, yields, and step count. In this work, we propose a general and principled framework via conditional residual energy-based models (EBMs), that focus on the quality of the entire synthetic route based on the specific criteria. By incorporating an additional energy-based function into our probabilistic model, our proposed algorithm can enhance the quality of the most probable synthetic routes (with higher probabilities) generated by various strategies in a plug-and-play fashion. Extensive experiments demonstrate that our framework can consistently boost performance across various strategies and outperforms previous state-of-the-art top-1 accuracy by a margin of 2.5%. Code is available at https://github.com/SongtaoLiu0823/CREBM.
Momentum Particle Maximum Likelihood
Jen Ning Lim, Juan Kuntz, Samuel Power, Adam Michael Johansen
Maximum likelihood estimation (MLE) of latent variable models is often recast as the minimization of a free energy functional over an extended space of parameters and probability distributions. This perspective was recently combined with insights from optimal transport to obtain novel particle-based algorithms for fitting latent variable models to data. Drawing inspiration from prior works which interpret `momentum-enriched' optimization algorithms as discretizations of ordinary differential equations, we propose an analogous dynamical-systems-inspired approach to minimizing the free energy functional. The result is a dynamical system that blends elements of Nesterov's Accelerated Gradient method, the underdamped Langevin diffusion, and particle methods. Under suitable assumptions, we prove that the continuous-time system minimizes the functional. By discretizing the system, we obtain a practical algorithm for MLE in latent variable models. The algorithm outperforms existing particle methods in numerical experiments and compares favourably with other MLE algorithms.
Best of Both Worlds Guarantees for Smoothed Online Quadratic Optimization
Neelkamal Bhuyan, Debankur Mukherjee, Adam Wierman
We study the smoothed online quadratic optimization (SOQO) problem where, at each round $t$, a player plays an action $x_t$ in response to a quadratic hitting cost and an additional squared $\ell_2$-norm cost for switching actions. This problem class has strong connections to a wide range of application domains including smart grid management, adaptive control, and data center management, where switching-efficient algorithms are highly sought after. We study the SOQO problem in both adversarial and stochastic settings, and in this process, perform the first stochastic analysis of this class of problems. We provide the online optimal algorithm when the minimizers of the hitting cost function evolve as a general stochastic process, which, for the case of martingale process, takes the form of a *distribution-agnostic dynamic interpolation algorithm* that we call Lazy Adaptive Interpolation (LAI). Next, we present the stochastic-adversarial trade-off by proving an $\Omega(T)$ expected regret for the adversarial optimal algorithm in the literature (ROBD) with respect to LAI and, a sub-optimal competitive ratio for LAI in the adversarial setting. Finally, we present a best-of-both-worlds algorithm that obtains a robust adversarial performance while simultaneously achieving a near-optimal stochastic performance.
Improving Adversarial Energy-Based Model via Diffusion Process
Cong Geng, Tian Han, Peng-Tao Jiang, Hao Zhang, Jinwei Chen, Søren Hauberg, Bo Li
Generative models have shown strong generation ability while efficient likelihood estimation is less explored. Energy-based models (EBMs) define a flexible energy function to parameterize unnormalized densities efficiently but are notorious for being difficult to train. Adversarial EBMs introduce a generator to form a minimax training game to avoid expensive MCMC sampling used in traditional EBMs, but a noticeable gap between adversarial EBMs and other strong generative models still exists. Inspired by diffusion-based models, we embedded EBMs into each denoising step to split a long-generated process into several smaller steps. Besides, we employ a symmetric Jeffrey divergence and introduce a variational posterior distribution for the generator's training to address the main challenges that exist in adversarial EBMs. Our experiments show significant improvement in generation compared to existing adversarial EBMs, while also providing a useful energy function for efficient density estimation.
Geometry-Calibrated DRO: Combating Over-Pessimism with Free Energy Implications
Jiashuo Liu, Jiayun Wu, Tianyu Wang, Hao Zou, Bo Li, Peng Cui
Machine learning algorithms minimizing average risk are susceptible to distributional shifts. Distributionally Robust Optimization (DRO) addresses this issue by optimizing the worst-case risk within an uncertainty set. However, DRO suffers from over-pessimism, leading to low-confidence predictions, poor parameter estimations as well as poor generalization. In this work, we conduct a theoretical analysis of a probable root cause of over-pessimism: excessive focus on noisy samples. To alleviate the impact of noise, we incorporate data geometry into calibration terms in DRO, resulting in our novel Geometry-Calibrated DRO (GCDRO) for regression. We establish the connection between our risk objective and the Helmholtz free energy in statistical physics, and this free-energy-based risk can extend to standard DRO methods. Leveraging gradient flow in Wasserstein space, we develop an approximate minimax optimization algorithm with a bounded error ratio and elucidate how our approach mitigates noisy sample effects. Comprehensive experiments confirm GCDRO's superiority over conventional DRO methods.
Differentiable Distributionally Robust Optimization Layers
Xutao Ma, Chao Ning, WenLi Du
In recent years, there has been a growing research interest in decision-focused learning, which embeds optimization problems as a layer in learning pipelines and demonstrates a superior performance than the prediction-focused approach. However, for distributionally robust optimization (DRO), a popular paradigm for decision-making under uncertainty, it is still unknown how to embed it as a layer, i.e., how to differentiate decisions with respect to an ambiguity set. In this paper, we develop such differentiable DRO layers for generic mixed-integer DRO problems with parameterized second-order conic ambiguity sets and discuss its extension to Wasserstein ambiguity sets. To differentiate the mixed-integer decisions, we propose a novel dual-view methodology by handling continuous and discrete parts of decisions via different principles. Specifically, we construct a differentiable energy-based surrogate to implement the dual-view methodology and use importance sampling to estimate its gradient. We further prove that such a surrogate enjoys the asymptotic convergency under regularization. As an application of the proposed differentiable DRO layers, we develop a novel decision-focused learning pipeline for contextual distributionally robust decision-making tasks and compare it with the prediction-focused approach in experiments
Evaluation of Trajectory Distribution Predictions with Energy Score
Novin Shahroudi, Mihkel Lepson, Meelis Kull
Predicting the future trajectory of surrounding objects is inherently uncertain and vital in the safe and reliable planning of autonomous systems such as in self-driving cars. Although trajectory prediction models have become increasingly sophisticated in dealing with the complexities of spatiotemporal data, the evaluation methods used to assess these models have not kept pace. "Minimum of N" is a common family of metrics used to assess the rich outputs of such models. We critically examine the Minimum of N within the proper scoring rules framework to show that it is not strictly proper and demonstrate how that could lead to a misleading assessment of multimodal trajectory predictions. As an alternative, we propose using Energy Score-based evaluation measures, leveraging their proven propriety for a more reliable evaluation of trajectory distribution predictions.
Learning Iterative Reasoning through Energy Diffusion
Yilun Du, Jiayuan Mao, Joshua B. Tenenbaum
We introduce iterative reasoning through energy diffusion (IRED), a novel framework for learning to reason for a variety of tasks by formulating reasoning and decision-making problems with energy-based optimization. IRED learns energy functions to represent the constraints between input conditions and desired outputs. After training, IRED adapts the number of optimization steps during inference based on problem difficulty, enabling it to solve problems outside its training distribution --- such as more complex Sudoku puzzles, matrix completion with large value magnitudes, and path finding in larger graphs. Key to our method’s success is two novel techniques: learning a sequence of annealed energy landscapes for easier inference and a combination of score function and energy landscape supervision for faster and more stable training. Our experiments show that IRED outperforms existing methods in continuous-space reasoning, discrete-space reasoning, and planning tasks, particularly in more challenging scenarios.