芯片设计 ML

Diffusion models (DMs) have emerged as powerful tools for modeling complex data distributions and generating realistic new samples. Over the years, advanced architectures and sampling methods have been developed to make these models practically usable. However, certain synthesis process decisions still rely on heuristics without a solid theoretical foundation. In our work, we offer a novel analysis of the DM's inference process, introducing a comprehensive frequency response perspective. Specifically, by relying on Gaussianity assumption, we present the inference process as a closed-form spectral transfer function, capturing how the generated signal evolves in response to the initial noise. We demonstrate how the proposed analysis can be leveraged to design a noise schedule that aligns effectively with the characteristics of the data. The spectral perspective also provides insights into the underlying dynamics and sheds light on the relationship between spectral properties and noise schedule structure. Our results lead to scheduling curves that are dependent on the spectral content of the data, offering a theoretical justification for some of the heuristics taken by practitioners.

With the development of biotechnology, RNA therapies have shown great potential. However, different from proteins, the sequences corresponding to a single RNA three-dimensional structure are more abundant. Most of the existing RNA design methods merely take into account the secondary structure of RNA, or are only capable of generating a limited number of candidate sequences. To address these limitations, we propose a geometric-algebra-enhanced $\textbf{B}$ayesian $\textbf{F}$low $\textbf{N}$etwork for the inverse design of $\textbf{R}$NA, called $\textbf{RBFN}$. RBFN uses a Bayesian Flow Network to model the distribution of nucleotide sequences in RNA, enabling the generation of more reasonable RNA sequences. Meanwhile, considering the more flexible characteristics of RNA conformations, we utilize geometric algebra to enhance the modeling ability of the RNA three-dimensional structure, facilitating a better understanding of RNA structural properties. In addition, due to the scarcity of RNA structures and the limitation that there are only four types of nucleic acids, we propose a new time-step distribution sampling to address the scarcity of RNA structure data and the relatively small number of nucleic acid types. Evaluation on the single-state fixed-backbone re-design benchmark and multi-state fixed-backbone benchmark indicates that RBFN can outperform existing RNA design methods in various RNA design tasks, enabling effective RNA sequence design.

Recent work in Bayesian Experiment Design (BED) has shown the value of using Deep Learning (DL) to obtain highly efficient adaptive experiment designs. In this paper, we argue that a central bottleneck of DL training for BED is belief explosion. Specifically, as an agent progresses deeper into an experiment, the effective number of realisable beliefs grows enormously, placing significant sampling burdens on offline training schemes in an effort to gather experience from all regions of belief space. We argue that choosing an appropriate inductive bias for actor/critic networks is a critical component in mitigating the effects of belief explosion and has so far been overlooked in the BED literature. We show how Graph Neural Networks are particularly well-suited for BED DL training due to their domain permutation equivariance properties, resulting in multiple orders of magnitude improvement to sample efficiency compared to naive parameterizations.

We study the problem of designing procurement auctions for the strategic uncapacitated facility location problem: a company needs to procure a set of facility locations in order to serve its customers and each facility location is owned by a strategic agent. Each owner has a private cost for providing access to their facility (e.g., renting it or selling it to the company) and needs to be compensated accordingly. The goal is to design truthful auctions that decide which facilities the company should procure and how much to pay the corresponding owners, aiming to minimize the total cost, i.e., the monetary cost paid to the owners and the connection cost suffered by the customers (their distance to the nearest facility). We evaluate the performance of these auctions using the \emph{frugality ratio}. We first analyze the performance of the classic VCG auction in this context and prove that its frugality ratio is exactly $3$. We then leverage the learning-augmented framework and design auctions that are augmented with predictions regarding the owners' private costs. Specifically, we propose a family of learning-augmented auctions that achieve significant payment reductions when the predictions are accurate, leading to much better frugality ratios. At the same time, we demonstrate that these auctions remain robust even if the predictions are arbitrarily inaccurate, and maintain reasonable frugality ratios even under adversarially chosen predictions. We finally provide a family of ``error-tolerant'' auctions that maintain improved frugality ratios even if the predictions are only approximately accurate, and we provide upper bounds on their frugality ratio as a function of the prediction error.

Modern machine learning algorithms, especially deep learning-based techniques, typically involve careful hyperparameter tuning to achieve the best performance. Despite the surge of intense interest in practical techniques like Bayesian optimization and random search-based approaches to automating this laborious and compute-intensive task, the fundamental learning-theoretic complexity of tuning hyperparameters for deep neural networks is poorly understood. Inspired by this glaring gap, we initiate the formal study of hyperparameter tuning complexity in deep learning through a recently introduced data-driven setting. We assume that we have a series of learning tasks, and we have to tune hyperparameters to do well on average over the distribution of tasks. A major difficulty is that the utility function as a function of the hyperparameter is very volatile, and furthermore, it is given implicitly by an optimization problem over the model parameters. To tackle this challenge, we introduce a new technique to characterize the discontinuities and oscillations of the utility function on any fixed problem instance as we vary the hyperparameter; our analysis relies on subtle concepts, including tools from algebraic geometry, differential geometry, and constrained optimization. We use this to show that the learning-theoretic complexity of the corresponding family of utility functions is bounded. We instantiate our results and provide sample complexity bounds for concrete applications—tuning a hyperparameter that interpolates neural activation functions and setting the kernel parameter in graph neural networks.

Modern chip design is complex, and there is a crucial need for early-stage prediction of key design-quality metrics like timing and routing congestion directly from Verilog code (a commonly used programming language for hardware design). It is especially important yet complex to predict individual lines of code that cause timing violations or downstream routing congestion. Prior works have tried approaches like converting Verilog into an intermediate graph representation and using LLM embeddings alongside other features to predict module-level quality, but did not consider line-level quality prediction. We propose VeriLoC, the first method that predicts design quality directly from Verilog at both the line- and module-level. To this end, VeriLoC leverages recent Verilog code-generation LLMs to extract local line-level and module-level embeddings, and trains downstream classifiers/regressors on concatenations of these embeddings. VeriLoC achieves high F1-scores of 0.86-0.95 for line-level congestion and timing prediction, and reduces the mean average percentage error from 14%-18% for SOTA methods down to only 4%. We believe that VeriLoC embeddings and insights from our work will also be of value for other predictive and optimization tasks for complex hardware design.

Neural network architectures have a large impact in machine learning. However, in the specific case of reinforcement learning, network architectures have remained notably simple, as changes often lead to small gains in performance. This work introduces a novel encoder architecture for pixel-based model-free reinforcement learning. The Hadamax (\textbf{Hada}mard \textbf{max}-pooling) encoder achieves state-of-the-art performance by max-pooling Hadamard products between GELU-activated parallel hidden layers. Based on the recent PQN algorithm, the Hadamax encoder achieves state-of-the-art model-free performance in the Atari-57 benchmark. Specifically, without applying any algorithmic hyperparameter modifications, Hadamax-PQN achieves an 80\% performance gain over vanilla PQN and significantly surpasses Rainbow-DQN. For reproducibility, the full code is available on GitHub.

Chip placement is a critical step in the Electronic Design Automation (EDA) workflow, which aims to arrange chip modules on the canvas to optimize the performance, power, and area (PPA) metrics of final designs. Recent advances show great potential of AI-based algorithms in chip placement. However, due to the lengthy EDA workflow, evaluations of these algorithms often focus on intermediate surrogate metrics, which are computationally efficient but often misalign with the final end-to-end performance (i.e., the final design PPA). To address this challenge, we propose to build ChiPBench, a comprehensive benchmark specifically designed to evaluate the effectiveness of AI-based algorithms in final design PPA metrics. Specifically, we generate a diverse evaluation dataset from $20$ circuits across various domains, such as CPUs, GPUs, and NPUs. We then evaluate six state-of-the-art AI-based chip placement algorithms on the dataset and conduct a thorough analysis of their placement behavior. Extensive experiments show that AI-based chip placement algorithms produce unsatisfactory final PPA results, highlighting the significant influence of often-overlooked factors like regularity and dataflow. We believe ChiPBench will effectively bridge the gap between academia and industry.

Network interference has attracted significant attention in the field of causal inference, encapsulating various sociological behaviors in which the treatment assigned to one individual within a network may affect the outcomes of others, such as their neighbors. A key challenge in this setting is that standard causal inference methods often assume independent treatment effects among individuals, which may not hold in networked environments. To estimate interference-aware causal effects, a traditional approach is to inherit the independent settings, where practitioners randomly assign experimental participants to different groups and compare their outcomes. Although effective in offline settings, this strategy becomes problematic in sequential experiments, where suboptimal decisions persist, leading to substantial regret. To address this issue, we introduce a unified interference-aware framework for online experimental design. Compared to existing studies, we extend the definition of arm space using the statistical concept of exposure mapping, which allows for a more flexible and context-aware representation of treatment effects in network settings. Crucially, we establish a Pareto-optimal trade-off between estimation accuracy and regret under the network concerning both time period and arm space, which remains superior to baseline models even without network interference. Furthermore, we propose an algorithmic implementation and discuss its generalization in different learning settings and network topology.

Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing RNA’s conformational flexibility, ensuring structural validity, and overcoming data scarcity. To address these challenges, we introduce RiboFlow, a synergistic flow matching model to co-design RNA structures and sequences based on target molecules. By integrating RNA backbone frames, torsion angles, and sequence features in an unified architecture, RiboFlow explicitly models RNA’s dynamic conformations while enforcing sequence-structure consistency to improve validity. Additionally, we curate RiboBind, a large-scale dataset of RNA-molecule interactions, to resolve the scarcity of high-quality structural data. Extensive experiments reveal that RiboFlow not only outperforms state-of-the-art RNA design methods by a large margin but also showcases controllable capabilities for achieving high binding affinity to target ligands. Our work bridges critical gaps in controllable RNA design, offering a framework for structure-aware, data-efficient generation.

With AI advancement and increasing circuit complexity, efficient chip design through Electronic Design Automation (EDA) is critical. Fast and accurate congestion prediction in chip layout and routing can significantly enhance automated design performance. Existing congestion modeling methods are limited by **(i)** ineffective processing and fusion of multi-view circuit data information, and **(ii)** insufficient reliability and interpretability in the prediction process. To address these challenges, We propose **M**ulti-view **I**nterpretable **H**ypergraph for **C**hip (**MIHC**), a trustworthy 'multi-view hypergraph neural network'-based framework that **(i)** processes both graph and image information in unified hypergraph representations, capturing topological and geometric circuit data, and **(ii)** implements a novel subgraph Information Bottleneck mechanism identifying critical congestion-correlated regions to guide predictions. This represents the first attempt to incorporate such interpretability into congestion prediction through informative graph reasoning. Experiments show our model reduces NMAE by 16.67% and 8.57% in cell-based and grid-based predictions on ISPD2015, and 5.26% and 2.44% on CircuitNet-N28, respectively, compared to state-of-the-art methods. Rigorous cross-design generalization experiments further validate our method’s capability to handle entirely unseen circuit designs.

In multi-armed bandits with network interference (MABNI), the action taken by one node can influence the rewards of others, creating complex interdependence. While existing research on MABNI largely concentrates on minimizing regret, it often overlooks the crucial concern that an excessive emphasis on the optimal arm can undermine the inference accuracy for sub-optimal arms. Although initial efforts have been made to address this trade-off in single-unit scenarios, these challenges have become more pronounced in the context of MABNI. In this paper, we establish, for the first time, a theoretical Pareto frontier characterizing the trade-off between regret minimization and inference accuracy in adversarial (design-based) MABNI. We further introduce an anytime-valid asymptotic confidence sequence along with a corresponding algorithm, $\texttt{EXP3-N-CS}$, specifically designed to balance the trade-off between regret minimization and inference accuracy in this setting.

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce ProDVa, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, ProDVa achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.62%.

We study revenue maximization for agents with additive preferences, subject to downward-closed constraints on the set of feasible allocations. In seminal work,~\citet{alaei2014bayesian} introduced a powerful multi-to-single agent reduction based on an ex-ante relaxation of the multi-agent problem. This reduction employs a rounding procedure which is an online contention resolution scheme (OCRS) in disguise, a now widely-used method for rounding fractional solutions in online Bayesian and stochastic optimization problems. In this paper, we leverage our vantage point, 10 years after the work of Alaei, with a rich OCRS toolkit and modern approaches to analyzing multi-agent mechanisms; we introduce a general framework for designing non-sequential and sequential multi-agent, revenue-maximizing mechanisms, capturing a wide variety of problems Alaei's framework could not address. Our framework uses an \emph{interim} relaxation, that is rounded to a feasible mechanism using what we call a two-level OCRS, which allows for some structured dependence between the activation of its input elements. For a wide family of constraints, we can construct such schemes using existing OCRSs as a black box; for other constraints, such as knapsack, we construct such schemes from scratch. We demonstrate numerous applications of our framework, including a sequential mechanism that guarantees a $\frac{2e}{e-1} \approx 3.16$ approximation to the optimal revenue for the case of additive agents subject to matroid feasibility constraints. Finally, we show how our framework can be easily extended to multi-parameter procurement auctions, where we provide an OCRS for Stochastic Knapsack that might be of independent interest.

Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can effectively capture patterns in regulatory DNA, their generative approaches often struggle to produce novel sequences with reliable cell-specific activity. Here, we introduce Ctrl-DNA, a novel constrained reinforcement learning (RL) framework tailored for designing regulatory DNA sequences with controllable cell-type specificity. By formulating regulatory sequence design as a biologically informed constrained optimization problem, we apply RL to autoregressive genomic LMs, enabling the models to iteratively refine sequences that maximize regulatory activity in targeted cell types while constraining off-target effects. Our evaluation on human promoters and enhancers demonstrates that Ctrl-DNA consistently outperforms existing generative and RL-based approaches, generating high-fitness regulatory sequences and achieving state-of-the-art cell-type specificity. Moreover, Ctrl-DNA-generated sequences capture key cell-type-specific transcription factor binding sites (TFBS), short DNA motifs recognized by regulatory proteins that control gene expression, demonstrating the biological plausibility of the generated sequences.

Visual In-Context Learning (VICL) has emerged as a prominent approach for adapting visual foundation models to novel tasks, by effectively exploiting contextual information embedded in in-context examples, which can be formulated as a global ranking problem of potential candidates. Current VICL methods, such as Partial2Global and VPR, are grounded in the similarity-priority assumption that images more visually similar to a query image serve as better in-context examples. This foundational assumption, while intuitive, lacks sufficient justification for its efficacy in selecting optimal in-context examples. Furthermore, Partial2Global constructs its global ranking from a series of randomly sampled pairwise preference predictions. Such a reliance on random sampling can lead to incomplete coverage and redundant samplings of comparisons, thus further adversely impacting the final global ranking. To address these issues, this paper introduces an enhanced variant of Partial2Global designed for reliable and holistic selection of in-context examples in VICL. Our proposed method, dubbed RH-Partial2Global, leverages a jackknife conformal prediction-guided strategy to construct reliable alternative sets and a covering design-based sampling approach to ensure comprehensive and uniform coverage of pairwise preferences. Extensive experiments demonstrate that RH-Partial2Global achieves excellent performance and outperforms Partial2Global across diverse visual tasks.

The efficiency of Bayesian optimization (BO) relies heavily on the choice of the Gaussian process (GP) kernel, which plays a central role in balancing exploration and exploitation under limited evaluation budgets. Traditional BO methods often rely on fixed or heuristic kernel selection strategies, which can result in slow convergence or suboptimal solutions when the chosen kernel is poorly suited to the underlying objective function. To address this limitation, we propose a freshly-baked Context-Aware Kernel Evolution (CAKE) to enhance BO with large language models (LLMs). Concretely, CAKE leverages LLMs as the crossover and mutation operators to adaptively generate and refine GP kernels based on the observed data throughout the optimization process. To maximize the power of CAKE, we further propose BIC-Acquisition Kernel Ranking (BAKER) to select the most effective kernel through balancing the model fit measured by the Bayesian information criterion (BIC) with the expected improvement at each iteration of BO. Extensive experiments demonstrate that our fresh CAKE-based BO method consistently outperforms established baselines across a range of real-world tasks, including hyperparameter optimization, controller tuning, and photonic chip design. Our code is publicly available at https://github.com/richardcsuwandi/cake.

We introduce LOKI, a compute-efficient framework for co-designing morphologies and control policies that generalize across unseen tasks. Inspired by biological adaptation—where animals quickly adjust to morphological changes—our method overcomes the inefficiencies of traditional evolutionary and quality-diversity algorithms. We propose learning convergent functions: shared control policies trained across clusters of morphologically similar designs in a learned latent space, drastically reducing the training cost per design. Simultaneously, we promote divergent forms by replacing mutation with dynamic local search, enabling broader exploration and preventing premature convergence. The policy reuse allows us to explore $\sim780\times$ more designs using 78\% fewer simulation steps and 40\% less compute per design. Local competition paired with a broader search results in a diverse set of high-performing final morphologies. Using the UNIMAL design space and a flat-terrain locomotion task, LOKI discovers a rich variety of designs—ranging from quadrupeds to crabs, bipedals, and spinners—far more diverse than those produced by prior work. These morphologies also transfer better to unseen downstream tasks in agility, stability, and manipulation domains (e.g. $2 \times$ higher reward on bump and push box incline tasks). Overall, our approach produces designs that are both diverse and adaptable, with substantially greater sample efficiency than existing co-design methods.

Diffusion bridge models and stochastic interpolants enable high-quality image-to-image (I2I) translation by creating paths between distributions in pixel space. However, recent diffusion bridge models excel in image translation but suffer from restricted design flexibility and complicated hyperparameter tuning, whereas Stochastic Interpolants offer greater flexibility but lack essential refinements. We show that these complementary strengths can be unified by interpreting all existing methods within a single SI-based framework. In this work, we unify and expand the space of bridge models by extending Stochastic Interpolants (SIs) with preconditioning, endpoint conditioning, and an optimized sampling algorithm. These enhancements expand the design space of diffusion bridge models, leading to state-of-the-art performance in both image quality and sampling efficiency across diverse I2I tasks. Furthermore, we identify and address a previously overlooked issue of low sample diversity under fixed conditions. We introduce a quantitative analysis for output diversity and demonstrate how we can modify the base distribution for further improvements.

Modern data marketplaces and data sharing consortia increasingly rely on incentive mechanisms to encourage agents to contribute data. However, schemes that reward agents based on the quantity of submitted data are vulnerable to manipulation, as agents may submit fabricated or low-quality data to inflate their rewards. Prior work has proposed comparing each agent’s data against others’ to promote honesty: when others contribute genuine data, the best way to minimize discrepancy is to do the same. Yet prior implementations of this idea rely on very strong assumptions about the data distribution (e.g. Gaussian), limiting their applicability. In this work, we develop reward mechanisms based on a novel, two-sample test statistic inspired by the Cramér-von Mises statistic. Our methods strictly incentivize agents to submit more genuine data, while disincentivizing data fabrication and other types of untruthful reporting. We establish that truthful reporting constitutes a (possibly approximate) Nash equilibrium in both Bayesian and prior-agnostic settings. We theoretically instantiate our method in two canonical data sharing problems and show that it relaxes key assumptions made by prior work. Empirically, we demonstrate that our mechanism incentivizes truthful data sharing via simulations and on real-world language and image data.