Optical proximity correction (OPC) is a widely-used resolution enhancement technique (RET) for printability optimization. Recently, rigorous numerical optimization and fast machine learning are the research focus of OPC in both academia and industry, each of which complements the other in terms of robustness or efficiency. We inspect the pattern distribution on a design layer and find that different sub-regions have different pattern complexity. Besides, we also find that many patterns repetitively appear in the design layout, and these patterns may possibly share optimized masks. We exploit these properties and propose a self-adaptive OPC framework to improve efficiency. Firstly we choose different OPC solvers adaptively for patterns of different complexity from an extensible solver pool to reach a speed/accuracy co-optimization. Apart from that, we prove the feasibility of reusing optimized masks for repeated patterns and hence, build a graph-based dynamic pattern library reusing stored masks to further speed up the OPC flow. Experimental results show that our framework achieves substantial improvement in both performance and efficiency.
With the feature size continuously shrinking in advanced technology nodes, mask optimization is increasingly crucial in the conventional design flow, accompanied by an explosive growth in prohibitive computational overhead in optical proximity correction (OPC) methods. Recently, inverse lithography technique (ILT) has drawn significant attention and is becoming prevalent in emerging OPC solutions. However, ILT methods are either time-consuming or in weak performance of mask printability and manufacturability. In this paper, we present DevelSet, a GPU and deep neural network (DNN) accelerated level set OPC framework for metal layer. We first improve the conventional level set-based ILT algorithm by introducing the curvature term to reduce mask complexity and applying GPU acceleration to overcome computational bottlenecks. To further enhance printability and fast iterative convergence, we propose a novel deep neural network delicately designed with level set intrinsic principles to facilitate the joint optimization of DNN and GPU accelerated level set optimizer. Experimental results show that DevelSet framework surpasses the state-of-the-art methods in printability and boost the runtime performance achieving instant level (around 1 second).
Molecular Dynamics (MD) is crucial in various fields such as materials science, chemistry, and pharmacology to name a few. Conventional MD software struggles with the balance between time cost and prediction accuracy, which restricts its wider application. Recently, data-driven approaches based on deep generative models have been devised for time-coarsened dynamics, which aim at learning dynamics of diverse molecular systems over a long timestep, enjoying both universality and efficiency. Nevertheless, most current methods are designed solely to learn from the data distribution regardless of the underlying Boltzmann distribution, and the physics priors such as energies and forces are constantly overlooked. In this work, we propose a conditional generative model called Force-guided Bridge Matching (FBM), which learns full-atom time-coarsened dynamics and targets the Boltzmann-constrained distribution. With the guidance of our delicately-designed intermediate force field, FBM leverages favourable physics priors into the generation process, giving rise to enhanced simulations. Experiments on two datasets consisting of peptides verify our superiority in terms of comprehensive metrics and demonstrate transferability to unseen systems.
Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.
The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.
Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models in a specific domain, either proteins or small molecules, missing the opportunity to leverage cross-domain knowledge. To mitigate this gap, we introduce Equivariant Pretrained Transformer (EPT), an all-atom foundation model that can be pretrained from multiple domain 3D molecules. Built upon an E(3)-equivariant transformer, EPT is able to not only process atom-level information but also incorporate block-level features (e.g. residuals in proteins). Additionally, we employ a block-level denoising task, rather than the conventional atom-level denoising, as the pretraining objective. To pretrain EPT, we construct a large-scale dataset of 5.89M entries, comprising small molecules, proteins, protein-protein complexes, and protein-molecule complexes. Experimental evaluations on downstream tasks including ligand binding affinity prediction, protein property prediction, and molecular property prediction, show that EPT significantly outperforms previous state-of-the-art methods in the first task and achieves competitively superior performance for the remaining two tasks. Furthermore, we demonstrate the potential of EPT in identifying small molecule drug candidates targeting 3CL protease, a critical target in the replication of SARS-CoV-2. Among 1,978 FDA-approved drugs, EPT ranks 7 out of 8 known anti-COVID-19 drugs in the top 200, indicating the high recall of EPT. By using Molecular Dynamics (MD) simulations, EPT further discoveries 7 novel compounds whose binding affinities are higher than that of the top-ranked known anti-COVID-19 drug, showcasing its powerful capabilities in drug discovery.
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based improvements have mostly focused on single-domain molecules, lacking transferability to unfamiliar molecular systems. Therefore, we propose \textbf{Uni}fied \textbf{Sim}ulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions. First, we employ a multi-head pretraining approach to learn a unified atomic representation model from a large and diverse set of molecular data. Then, based on the stochastic interpolant framework, we learn the state transition patterns over long timesteps from MD trajectories, and introduce a force guidance module for rapidly adapting to different chemical environments. Our experiments demonstrate that UniSim achieves highly competitive performance across small molecules, peptides, and proteins.
Deep learning models for skin disease classification require large, diverse, and well-annotated datasets. However, such resources are often limited due to privacy concerns, high annotation costs, and insufficient demographic representation. While text-to-image diffusion probabilistic models (T2I-DPMs) offer promise for medical data synthesis, their use in dermatology remains underexplored, largely due to the scarcity of rich textual descriptions in existing skin image datasets. In this work, we introduce LesionGen, a clinically informed T2I-DPM framework for dermatology image synthesis. Unlike prior methods that rely on simplistic disease labels, LesionGen is trained on structured, concept-rich dermatological captions derived from expert annotations and pseudo-generated, concept-guided reports. By fine-tuning a pretrained diffusion model on these high-quality image-caption pairs, we enable the generation of realistic and diverse skin lesion images conditioned on meaningful dermatological descriptions. Our results demonstrate that models trained solely on our synthetic dataset achieve classification accuracy comparable to those trained on real images, with notable gains in worst-case subgroup performance. Code and data are available here.
Despite the recent success of Large Language Models (LLMs), it remains challenging to feed LLMs with long prompts due to the fixed size of LLM inputs. As a remedy, prompt compression becomes a promising solution by removing redundant tokens in the prompt. However, using LLM in the existing works requires additional computation resources and leads to memory overheads. To address it, we propose ICPC (In-context Prompt Compression), a novel and scalable prompt compression method that adaptively reduces the prompt length. The key idea of ICPC is to calculate the probability of each word appearing in the prompt using encoders and calculate information carried by each word through the information function, which effectively reduces the information loss during prompt compression and increases the speed of compression. Empirically, we demonstrate that ICPC can effectively compress long texts of different categories and thus achieve better performance and speed on different types of NLP tasks.