Xingbo Du

Ruizhe Zhong, Xingbo Du, Junchi Yan

Floorplanning determines the coordinate and shape of each module in Integrated Circuits. With the scaling of technology nodes, in floorplanning stage especially 3D scenarios with multiple stacked layers, it has become increasingly challenging to adhere to complex hardware design rules. Current methods are only capable of handling specific and limited design rules, while violations of other rules require manual and meticulous adjustment. This leads to labor-intensive and time-consuming post-processing for expert engineers. In this paper, we propose an all-in-one deep reinforcement learning-based approach to tackle these challenges, and design novel representations for real-world IC design rules that have not been addressed by previous approaches. Specifically, the processing of various hardware design rules is unified into a single framework with three key components: 1) novel matrix representations to model the design rules, 2) constraints on the action space to filter out invalid actions that cause rule violations, and 3) quantitative analysis of constraint satisfaction as reward signals. Experiments on public benchmarks demonstrate the effectiveness and validity of our approach. Furthermore, transferability is well demonstrated on unseen circuits. Our framework is extensible to accommodate new design rules, thus providing flexibility to address emerging challenges in future chip design. Code will be available at: https://github.com/Thinklab-SJTU/EDA-AI

Ruizhe Zhong, Xingbo Du, Shixiong Kai et al.

Driven by Moore's Law, the complexity and scale of modern chip design are increasing rapidly. Electronic Design Automation (EDA) has been widely applied to address the challenges encountered in the full chip design process. However, the evolution of very large-scale integrated circuits has made chip design time-consuming and resource-intensive, requiring substantial prior expert knowledge. Additionally, intermediate human control activities are crucial for seeking optimal solutions. In system design stage, circuits are usually represented with Hardware Description Language (HDL) as a textual format. Recently, Large Language Models (LLMs) have demonstrated their capability in context understanding, logic reasoning and answer generation. Since circuit can be represented with HDL in a textual format, it is reasonable to question whether LLMs can be leveraged in the EDA field to achieve fully automated chip design and generate circuits with improved power, performance, and area (PPA). In this paper, we present a systematic study on the application of LLMs in the EDA field, categorizing it into the following cases: 1) assistant chatbot, 2) HDL and script generation, and 3) HDL verification and analysis. Additionally, we highlight the future research direction, focusing on applying LLMs in logic synthesis, physical design, multi-modal feature extraction and alignment of circuits. We collect relevant papers up-to-date in this field via the following link: https://github.com/Thinklab-SJTU/Awesome-LLM4EDA.

Loka Li, Duzhen Zhang, Xingbo Du et al.

Large language model (LLM) agents are increasingly capable of automating components of machine learning development, yet existing biomedical benchmarks mainly focus on question answering, reasoning, and tool usage, or evaluate only narrow aspects of biomedical ML coding. We present BioXArena, a biomedical machine learning benchmark designed to evaluate whether agents can generate task-specific model training pipelines for heterogeneous and multi-modal biomedical datasets. BioXArena contains 76 end-to-end tasks across 9 domains, including sequence modeling, single-cell analysis, structural biology, network biology, chemical biology, perturbation dynamics, phenotype-disease modeling, biomedical imaging, and text-integrated learning. Each task is curated from primary biomedical sources into a unified evaluation framework with hidden labels, held-out graders, and biology-aware metrics normalized to a 0 to 1 scale. Agents are required to write executable code, train predictive models, and generate submissions for private test samples. Most tasks involve multiple input modalities, including tabular data, images, natural language, molecular sequences, omics matrices, and protein structures. We evaluate 11 agent configurations in a standardized 2-hour single-GPU environment. MLEvolve with Gemini-3.1-Pro achieves the highest average score of 0.666, followed by GPT-5.4 with 0.636, while no single agent consistently dominates across all domains. We additionally perform extensive ablation studies, robustness evaluations, scaling analyses, cost analyses, and failure-mode investigations to better understand how model backbones, agent scaffolds, inference budgets, and biomedical domains influence BioML coding performance. We will publicly release all benchmark tasks, graders, execution runners, leaderboard results, and agent trajectories.

Xingbo Du, Loka Li, Duzhen Zhang et al.

Memory systems have been designed to leverage past experiences in Large Language Model (LLM) agents. However, many deployed memory systems primarily optimize compression and storage, with comparatively less emphasis on explicit, closed-loop control of memory retrieval. From this observation, we build memory retrieval as an autonomous, accurate, and compatible agent system, named MemR$^3$, which has two core mechanisms: 1) a router that selects among retrieve, reflect, and answer actions to optimize answer quality; 2) a global evidence-gap tracker that explicitly renders the answering process transparent and tracks the evidence collection process. This design departs from the standard retrieve-then-answer pipeline by introducing a closed-loop control mechanism that enables autonomous decision-making. Empirical results on the LoCoMo benchmark demonstrate that MemR$^3$ surpasses strong baselines on LLM-as-a-Judge score, and particularly, it improves existing retrievers across four categories with an overall improvement on RAG (+7.29%) and Zep (+1.94%) using GPT-4.1-mini backend, offering a plug-and-play controller for existing memory stores.

Xingbo Du, Qiantong Dou, Lei Fan et al.

Concept bottleneck models (CBMs) improve neural network interpretability by introducing an intermediate layer that maps human-understandable concepts to predictions. Recent work has explored the use of vision-language models (VLMs) to automate concept selection and annotation. However, existing VLM-based CBMs typically require full model retraining when new concepts are involved, which limits their adaptability and flexibility in real-world scenarios, especially considering the rapid evolution of vision-language foundation models. To address these issues, we propose Flexible Concept Bottleneck Model (FCBM), which supports dynamic concept adaptation, including complete replacement of the original concept set. Specifically, we design a hypernetwork that generates prediction weights based on concept embeddings, allowing seamless integration of new concepts without retraining the entire model. In addition, we introduce a modified sparsemax module with a learnable temperature parameter that dynamically selects the most relevant concepts, enabling the model to focus on the most informative features. Extensive experiments on five public benchmarks demonstrate that our method achieves accuracy comparable to state-of-the-art baselines with a similar number of effective concepts. Moreover, the model generalizes well to unseen concepts with just a single epoch of fine-tuning, demonstrating its strong adaptability and flexibility.

Ruiqing Yan, Xingbo Du, Haoyu Deng et al.

With the advent of large models based on the Transformer architecture, researchers have observed an anomalous phenomenon in the Attention mechanism--there is a very high attention on the first element, which is prevalent across Transformer-based models. It is crucial to understand it for the development of techniques focusing on attention distribution, such as Key-Value (KV) Cache compression and infinite extrapolation; however, the latent cause leaves to be unknown. In this paper, we analyze such a phenomenon from the perspective of waiver phenomenon, which involves reducing the internal values of certain elements in the sequence, allowing them to absorb excess attention without affecting their contribution to information. In specific models, due to differences in positional encoding and attention patterns, we have found that the selection of waiver elements by the model can be categorized into two methods: positional-encoding-based and feature-distribution-within-elements-based.