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Shuqi Wang

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7 papers

2 author rows

AAAI Conference 2026 Conference Paper

PET2Rep: Towards Vision-Language Model-Drived Automated Radiology Report Generation for Positron Emission Tomography

Yichi Zhang
Wenbo Zhang
Zehui Ling
Gang Feng
Sisi Peng
Deshu Chen
Yuchen Liu
Hongwei Zhang

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications. We believe PET2Rep will serve as a platform for the development and application of VLMs for PET imaging, accelerating the development of trustworthy reporting tools that can genuinely alleviate radiologist burden and enhance patient care.

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IROS Conference 2025 Conference Paper

Decentralized but Not Compromised: Modular Architecture with Refined Observation for Multi-Agent Model-Based Reinforcement Learning

Shuqi Wang
Meiqin Liu 0001
Ronghao Zheng
Shanling Dong
Ping Wei 0001

Multi-agent adversarial tasks such as swarm robotics and autonomous vehicle coordination, demand efficient decentralized collaboration under partial observability. While model-free multi-agent RL (MF-MARL) methods suffer from necessitating extensive environment interactions, most existing multi-agent model-based RL (MA-MBRL) methods fail to align with the Centralized Training with Decentralized Execution (CTDE) paradigm, which limits system flexibility. This paper proposes a novel modular architecture with refined observations (MARO) to achieve the CTDE paradigm by decoupling agents from the world model. Key innovations include: 1) an enhanced world model with weighted loss and history-augmented rollout for high-quality data generation; 2) a dual-stream semantic decomposition network (DSDN) that performs fine-grained decomposition of observations to refine action mapping and mitigate performance degradation from information loss. Extensive experiments on the StarCraft Multi-Agent Challenge (SMAC) demonstrate superior performance over opponents, validating the effectiveness and advancement of MARO.

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NeurIPS Conference 2025 Conference Paper

High-dimensional neuronal activity from low-dimensional latent dynamics: a solvable model

Valentin Schmutz
Ali Haydaroğlu
Shuqi Wang
Yixiao Feng
Matteo Carandini
Kenneth D Harris

Computation in recurrent networks of neurons has been hypothesized to occur at the level of low-dimensional latent dynamics, both in artificial systems and in the brain. This hypothesis seems at odds with evidence from large-scale neuronal recordings in mice showing that neuronal population activity is high-dimensional. To demonstrate that low-dimensional latent dynamics and high-dimensional activity can be two sides of the same coin, we present an analytically solvable recurrent neural network (RNN) model whose dynamics can be exactly reduced to a low-dimensional dynamical system, but generates an activity manifold that has a high linear embedding dimension. This raises the question: Do low-dimensional latents explain the high-dimensional activity observed in mouse visual cortex? Spectral theory tells us that the covariance eigenspectrum alone does not allow us to recover the dimensionality of the latents, which can be low or high, when neurons are nonlinear. To address this indeterminacy, we develop Neural Cross-Encoder (NCE), an interpretable, nonlinear latent variable modeling method for neuronal recordings, and find that high-dimensional neuronal responses to drifting gratings and spontaneous activity in visual cortex can be reduced to low-dimensional latents, while the responses to natural images cannot. We conclude that the high-dimensional activity measured in certain conditions, such as in the absence of a stimulus, is explained by low-dimensional latents that are nonlinearly processed by individual neurons.

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NeurIPS Conference 2025 Conference Paper

Inpainting the Neural Picture: Inferring Unrecorded Brain Area Dynamics from Multi-Animal Datasets

Ji Xia
Yizi Zhang
Shuqi Wang
Genevera Allen
Liam Paninski
Cole Hurwitz
Kenneth Miller

Characterizing interactions between brain areas is a fundamental goal of systems neuroscience. While such analyses are possible when areas are recorded simultaneously, it is rare to observe all combinations of areas of interest within a single animal or recording session. How can we leverage multi-animal datasets to better understand multi-area interactions? Building on recent progress in large-scale, multi-animal models, we introduce NeuroPaint, a masked autoencoding approach for inferring the dynamics of unobserved brain areas. By training across animals with overlapping subsets of recorded areas, NeuroPaint learns to reconstruct activity in missing areas based on shared structure across individuals. We train and evaluate our approach on both synthetic data and two multi-animal, multi-area Neuropixels datasets. Our results demonstrate that models trained across animals with partial observations can successfully in-paint the dynamics of unrecorded areas, enabling multi-area analyses that transcend the limitations of any single experiment.

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NeurIPS Conference 2022 Conference Paper

Mesoscopic modeling of hidden spiking neurons

Shuqi Wang
Valentin Schmutz
Guillaume Bellec
Wulfram Gerstner

Can we use spiking neural networks (SNN) as generative models of multi-neuronal recordings, while taking into account that most neurons are unobserved? Modeling the unobserved neurons with large pools of hidden spiking neurons leads to severely underconstrained problems that are hard to tackle with maximum likelihood estimation. In this work, we use coarse-graining and mean-field approximations to derive a bottom-up, neuronally-grounded latent variable model (neuLVM), where the activity of the unobserved neurons is reduced to a low-dimensional mesoscopic description. In contrast to previous latent variable models, neuLVM can be explicitly mapped to a recurrent, multi-population SNN, giving it a transparent biological interpretation. We show, on synthetic spike trains, that a few observed neurons are sufficient for neuLVM to perform efficient model inversion of large SNNs, in the sense that it can recover connectivity parameters, infer single-trial latent population activity, reproduce ongoing metastable dynamics, and generalize when subjected to perturbations mimicking optogenetic stimulation.

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JBHI Journal 2022 Journal Article

MFI-Net: Multiscale Feature Interaction Network for Retinal Vessel Segmentation

Yiwen Ye
Chengwei Pan
Yicheng Wu
Shuqi Wang
Yong Xia

Segmentation of retinal vessels on fundus images plays a critical role in the diagnosis of micro-vascular and ophthalmological diseases. Although being extensively studied, this task remains challenging due to many factors including the highly variable vessel width and poor vessel-background contrast. In this paper, we propose a multiscale feature interaction network (MFI-Net) for retinal vessel segmentation, which is a U-shaped convolutional neural network equipped with the pyramid squeeze-and-excitation (PSE) module, coarse-to-fine (C2F) module, deep supervision, and feature fusion. We extend the SE operator to multiscale features, resulting in the PSE module, which uses the channel attention learned at multiple scales to enhance multiscale features and enables the network to handle the vessels with variable width. We further design the C2F module to generate and re-process the residual feature maps, aiming to preserve more vessel details during the decoding process. The proposed MFI-Net has been evaluated against several public models on the DRIVE, STARE, CHASE_DB1, and HRF datasets. Our results suggest that both PSE and C2F modules are effective in improving the accuracy of MFI-Net, and also indicate that our model has superior segmentation performance and generalization ability over existing models on four public datasets.

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NeurIPS Conference 2021 Conference Paper

Fitting summary statistics of neural data with a differentiable spiking network simulator

Guillaume Bellec
Shuqi Wang
Alireza Modirshanechi
Johanni Brea
Wulfram Gerstner

Fitting network models to neural activity is an important tool in neuroscience. A popular approach is to model a brain area with a probabilistic recurrent spiking network whose parameters maximize the likelihood of the recorded activity. Although this is widely used, we show that the resulting model does not produce realistic neural activity. To correct for this, we suggest to augment the log-likelihood with terms that measure the dissimilarity between simulated and recorded activity. This dissimilarity is defined via summary statistics commonly used in neuroscience and the optimization is efficient because it relies on back-propagation through the stochastically simulated spike trains. We analyze this method theoretically and show empirically that it generates more realistic activity statistics. We find that it improves upon other fitting algorithms for spiking network models like GLMs (Generalized Linear Models) which do not usually rely on back-propagation. This new fitting algorithm also enables the consideration of hidden neurons which is otherwise notoriously hard, and we show that it can be crucial when trying to infer the network connectivity from spike recordings.

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