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Junyu Chen

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7 papers

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YNIMG Journal 2025 Journal Article

Deep learning-derived arterial input function for dynamic brain PET

Junyu Chen
Zirui Jiang
Jennifer M. Coughlin
Ian Cheong
Kelly A. Mills
Martin G. Pomper
Yong Du

Dynamic positron emission tomography (PET) imaging combined with radiotracer kinetic modeling is a powerful technique for visualizing biological processes in the brain, offering valuable insights into brain functions and neurological disorders such as Alzheimer's and Parkinson's diseases. Accurate kinetic modeling relies heavily on the use of a metabolite-corrected arterial input function (AIF), which typically requires invasive and labor-intensive arterial blood sampling. While alternative non-invasive approaches have been proposed, they often compromise accuracy or still necessitate at least one invasive blood sampling. In this study, we present the deep learning-derived arterial input function (DLIF), a deep learning framework capable of estimating a metabolite-corrected AIF directly from dynamic PET image sequences without any blood sampling. We validated DLIF using existing dynamic PET patient data. We compared DLIF and resulting parametric maps against ground truth measurements. Our evaluation shows that DLIF achieves accurate and robust AIF estimation. By leveraging deep learning's ability to capture complex temporal dynamics and incorporating prior knowledge of typical AIF shapes through basis functions, DLIF provides a rapid, accurate, and entirely non-invasive alternative to traditional AIF measurement methods.

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NeurIPS Conference 2025 Conference Paper

Jet-Nemotron: Efficient Language Model with Post Neural Architecture Search

Yuxian Gu
Qinghao Hu
Haocheng Xi
Junyu Chen
Shang Yang
Song Han
Han Cai

We present Jet-Nemotron, a new family of hybrid-architecture language models, which matches or exceeds the accuracy of leading full-attention models while significantly improving generation throughput. Jet-Nemotron is developed using Post Neural Architecture Search (PostNAS), a novel neural architecture exploration pipeline that enables efficient model design. Unlike prior approaches, PostNAS begins with a pre-trained full-attention model and freezes its MLP weights, allowing efficient exploration of attention block designs. The pipeline includes four key components: (1) learning optimal full-attention layer placement and elimination, (2) linear attention block selection, (3) designing new attention blocks, and (4) performing hardware-aware hyperparameter search. Our Jet-Nemotron-2B model achieves comparable or superior accuracy to Qwen3, Qwen2. 5, Gemma3, and Llama3. 2 across a comprehensive suite of benchmarks while delivering up to 53. 6× generation throughput speedup and 6. 1× prefilling speedup. It also achieves higher accuracy on MMLU and MMLU-Pro than recent advanced MoE full-attention models, such as DeepSeek-V3-Small and Moonlight, despite their larger scale with 15B total and 2. 2B activated parameters.

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NeurIPS Conference 2025 Conference Paper

LoTA-QAF: Lossless Ternary Adaptation for Quantization-Aware Fine-Tuning

Junyu Chen
Junzhuo Li
Zhen Peng
Wenjie Wang
Yuxiang Ren
Long Shi
Xuming Hu

Quantization and fine-tuning are crucial for deploying large language models (LLMs) on resource-constrained edge devices. However, fine-tuning quantized models presents significant challenges, primarily stemming from: First, the mismatch in data types between the low-precision quantized weights (e. g. , 4-bit) and the high-precision adaptation weights (e. g. , 16-bit). This mismatch limits the computational efficiency advantage offered by quantized weights during inference. Second, potential accuracy degradation when merging these high-precision adaptation weights into the low-precision quantized weights, as the adaptation weights often necessitate approximation or truncation. Third, as far as we know, no existing methods support the lossless merging of adaptation while adjusting all quantized weights. To address these challenges, we introduce lossless ternary adaptation for quantization-aware fine-tuning (LoTA-QAF). This is a novel fine-tuning method specifically designed for quantized LLMs, enabling the lossless merging of ternary adaptation weights into quantized weights and the adjustment of all quantized weights. LoTA-QAF operates through a combination of: i) A custom-designed ternary adaptation (TA) that aligns ternary weights with the quantization grid and uses these ternary weights to adjust quantized weights. ii) A TA-based mechanism that enables the lossless merging of adaptation weights. iii) Ternary signed gradient descent (t-SignSGD) for updating the TA weights. We apply LoTA-QAF to Llama-3. 1/3. 3 and Qwen-2. 5 model families and validate its effectiveness on several downstream tasks. On the MMLU benchmark, our method effectively recovers performance for quantized models, surpassing 16-bit LoRA by up to 5. 14\%. For task-specific fine-tuning, 16-bit LoRA achieves superior results, but LoTA-QAF still outperforms other methods. Code is available in github. com/KingdalfGoodman/LoTA-QAF.

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NeurIPS Conference 2025 Conference Paper

Optical Coherence Tomography Harmonization with Anatomy-Guided Latent Metric Schrödinger Bridges

Shuwen Wei
Samuel Remedios
Blake Dewey
Zhangxing Bian
Shimeng Wang
Junyu Chen
Bruno Jedynak
shiv saidha

Medical image harmonization aims to reduce the differences in appearance caused by scanner hardware variations to allow for consistent and reliable comparisons across devices. Harmonization based on paired images from different devices has limited applicability in real-world clinical settings. On the other hand, unpaired harmonization typically does not guarantee anatomy consistency, which is problematic because anatomical information preservation is paramount. The Schrödinger bridge framework has achieved state-of-the-art style transfer performance with natural images by matching distributions of unpaired images, but this approach can also introduce anatomy changes when applied to medical images. We show that such changes occur because the Schrödinger bridge uses the square of the Euclidean distance between images as the transport cost in an entropy-regularized optimal transport problem. Such a transport cost is not appropriate for measuring anatomical distances, as medical images with the same anatomy need not have a small Euclidean distance between them. In this paper, we propose a latent metric Schrödinger bridge (LMSB) framework to improve the anatomical consistency for the harmonization of medical images. We develop an invertible network that maps medical images into a latent Euclidean metric space where the distances among images with the same anatomy are minimized using the pullback latent metric. Within this latent space, we train a Schrödinger bridge to match distributions. We show that the proposed LMSB is superior to the direct application of a Schrödinger bridge to harmonize optical coherence tomography (OCT) images.

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AAAI Conference 2024 Conference Paper

Semantic Complete Scene Forecasting from a 4D Dynamic Point Cloud Sequence

Zifan Wang
Zhuorui Ye
Haoran Wu
Junyu Chen
Li Yi

We study a new problem of semantic complete scene forecasting (SCSF) in this work. Given a 4D dynamic point cloud sequence, our goal is to forecast the complete scene corresponding to the future next frame along with its semantic labels. To tackle this challenging problem, we properly model the synergetic relationship between future forecasting and semantic scene completion through a novel network named SCSFNet. SCSFNet leverages a hybrid geometric representation for high-resolution complete scene forecasting. To leverage multi-frame observation as well as the understanding of scene dynamics to ease the completion task, SCSFNet introduces an attention-based skip connection scheme. To ease the need to model occlusion variations and to better focus on the occluded part, SCSFNet utilizes auxiliary visibility grids to guide the forecasting task. To evaluate the effectiveness of SCSFNet, we conduct experiments on various benchmarks including two large-scale indoor benchmarks we contributed and the outdoor SemanticKITTI benchmark. Extensive experiments show SCSFNet outperforms baseline methods on multiple metrics by a large margin, and also prove the synergy between future forecasting and semantic scene completion.The project page with code is available at scsfnet.github.io.

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NeurIPS Conference 2024 Conference Paper

Semidefinite Relaxations of the Gromov-Wasserstein Distance

Junyu Chen
Binh T. Nguyen
Shang H. Koh
Yong S. Soh

The Gromov-Wasserstein (GW) distance is an extension of the optimal transport problem that allows one to match objects between incomparable spaces. At its core, the GW distance is specified as the solution of a non-convex quadratic program and is not known to be tractable to solve. In particular, existing solvers for the GW distance are only able to find locally optimal solutions. In this work, we propose a semi-definite programming (SDP) relaxation of the GW distance. The relaxation can be viewed as the Lagrangian dual of the GW distance augmented with constraints that relate to the linear and quadratic terms of transportation plans. In particular, our relaxation provides a tractable (polynomial-time) algorithm to compute globally optimal transportation plans (in some instances) together with an accompanying proof of global optimality. Our numerical experiments suggest that the proposed relaxation is strong in that it frequently computes the globally optimal solution. Our Python implementation is available at https: //github. com/tbng/gwsdp.

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JAIR Journal 2021 Journal Article

Hybrid-order Network Consensus for Distributed Multi-agent Systems

Guangqiang Xie
Junyu Chen
Yang Li

As an important field of Distributed artificial intelligence (DAI), multi-agent systems (MASs) have attracted the attention of extensive research scholars. Consensus as the most important issue in MAS, much progress has been made in studying the consensus control of MAS, but there are some problems remained largely unaddressed which cause the MAS to lose some useful network structure information. First, multi-agent consensus protocol usually proceeds over the low-order structure by only considering the direct edges between agents, but ignores the higher-order structure of the whole topology network. Second, the existing work assumes all the edges in a topology network have the same weight without exploring the potential diversity of the connections. In this way, multi-agent systems fail to enforce consensus, resulting in fragmentation into multiple clusters. To address the above issues, this paper proposes a Motif-aware Weighted Multi-agent System (MWMS) method for consensus control. We focus more on triangle motif in the network, but it can be extended to other kinds of motifs as well. First, a novel weighted network is used which is the combination of the edge-based lower-order structure and the motif-based higher-order structure, i.e., hybrid-order structure. Subsequently, by simultaneously considering the quantity and the quality of the connections in the network, a novel consensus framework for MAS is designed to update agents. Then, two baseline consensus algorithms are used in MWMS. In our experiments, we use ten topologies of different shapes, densities and ranges to comprehensively analyze the performance of our proposed algorithms. The simulation results show that the hybrid higher-order network can effectively enhance the consensus of the multi-agent system in different network topologies.

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