Researcher profile

Chien-Yu Lin

Chien-Yu Lin contributes to research discovery and scholarly infrastructure.

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Published work

4 published item(s)

preprint2026arXiv

Agentic Discovery of Neural Architectures: AIRA-Compose and AIRA-Design

Toward recursive self-improvement, we investigate LLM agents autonomously designing foundation models beyond standard Transformers. We introduce a dual-framework approach: AIRA-Compose for high-level architecture search, and AIRA-Design for low-level mechanistic implementation. AIRA-Compose uses 11 agents to explore fundamental computational primitives under a 24-hour budget. Agents evaluate million-parameter candidates, extrapolating top designs to 350M, 1B, and 3B scales. This yields 14 architectures across two families: AIRAformers (Transformer-based) and AIRAhybrids (Transformer-Mamba). Pre-trained at 1B scale, these consistently outperform Llama 3.2 and Composer-found baselines. On downstream tasks, AIRAformer-D and AIRAhybrid-D improve accuracy by 2.4% and 3.8% over Llama 3.2. Furthermore, AIRA-Compose finds models with highly efficient scaling frontiers: AIRAformer-C scales 54% and 71% faster than Llama 3.2 and Composer's best Transformer, while AIRAhybrid-C outscales Nemotron-2 by 23% and Composer's best hybrid by 37%. AIRA-Design tasks 20 agents with writing novel attention mechanisms for long-range dependencies and high-performing training scripts. On the Long Range Arena benchmark, agent-designed architectures reach within 2.3% and 2.6% of human state-of-the-art on document matching and text classification. On the Autoresearch benchmark, Greedy Opus 4.5 achieves 0.968 validation bits-per-byte under a fixed time budget, surpassing the published minimum. Together, these frameworks show AI agents can autonomously discover architectures and algorithmic optimizations matching or surpassing hand-designed baselines. This establishes a powerful paradigm for discovering next-generation foundation models, marking a clear step toward recursive self-improvement.

preprint2023arXiv

Proton FLASH irradiation platform for small animal setup at Chang Gung Memorial Hospital

Background : Proton flash therapy is an emergency research topic in radiation therapy since the Varian announced the promising results from the first in human clinical trial of Flash therapy recently. However, it still needs a lot of researches on this topic, not only to understand the mechanism of the radiobiological effects but also to develop an appropriate dose monitoring system. Purpose : In this study we setup an experimental station for small animal proton Flash irradiation in a clinical machine. The dose monitoring system is able to provide real-time irradiation dose and irradiation time structure. Methods : The dose monitoring system includes homebrewed transmission ionization chamber (TIC), plastic scintillator based beam position monitor, and Poor Man Faraday Cup (FC). Both TIC and FC are equipped with a homebrewed fast reading current integral electronics device. The imaging guidance system comprises a moveable CT, laser, as well as attaching a bead on the body surface of the mouse can accurately guide the testing small animal in position. Results : The dose monitoring system can provide the time structure of delivered dose rate within 1 ms time resolution. Experimental testing results show that the highest dose in one pulse of 230 MeV proton that can be delivered to the target is about 20 Gy during 199 ms pulse period at 100 Gy/s dose rate. Conclusion : A proton research irradiation platform dedicated for studying small animal Flash biological effects has been established at Chang Gung Memorial Hospital. The final setup data represent a reference for the beam users to plan the experiments as well as for the improvement of the facility.

preprint2022arXiv

SPIN: An Empirical Evaluation on Sharing Parameters of Isotropic Networks

Recent isotropic networks, such as ConvMixer and vision transformers, have found significant success across visual recognition tasks, matching or outperforming non-isotropic convolutional neural networks (CNNs). Isotropic architectures are particularly well-suited to cross-layer weight sharing, an effective neural network compression technique. In this paper, we perform an empirical evaluation on methods for sharing parameters in isotropic networks (SPIN). We present a framework to formalize major weight sharing design decisions and perform a comprehensive empirical evaluation of this design space. Guided by our experimental results, we propose a weight sharing strategy to generate a family of models with better overall efficiency, in terms of FLOPs and parameters versus accuracy, compared to traditional scaling methods alone, for example compressing ConvMixer by 1.9x while improving accuracy on ImageNet. Finally, we perform a qualitative study to further understand the behavior of weight sharing in isotropic architectures. The code is available at https://github.com/apple/ml-spin.

preprint2020arXiv

Organ at Risk Segmentation for Head and Neck Cancer using Stratified Learning and Neural Architecture Search

OAR segmentation is a critical step in radiotherapy of head and neck (H&N) cancer, where inconsistencies across radiation oncologists and prohibitive labor costs motivate automated approaches. However, leading methods using standard fully convolutional network workflows that are challenged when the number of OARs becomes large, e.g. > 40. For such scenarios, insights can be gained from the stratification approaches seen in manual clinical OAR delineation. This is the goal of our work, where we introduce stratified organ at risk segmentation (SOARS), an approach that stratifies OARs into anchor, mid-level, and small & hard (S&H) categories. SOARS stratifies across two dimensions. The first dimension is that distinct processing pipelines are used for each OAR category. In particular, inspired by clinical practices, anchor OARs are used to guide the mid-level and S&H categories. The second dimension is that distinct network architectures are used to manage the significant contrast, size, and anatomy variations between different OARs. We use differentiable neural architecture search (NAS), allowing the network to choose among 2D, 3D or Pseudo-3D convolutions. Extensive 4-fold cross-validation on 142 H&N cancer patients with 42 manually labeled OARs, the most comprehensive OAR dataset to date, demonstrates that both pipeline- and NAS-stratification significantly improves quantitative performance over the state-of-the-art (from 69.52% to 73.68% in absolute Dice scores). Thus, SOARS provides a powerful and principled means to manage the highly complex segmentation space of OARs.