芯片设计 ML

Distributed execution of deep learning training involves a dynamic interplay between hardware accelerator architecture and device placement strategy. This is the first work to explore the co-optimization of determining the optimal architecture and device placement strategy through novel algorithms, improving the balance of computational resources, memory usage, and data distribution. Our architecture search leverages tensor and vector units, determining their quantity and dimensionality, and on-chip and off-chip memory configurations. It also determines the microbatch size and decides whether to recompute or stash activations, balancing the memory footprint of training and storage size. For each explored architecture configuration, we use an Integer Linear Program (ILP) to find the optimal schedule for executing operators on the accelerator. The ILP results then integrate with a dynamic programming solution to identify the most effective device placement strategy, combining data, pipeline, and tensor model parallelism across multiple accelerators. Our approach achieves higher throughput on large language models compared to the state-of-the-art TPUv4 and the Spotlight accelerator search framework. The entire source code of PHAZE is available at https://github.com/msr-fiddle/phaze.

We propose a new procedure named PASOA, for Bayesian experimental design, that performs sequential design optimization by simultaneously providing accurate estimates of successive posterior distributions for parameter inference. The sequential design process is carried out via a contrastive estimation principle, using stochastic optimization and Sequential Monte Carlo (SMC) samplers to maximise the Expected Information Gain (EIG). As larger information gains are obtained for larger distances between successive posterior distributions, this EIG objective may worsen classical SMC performance. To handle this issue, tempering is proposed to have both a large information gain and an accurate SMC sampling, that we show is crucial for performance. This novel combination of stochastic optimization and tempered SMC allows to jointly handle design optimization and parameter inference. We provide a proof that the obtained optimal design estimators benefit from some consistency property. Numerical experiments confirm the potential of the approach, which outperforms other recent existing procedures.

In this paper, we propose a novel approach to Bayesian experimental design for non-exchangeable data that formulates it as risk-sensitive policy optimization. We develop the Inside-Out SMC$^2$ algorithm, a nested sequential Monte Carlo technique to infer optimal designs, and embed it into a particle Markov chain Monte Carlo framework to perform gradient-based policy amortization. Our approach is distinct from other amortized experimental design techniques, as it does not rely on contrastive estimators. Numerical validation on a set of dynamical systems showcases the efficacy of our method in comparison to other state-of-the-art strategies.

The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA presents new challenges due to RNA's conformational flexibility and the computational cost of fine-tuning large structure prediction models. To this end, we propose RNAFlow, a flow matching model for protein-conditioned RNA sequence-structure design. Its denoising network integrates an RNA inverse folding model and a pre-trained RosettaFold2NA network for generation of RNA sequences and structures. The integration of inverse folding in the structure denoising process allows us to simplify training by fixing the structure prediction network. We further enhance the inverse folding model by conditioning it on inferred conformational ensembles to model dynamic RNA conformations. Evaluation on protein-conditioned RNA structure and sequence generation tasks demonstrates RNAFlow's advantage over existing RNA design methods.

Lithography, transferring chip design masks to the silicon wafer, is the most important phase in modern semiconductor manufacturing flow. Due to the limitations of lithography systems, Extensive design optimizations are required to tackle the design and silicon mismatch. Inverse lithography technology (ILT) is one of the promising solutions to perform pre-fabrication optimization, termed mask optimization. Because of mask optimization problems’ constrained non-convexity, numerical ILT solvers rely heavily on good initialization to avoid getting stuck on sub-optimal solutions. Machine learning (ML) techniques are hence proposed to generate mask initialization for ILT solvers with one-shot inference, targeting faster and better convergence during ILT. This paper addresses the question of whether ML models can directly generate high-quality optimized masks without engaging ILT solvers in the loop. We propose an implicit learning ILT framework: ILILT, which leverages the implicit layer learning method and lithography-conditioned inputs to ground the model. Trained to understand the ILT optimization procedure, ILILT can outperform the state-of-the-art machine learning solutions, significantly improving efficiency and quality.

How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to generate functional proteins given a desired surface and its associated biochemical properties. SurfPro comprises a hierarchical encoder that progressively models the geometric shape and biochemical features of a protein surface, and an autoregressive decoder to produce an amino acid sequence. We evaluate SurfPro on a standard inverse folding benchmark CATH 4.2 and two functional protein design tasks: protein binder design and enzyme design. Our SurfPro consistently surpasses previous state-of-the-art inverse folding methods, achieving a recovery rate of 57.78% on CATH 4.2 and higher success rates in terms of protein-protein binding and enzyme-substrate interaction scores

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in *false positives*. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

We presents VoxBind, a new score-based generative model for 3D molecules conditioned on protein structures. Our approach represents molecules as 3D atomic density grids and leverages a 3D voxel-denoising network for learning and generation. We extend the neural empirical Bayes formalism (Saremi & Hyvärinen, 2019) to the conditional setting and generate structure-conditioned molecules with a two-step procedure: (i) sample noisy molecules from the Gaussian-smoothed conditional distribution with underdamped Langevin MCMC using the learned score function and (ii) estimate clean molecules from the noisy samples with single-step denoising. Compared to the current state of the art, our model is simpler to train, significantly faster to sample from, and achieves better results on extensive in silico benchmarks—the generated molecules are more diverse, exhibit fewer steric clashes, and bind with higher affinity to protein pockets.

As Large Language Models (LLMs) become more integrated into our daily lives, it is crucial to identify and mitigate their risks, especially when the risks can have profound impacts on human users and societies. Guardrails, which filter the inputs or outputs of LLMs, have emerged as a core safeguarding technology. This position paper takes a deep look at current open-source solutions (Llama Guard, Nvidia NeMo, Guardrails AI), and discusses the challenges and the road towards building more complete solutions. Drawing on robust evidence from previous research, we advocate for a systematic approach to construct guardrails for LLMs, based on comprehensive consideration of diverse contexts across various LLMs applications. We propose employing socio-technical methods through collaboration with a multi-disciplinary team to pinpoint precise technical requirements, exploring advanced neural-symbolic implementations to embrace the complexity of the requirements, and developing verification and testing to ensure the utmost quality of the final product.

Offline reinforcement learning (RL) is crucial for real-world applications where exploration can be costly or unsafe. However, offline learned policies are often suboptimal, and further online fine-tuning is required. In this paper, we tackle the fundamental dilemma of offline-to-online fine-tuning: if the agent remains pessimistic, it may fail to learn a better policy, while if it becomes optimistic directly, performance may suffer from a sudden drop. We show that Bayesian design principles are crucial in solving such a dilemma. Instead of adopting optimistic or pessimistic policies, the agent should act in a way that matches its belief in optimal policies. Such a probability-matching agent can avoid a sudden performance drop while still being guaranteed to find the optimal policy. Based on our theoretical findings, we introduce a novel algorithm that outperforms existing methods on various benchmarks, demonstrating the efficacy of our approach. Overall, the proposed approach provides a new perspective on offline-to-online RL that has the potential to enable more effective learning from offline data.

The development of deep learning architectures is a resource-demanding process, due to a vast design space, long prototyping times, and high compute costs associated with at-scale model training and evaluation. We set out to simplify this process by grounding it in an end-to-end mechanistic architecture design (MAD) pipeline, encompassing small-scale capability unit tests predictive of scaling laws. Through a suite of synthetic token manipulation tasks such as compression and recall, designed to probe capabilities, we identify and test new hybrid architectures constructed from a variety of computational primitives. We experimentally validate the resulting architectures via an extensive compute-optimal and a new state-optimal scaling law analysis, training over 500 language models between 70M to 7B parameters. Surprisingly, we find MAD synthetics to correlate with compute-optimal perplexity, enabling accurate evaluation of new architectures via isolated proxy tasks. The new architectures found via MAD, based on simple ideas such as hybridization and sparsity, outperform state-of-the-art Transformer, convolutional, and recurrent architectures (Transformer++, Hyena, Mamba) in scaling, both at compute-optimal budgets and in overtrained regimes. Overall, these results provide evidence that performance on curated synthetic tasks can be predictive of scaling laws, and that an optimal architecture should leverage specialized layers via a hybrid topology.

De novo protein design aims to create novel protein structures and sequences unseen in nature. Recent structure-oriented design methods typically employ a two-stage strategy, where structure design and sequence design modules are trained separately, and the backbone structures and sequences are generated sequentially in inference. While diffusion-based generative models like RFdiffusion show great promise in structure design, they face inherent limitations within the two-stage framework. First, the sequence design module risks overfitting, as the accuracy of the generated structures may not align with that of the crystal structures used for training. Second, the sequence design module lacks interaction with the structure design module to further optimize the generated structures. To address these challenges, we propose CarbonNovo, a unified energy-based model for jointly generating protein structure and sequence. Specifically, we leverage a score-based generative model and Markov Random Fields for describing the energy landscape of protein structure and sequence. In CarbonNovo, the structure and sequence design module communicates at each diffusion step, encouraging the generation of more coherent structure-sequence pairs. Moreover, the unified framework allows for incorporating the protein language models as evolutionary constraints for generated proteins. The rigorous evaluation demonstrates that CarbonNovo outperforms two-stage methods across various metrics, including designability, novelty, sequence plausibility, and Rosetta Energy.

Heuristics are widely used for dealing with complex search and optimization problems. However, manual design of heuristics can be often very labour extensive and requires rich working experience and knowledge. This paper proposes Evolution of Heuristic (EoH), a novel evolutionary paradigm that leverages both Large Language Models (LLMs) and Evolutionary Computation (EC) methods for Automatic Heuristic Design (AHD). EoH represents the ideas of heuristics in natural language, termed thoughts. They are then translated into executable codes by LLMs. The evolution of both thoughts and codes in an evolutionary search framework makes it very effective and efficient for generating high-performance heuristics. Experiments on three widely studied combinatorial optimization benchmark problems demonstrate that EoH outperforms commonly used handcrafted heuristics and other recent AHD methods including FunSearch. Particularly, the heuristic produced by EoH with a low computational budget (in terms of the number of queries to LLMs) significantly outperforms widely-used human hand-crafted baseline algorithms for the online bin packing problem.

Learning a reward function from demonstrations suffers from low sample-efficiency. Even with abundant data, current inverse reinforcement learning methods that focus on learning from a single environment can fail to handle slight changes in the environment dynamics. We tackle these challenges through adaptive environment design. In our framework, the learner repeatedly interacts with the expert, with the former selecting environments to identify the reward function as quickly as possible from the expert’s demonstrations in said environments. This results in improvements in both sample-efficiency and robustness, as we show experimentally, for both exact and approximate inference.

Macro placement is a crucial step in modern chip design, and reinforcement learning (RL) has recently emerged as a promising technique for improving the placement quality. However, existing RL-based techniques are hindered by their low sample efficiency, requiring numerous online rollouts or substantial offline expert data to achieve bootstrap, which are often impractical in industrial scenarios. To address this challenge, we propose a novel sample-efficient framework, namely **EfficientPlace**, for fast macro placement. EfficientPlace integrates a global tree search algorithm to strategically direct the optimization process, as well as a RL agent for local policy learning to advance the tree search. Experiments on commonly used benchmarks demonstrate that EfficientPlace achieves remarkable placement quality within a short timeframe, outperforming recent state-of-the-art approaches.

Increasing works for antibody design are emerging to generate sequences and structures in Complementarity Determining Regions (CDRs), but problems still exist. We focus on two of them: (i) authenticity of the generated structure and (ii) rationality of the affinity maturation, and propose GeoAB as a solution. In specific, GeoAB-Designergenerates CDR structures with realistic internal geometries, composed of a generative geometry initializer (Geo-Initializer) and a position refiner (Geo-Refiner); GeoAB-Optimizer achieves affinity maturation by accurately predicting both the mutation effects and structures of mutant antibodies with the same network architecture as Geo-Refiner. Experiments show that GeoAB achieves state-of-the-art performance in CDR co-design and mutation effect predictions, and fulfills the discussed tasks effectively.

Visually-conditioned language models (VLMs) have seen growing adoption in applications such as visual dialogue, scene understanding, and robotic task planning; adoption that has fueled a wealth of new models such as LLaVa, InstructBLIP, and PaLI-3. Despite the volume of new releases, key design decisions around image preprocessing, architecture, and optimization are under-explored, making it challenging to understand what factors account for model performance – a challenge further complicated by the lack of objective, consistent evaluations. To address these gaps, we first compile a suite of standardized evaluations spanning visual question answering, object localization, and challenge sets that probe properties such as hallucination; evaluations that provide fine-grained insight VLM capabilities. Second, we rigorously investigate VLMs along key design axes, including pretrained visual representations and training from base vs. instruct-tuned language models, amongst others. We couple our analysis with three resource contributions: (1) a unified framework for evaluating VLMs, (2) optimized, flexible training code, and (3) checkpoints for all models, including a family of VLMs at the 7-13B scale that strictly outperform InstructBLIP and LLaVa v1.5, the state-of-the-art in open VLMs.

This paper addresses the complex issue of resource-constrained scheduling, an NP-hard problem that spans critical areas including chip design and high-performance computing. Traditional scheduling methods often stumble over scalability and applicability challenges. We propose a novel approach using a differentiable combinatorial scheduling framework, utilizing Gumbel-Softmax differentiable sampling technique. This new technical allows for a fully differentiable formulation of linear programming (LP) based scheduling, extending its application to a broader range of LP formulations. To encode inequality constraints for scheduling tasks, we introduce *constrained Gumbel Trick*, which adeptly encodes arbitrary inequality constraints. Consequently, our method facilitates an efficient and scalable scheduling via gradient descent without the need for training data. Comparative evaluations on both synthetic and real-world benchmarks highlight our capability to significantly improve the optimization efficiency of scheduling, surpassing state-of-the-art solutions offered by commercial and open-source solvers such as CPLEX, Gurobi, and CP-SAT in the majority of the designs.

Logic Synthesis (LS) plays a vital role in chip design. A key task in LS is to simplify circuits---modeled by directed acyclic graphs (DAGs)---with functionality-equivalent transformations. To tackle this task, many LS heuristics apply transformations to subgraphs---rooted at each node on an input DAG---sequentially. However, we found that a large number of transformations are ineffective, which makes applying these heuristics highly time-consuming. In particular, we notice that the runtime of the Resub and Mfs2 heuristics often dominates the overall runtime of LS optimization processes. To address this challenge, we propose a novel data-driven LS heuristic paradigm, namely PruneX, to reduce ineffective transformations. The major challenge of developing PruneX is to learn models that well generalize to unseen circuits, i.e., the out-of-distribution (OOD) generalization problem. Thus, the major technical contribution of PruneX is the novel circuit domain generalization framework, which learns domain-invariant representations based on the transformation-invariant domain-knowledge. To the best of our knowledge, PruneX is the first approach to tackle the OOD problem in LS heuristics. We integrate PruneX with the aforementioned Resub and Mfs2 heuristics. Experiments demonstrate that PruneX significantly improves their efficiency while keeping comparable optimization performance on industrial and very large-scale circuits, achieving up to $3.1\times$ faster runtime.

Dynamic convolution learns a linear mixture of $n$ static kernels weighted with their input-dependent attentions, demonstrating superior performance than normal convolution. However, it increases the number of convolutional parameters by $n$ times, and thus is not parameter efficient. This leads to no research progress that can allow researchers to explore the setting $n > 100$ (an order of magnitude larger than the typical setting $n < 10$) for pushing forward the performance boundary of dynamic convolution while enjoying parameter efficiency. To fill this gap, in this paper, we propose KernelWarehouse, a more general form of dynamic convolution, which redefines the basic concepts of “kernels”, “assembling kernels” and “attention function” through the lens of exploiting convolutional parameter dependencies within the same layer and across neighboring layers of a ConvNet. We testify the effectiveness of KernelWarehouse on ImageNet and MS-COCO datasets using various ConvNet architectures. Intriguingly, KernelWarehouse is also applicable to Vision Transformers, and it can even reduce the model size of a backbone while improving the model accuracy. For instance, KernelWarehouse ($n = 4$) achieves 5.61%|3.90%|4.38% absolute top-1 accuracy gain on the ResNet18|MobileNetV2|DeiT-Tiny backbone, and KernelWarehouse ($n = 1/4$) with 65.10% model size reduction still achieves 2.29% gain on the ResNet18 backbone. The code and models are available at https://github.com/OSVAI/KernelWarehouse.