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Dec 12

Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

  • 5 authors
·
Sep 29, 2023

Efficient Model Development through Fine-tuning Transfer

Modern LLMs struggle with efficient updates, as each new pretrained model version requires repeating expensive alignment processes. This challenge also applies to domain- or language-specific models, where fine-tuning on specialized data must be redone for every new base model release. In this paper, we explore the transfer of fine-tuning updates between model versions. Specifically, we derive the diff vector from one source model version, which represents the weight changes from fine-tuning, and apply it to the base model of a different target version. Through empirical evaluations on various open-weight model versions, we show that transferring diff vectors can significantly improve the target base model, often achieving performance comparable to its fine-tuned counterpart. For example, reusing the fine-tuning updates from Llama 3.0 8B leads to an absolute accuracy improvement of 10.7% on GPQA over the base Llama 3.1 8B without additional training, surpassing Llama 3.1 8B Instruct. In a multilingual model development setting, we show that this approach can significantly increase performance on target-language tasks without retraining, achieving an absolute improvement of 4.7% and 15.5% on Global MMLU for Malagasy and Turkish, respectively, compared to Llama 3.1 8B Instruct. Our controlled experiments reveal that fine-tuning transfer is most effective when the source and target models are linearly connected in the parameter space. Additionally, we demonstrate that fine-tuning transfer offers a stronger and more computationally efficient starting point for further fine-tuning. Finally, we propose an iterative recycling-then-finetuning approach for continuous model development, which improves both efficiency and effectiveness. Our findings suggest that fine-tuning transfer is a viable strategy to reduce training costs while maintaining model performance.

  • 5 authors
·
Mar 25 2

diff History for Neural Language Agents

Neural Language Models (LMs) offer an exciting solution for general-purpose embodied control. However, a key technical issue arises when using an LM-based controller: environment observations must be converted to text, which coupled with history, results in long and verbose textual prompts. As a result, prior work in LM agents is limited to restricted domains with small observation size as well as minimal needs for interaction history or instruction tuning. In this paper, we introduce diff history, a simple and highly effective solution to these issues. By applying the Unix diff command on consecutive text observations in the interaction histories used to prompt LM policies, we can both abstract away redundant information and focus the content of textual inputs on the salient changes in the environment. On NetHack, an unsolved video game that requires long-horizon reasoning for decision-making, LMs tuned with diff history match state-of-the-art performance for neural agents while needing 1800x fewer training examples compared to prior work. Even on the simpler BabyAI-Text environment with concise text observations, we find that although diff history increases the length of prompts, the representation it provides offers a 25% improvement in the efficiency of low-sample instruction tuning. Further, we show that diff history scales favorably across different tuning dataset sizes. We open-source our code and data to https://diffhistory.github.io.

  • 3 authors
·
Dec 12, 2023

PFB-Diff: Progressive Feature Blending Diffusion for Text-driven Image Editing

Diffusion models have demonstrated their ability to generate diverse and high-quality images, sparking considerable interest in their potential for real image editing applications. However, existing diffusion-based approaches for local image editing often suffer from undesired artifacts due to the latent-level blending of the noised target images and diffusion latent variables, which lack the necessary semantics for maintaining image consistency. To address these issues, we propose PFB-Diff, a Progressive Feature Blending method for Diffusion-based image editing. Unlike previous methods, PFB-Diff seamlessly integrates text-guided generated content into the target image through multi-level feature blending. The rich semantics encoded in deep features and the progressive blending scheme from high to low levels ensure semantic coherence and high quality in edited images. Additionally, we introduce an attention masking mechanism in the cross-attention layers to confine the impact of specific words to desired regions, further improving the performance of background editing and multi-object replacement. PFB-Diff can effectively address various editing tasks, including object/background replacement and object attribute editing. Our method demonstrates its superior performance in terms of editing accuracy and image quality without the need for fine-tuning or training. Our implementation is available at https://github.com/CMACH508/PFB-Diff.

  • 3 authors
·
Jun 28, 2023