Chip Design ML

Machine Learning Force Fields (MLFFs) are of great importance for chemistry, physics, materials science, and many other related fields. The Clebsch–Gordan transform (CG transform) effectively encodes many-body interactions and is thus an important building block for many models of MLFFs. However, the permutation-equivariance requirement of MLFFs limits the design space of CG transform, that is, intensive CG transform has to be conducted for each neighboring edge and the operations should be performed in the same manner for all edges. Freeing up the design space can greatly improve the model's expressiveness while simultaneously decreasing computational demands. To reach this goal, we utilize a mathematical proposition, invariance transitivity, to show that implementing the CG transform layer on the permutation-invariant abstract edges allows complete freedom in the design of the layer without compromising the overall permutation equivariance. Developing on this free design space, we further propose group CG transform with sparse path, abstract edges shuffling, and attention enhancer to form a powerful and efficient CG transform layer. Our method, known as FreeCG, achieves state-of-the-art (SOTA) results in force prediction for MD17, rMD17, MD22, and is well extended to property prediction in QM9 datasets with several improvements greater than 15% and the maximum beyond 20%. The extensive real-world applications showcase high practicality. FreeCG introduces a novel paradigm for carrying out efficient and expressive CG transform in future geometric network designs. To demonstrate this, the recent SOTA, QuinNet, is also enhanced under our paradigm. Code: https://github.com/ShihaoShao-GH/FreeCG.

The rapid advancements of AI rely on the support of integrated circuits (ICs). However, the growing complexity of digital ICs makes the traditional IC design process costly and time-consuming. In recent years, AI-assisted IC design methods have demonstrated great potential, but most methods are task-specific or focus solely on the circuit structure in graph format, overlooking other circuit modalities with rich functional information. In this paper, we introduce CircuitFusion, the first multimodal and implementation-aware circuit encoder. It encodes circuits into general representations that support different downstream circuit design tasks. To learn from circuits, we propose to fuse three circuit modalities: hardware code, structural graph, and functionality summary. More importantly, we identify four unique properties of circuits: parallel execution, functional equivalent transformation, multiple design stages, and circuit reusability. Based on these properties, we propose new strategies for both the development and application of CircuitFusion: 1) During circuit preprocessing, utilizing the parallel nature of circuits, we split each circuit into multiple sub-circuits based on sequential-element boundaries, each sub-circuit in three modalities. It enables fine-grained encoding at the sub-circuit level. 2) During CircuitFusion pre-training, we introduce three self-supervised tasks that utilize equivalent transformations both within and across modalities. We further utilize the multi-stage property of circuits to align representation with ultimate circuit implementation. 3) When applying CircuitFusion to downstream tasks, we propose a new retrieval-augmented inference method, which retrieves similar known circuits as a reference for predictions. It improves fine-tuning performance and even enables zero-shot inference. Evaluated on five different circuit design tasks, CircuitFusion consistently outperforms the state-of-the-art supervised method specifically developed for every single task, demonstrating its generalizability and ability to learn circuits' inherent properties.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. gRNAde uses a multi-state Graph Neural Network and autoregressive decoding to generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. (2010), gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Experimental wet lab validation on 10 different structured RNA backbones finds that gRNAde has a success rate of 50% at designing pseudoknotted RNA structures, a significant advance over 35% for Rosetta. Open source code and tutorials are available at: github.com/chaitjo/geometric-rna-design

Bayesian Optimal Experimental Design (BOED) is a powerful tool to reduce the cost of running a sequence of experiments. When based on the Expected Information Gain (EIG), design optimization corresponds to the maximization of some intractable expected *contrast* between prior and posterior distributions. Scaling this maximization to high dimensional and complex settings has been an issue due to BOED inherent computational complexity. In this work, we introduce an *pooled posterior* distribution with cost-effective sampling properties and provide a tractable access to the EIG contrast maximization via a new EIG gradient expression. Diffusion-based samplers are used to compute the dynamics of the pooled posterior and ideas from bi-level optimization are leveraged to derive an efficient joint sampling-optimization loop, without resorting to lower bound approximations of the EIG. The resulting efficiency gain allows to extend BOED to the well-tested generative capabilities of diffusion models. By incorporating generative models into the BOED framework, we expand its scope and its use in scenarios that were previously impractical. Numerical experiments and comparison with state-of-the-art methods show the potential of the approach.

Circuit representation learning has become pivotal in electronic design automation, enabling critical tasks such as testability analysis, logic reasoning, power estimation, and SAT solving. However, existing models face significant challenges in scaling to large circuits due to limitations like over-squashing in graph neural networks and the quadratic complexity of transformer-based models. To address these issues, we introduce \textbf{DeepGate4}, a scalable and efficient graph transformer specifically designed for large-scale circuits. DeepGate4 incorporates several key innovations: (1) an update strategy tailored for circuit graphs, which reduce memory complexity to sub-linear and is adaptable to any graph transformer; (2) a GAT-based sparse transformer with global and local structural encodings for AIGs; and (3) an inference acceleration CUDA kernel that fully exploit the unique sparsity patterns of AIGs. Our extensive experiments on the ITC99 and EPFL benchmarks show that DeepGate4 significantly surpasses state-of-the-art methods, achieving 15.5\% and 31.1\% performance improvements over the next-best models. Furthermore, the Fused-DeepGate4 variant reduces runtime by 35.1\% and memory usage by 46.8\%, making it highly efficient for large-scale circuit analysis. These results demonstrate the potential of DeepGate4 to handle complex EDA tasks while offering superior scalability and efficiency.

Machine learning techniques have shown great potential in enhancing macro placement, a critical stage in modern chip design. However, existing methods primarily focus on *online* optimization of *intermediate surrogate metrics* that are available at the current placement stage, rather than directly targeting the *cross-stage metrics*---such as the timing performance---that measure the final chip quality. This is mainly because of the high computational costs associated with performing post-placement stages for evaluating such metrics, making the *online* optimization impractical. Consequently, these optimizations struggle to align with actual performance improvements and can even lead to severe manufacturing issues. To bridge this gap, we propose **LaMPlace**, which **L**earns **a** **M**ask for optimizing cross-stage metrics in macro placement. Specifically, LaMPlace trains a predictor on *offline* data to estimate these *cross-stage metrics* and then leverages the predictor to quickly generate a mask, i.e., a pixel-level feature map that quantifies the impact of placing a macro in each chip grid location on the design metrics. This mask essentially acts as a fast evaluator, enabling placement decisions based on *cross-stage metrics* rather than *intermediate surrogate metrics*. Experiments on commonly used benchmarks demonstrate that LaMPlace significantly improves the chip quality across several key design metrics, achieving an average improvement of 9.6\%, notably 43.0\% and 30.4\% in terms of WNS and TNS, respectively, which are two crucial cross-stage metrics that reflect the final chip quality in terms of the timing performance.

Motif-scaffolding is a fundamental component of protein design, which aims to construct the scaffold structure that stabilizes motifs conferring desired functions. Recent advances in generative models are promising for designing scaffolds, with two main approaches: training-based and sampling-based methods. Training-based methods are resource-heavy and slow, while training-free sampling-based methods are flexible but require numerous sampling steps and costly, unstable guidance. To speed up and improve sampling-based methods, we analyzed failure cases and found that errors stem from the trade-off between generation and guidance. Thus we proposed to exploit the spatial context and adjust the generative direction to be consistent with guidance to overcome this trade-off. Motivated by this, we formulate motif-scaffolding as a Geometric Inverse Design task inspired by the image inverse problem, and present Evolution-ViA-reconstruction (EVA), a novel sampling-based coupled flow framework on geometric manifolds, which starts with a pretrained flow-based generative model. EVA uses motif-coupled priors to leverage spatial contexts, guiding the generative process along a straighter probability path, with generative directions aligned with guidance in the early sampling steps. EVA is 70× faster than SOTA model RFDiffusion with competitive and even better performance on benchmark tests. Further experiments on real-world cases including vaccine design, multi-motif scaffolding and motif optimal placement searching demonstrate EVA's superior efficiency and effectiveness.

Recent advances in Large Language Models (LLMs) have stimulated a significant paradigm shift in evolutionary optimization, where hand-crafted search heuristics are gradually replaced with LLMs serving as intelligent search operators. However, these studies still bear some notable limitations, including a challenge to balance exploitation with exploration, often leading to inferior solution diversity, as well as poor generalizability of problem solving across different task settings. These unsolved issues render the prowess of LLMs in robot design automation largely untapped. In this work, we present LASeR -- Large Language Model-Aided Evolutionary Search for Robot Design Automation. Leveraging a novel reflection mechanism termed DiRect, we elicit more knowledgeable exploratory behaviors from LLMs based on past search trajectories, reshaping the exploration-exploitation tradeoff with dual improvements in optimization efficiency and solution diversity. Additionally, with evolution fully grounded in task-related background information, we unprecedentedly uncover the inter-task reasoning capabilities of LLMs, facilitating generalizable design processes that effectively inspire zero-shot robot proposals for new applications. Our simulated experiments on voxel-based soft robots showcase distinct advantages of LASeR over competitive baselines. Code at https://github.com/WoodySJR/LASeR.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.