Aniketh Iyengar

Aniketh Iyengar, Jiaqi Han, Pengwei Sun et al.

Generating molecular dynamics (MD) trajectories using deep generative models has attracted increasing attention, yet remains inherently challenging due to the limited availability of MD data and the complexities involved in modeling high-dimensional MD distributions. To overcome these challenges, we propose a novel framework that leverages structure pretraining for MD trajectory generation. Specifically, we first train a diffusion-based structure generation model on a large-scale conformer dataset, on top of which we introduce an interpolator module trained on MD trajectory data, designed to enforce temporal consistency among generated structures. Our approach effectively harnesses abundant structural data to mitigate the scarcity of MD trajectory data and effectively decomposes the intricate MD modeling task into two manageable subproblems: structural generation and temporal alignment. We comprehensively evaluate our method on the QM9 and DRUGS small-molecule datasets across unconditional generation, forward simulation, and interpolation tasks, and further extend our framework and analysis to tetrapeptide and protein monomer systems. Experimental results confirm that our approach excels in generating chemically realistic MD trajectories, as evidenced by remarkable improvements of accuracy in geometric, dynamical, and energetic measurements.

Zhuoran Qiao, Feizhi Ding, Thomas Dresselhaus et al.

Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting protein and bioassembly structures from sequences and molecular topology alone. Despite substantial progress in the field, challenges remain to deliver structure prediction models to real-world drug discovery. Here, we present NeuralPLexer3 -- a physics-inspired flow-based generative model that achieves state-of-the-art prediction accuracy on key biomolecular interaction types and improves training and sampling efficiency compared to its predecessors and alternative methodologies. Examined through newly developed benchmarking strategies, NeuralPLexer3 excels in vital areas that are crucial to structure-based drug design, such as physical validity and ligand-induced conformational changes.

Aniketh Iyengar, Jiaqi Han, Boris Ruf et al.

The rapidly growing computational demands of diffusion models for image generation have raised significant concerns about energy consumption and environmental impact. While existing approaches to energy optimization focus on architectural improvements or hardware acceleration, there is a lack of principled methods to predict energy consumption across different model configurations and hardware setups. We propose an adaptation of Kaplan scaling laws to predict GPU energy consumption for diffusion models based on computational complexity (FLOPs). Our approach decomposes diffusion model inference into text encoding, iterative denoising, and decoding components, with the hypothesis that denoising operations dominate energy consumption due to their repeated execution across multiple inference steps. We conduct comprehensive experiments across four state-of-the-art diffusion models (Stable Diffusion 2, Stable Diffusion 3.5, Flux, and Qwen) on three GPU architectures (NVIDIA A100, A4000, A6000), spanning various inference configurations including resolution (256x256 to 1024x1024), precision (fp16/fp32), step counts (10-50), and classifier-free guidance settings. Our energy scaling law achieves high predictive accuracy within individual architectures (R-squared > 0.9) and exhibits strong cross-architecture generalization, maintaining high rank correlations across models and enabling reliable energy estimation for unseen model-hardware combinations. These results validate the compute-bound nature of diffusion inference and provide a foundation for sustainable AI deployment planning and carbon footprint estimation.