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Zhichao Liang

Publications and source records attributed to Zhichao Liang.

18 recordsLinked to original sources

QuarkMedSearch: A Long-Horizon Deep Search Agent for Exploring Medical Intelligence

As agentic foundation models continue to evolve, how to further improve their performance in vertical domains has become an important challenge. To this end, building upon Tongyi DeepResearch, a powerful agentic foundation model, we focus on the Chinese medical deep search scenario and propose QuarkMedSearch, systematically exploring a full-pipeline approach spanning medical multi-hop data construction, training strategies, and evaluation benchmarks to further push and assess its performance upper bound in vertical domains. Specifically, for data synthesis, to address the scarcity of deep search training data in the medical domain, we combine a large-scale medical knowledge graph with real-time online exploration to construct long-horizon medical deep search training data; for post-training, we adopt a two-stage SFT and RL training strategy that progressively enhances the model's planning, tool invocation, and reflection capabilities required for deep search, while maintaining search efficiency; for evaluation, we collaborate with medical experts to construct the QuarkMedSearch Benchmark through rigorous manual verification. Experimental results demonstrate that QuarkMedSearch achieves state-of-the-art performance among open-source models of comparable scale on the QuarkMedSearch Benchmark, while also maintaining strong competitiveness on general benchmarks.

cs.AI

Inferring brain plasticity rule under long-term stimulation with structured recurrent dynamics

Understanding how long-term stimulation reshapes neural circuits requires uncovering the rules of brain plasticity. While short-term synaptic modifications have been extensively characterized, the principles that drive circuit-level reorganization across hours to weeks remain unknown. Here, we formalize these principles as a latent dynamical law that governs how recurrent connectivity evolves under repeated interventions. To capture this law, we introduce the Stimulus-Evoked Evolution Recurrent dynamics (STEER) framework, a dual-timescale model that disentangles fast neural activity from slow plastic changes. STEER represents plasticity as low-dimensional latent coefficients evolving under a learnable recurrence, enabling testable inference of plasticity rules rather than absorbing them into black-box parameters. We validate STEER with four benchmarks: synthetic Lorenz systems with controlled parameter shifts, BCM-based networks with biologically grounded plasticity, a task learning setting with adaptively optimized external stimulation and longitudinal recordings from Parkinsonian rats receiving closed-loop DBS. Our results demonstrate that STEER recovers interpretable update equations, predicts network adaptation under unseen stimulation schedules, and supports the design of improved intervention protocols. By elevating long-term plasticity from a hidden confound to an identifiable dynamical object, STEER provides a data-driven foundation for both mechanistic insight and principled optimization of brain stimulation.

q-bio.NC

Robust, High-Contrast, Recyclable Zinc-Based Dynamic Windows via Synergistic Electrolyte and Interfacial Engineering

Zinc-based electrochromic devices offer a sustainable route for dynamic optical management but are plagued by poor cycling stability due to irreversible zinc plating/stripping and side reactions. Herein, we report a robust, high-contrast, and recyclable zinc-based dynamic window enabled by a synergistic electrolyte and interfacial engineering strategy. Molecular dynamics simulations and electrochemical analyses reveal a dual-ion cooperative mechanism that governs the reversibility: anions with the strongest binding affinity guide uniform Zn deposition by stabilizing the inner solvation shell, while formate anions co-enriched at the interface facilitate smooth stripping via protonation during the oxidation process. This orchestrated interplay effectively eliminates "dead Zn" accumulation and dendrite growth. Consequently, the device demonstrates a record-high lifespan of 15,000 cycles with negligible degradation and maintains a large optical modulation of >50%, along with multiple optical states (transparent, gray, black, and mirror). Furthermore, it achieves a large reflectance modulation (>50%) stable for over 2,000 cycles. This work establishes the recyclable zinc-based dynamic window as a scalable, high-performance alternative to conventional electrochromic systems, advancing the feasibility of solution-processed energy-saving windows in sustainable buildings.

cond-mat.mtrl-sci

Understanding Mental States to Guide Social Influence in Multi-Person Group Dialogue

Existing dynamic Theory of Mind (ToM) benchmarks mostly place language models in a passive role: the model reads a sequence of connected scenarios and reports what people believe, feel, intend, and do as these states change. In real social interaction, ToM is also used for action: a speaker plans what to say in order to shift another person's mental-state trajectory toward a goal. We introduce SocialMindChange, a benchmark that moves from tracking minds to changing minds in social interaction. Each instance defines a social context with 4 characters and five connected scenes. The model plays one character and generates dialogue across the five scenes to reach the target while remaining consistent with the evolving states of all participants. SocialMindChange also includes selected higher-order states. Using a structured four-step framework, we construct 1,200 social contexts, covering 6000 scenarios and over 90,000 questions, each validated for realism and quality. Evaluations on ten state-of-the-art LLMs show that their average performance is 54.2% below human performance. This gap suggests that current LLMs still struggle to maintain and change mental-state representations across long, linked interactions.

cs.AI

Artificial intelligence as a surrogate brain: Bridging neural dynamical models and data

Recent breakthroughs in artificial intelligence (AI) are reshaping the way we construct computational counterparts of the brain, giving rise to a new class of ``surrogate brains''. In contrast to conventional hypothesis-driven biophysical models, the AI-based surrogate brain encompasses a broad spectrum of data-driven approaches to solve the inverse problem, with the primary objective of accurately predicting future whole-brain dynamics with historical data. Here, we introduce a unified framework of constructing an AI-based surrogate brain that integrates forward modeling, inverse problem solving, and model evaluation. Leveraging the expressive power of AI models and large-scale brain data, surrogate brains open a new window for decoding neural systems and forecasting complex dynamics with high dimensionality, nonlinearity, and adaptability. We highlight that the learned surrogate brain serves as a simulation platform for dynamical systems analysis, virtual perturbation, and model-guided neurostimulation. We envision that the AI-based surrogate brain will provide a functional bridge between theoretical neuroscience and translational neuroengineering.

q-bio.NC

Medical Image Fusion for High-Level Analysis: A Mutual Enhancement Framework for Unaligned PAT and MRI

Photoacoustic tomography (PAT) offers optical contrast, whereas magnetic resonance imaging (MRI) excels in imaging soft tissue and organ anatomy. The fusion of PAT with MRI holds promising application prospects due to their complementary advantages. Existing image fusion have made considerable progress in pre-registered images, yet spatial deformations are difficult to avoid in medical imaging scenarios. More importantly, current algorithms focus on visual quality and statistical metrics, thus overlooking the requirements of high-level tasks. To address these challenges, we propose an unsupervised fusion model, termed PAMRFuse+, which integrates image generation and registration. Specifically, a cross-modal style transfer network is introduced to simplify cross-modal registration to single-modal registration. Subsequently, a multi-level registration network is employed to predict displacement vector fields. Furthermore, a dual-branch feature decomposition fusion network is proposed to address the challenges of cross-modal feature modeling and decomposition by integrating modality-specific and modality-shared features. PAMRFuse+ achieves satisfactory results in registering and fusing unaligned PAT-MRI datasets. Moreover, for the first time, we evaluate the performance of medical image fusion with multi-organ instance segmentation. Extensive experimental demonstrations reveal the advantages of PAMRFuse+ in improving the performance of medical image analysis tasks.

eess.IV

ColorDynamic: Generalizable, Scalable, Real-time, End-to-end Local Planner for Unstructured and Dynamic Environments

Deep Reinforcement Learning (DRL) has demonstrated potential in addressing robotic local planning problems, yet its efficacy remains constrained in highly unstructured and dynamic environments. To address these challenges, this study proposes the ColorDynamic framework. First, an end-to-end DRL formulation is established, which maps raw sensor data directly to control commands, thereby ensuring compatibility with unstructured environments. Under this formulation, a novel network, Transqer, is introduced. The Transqer enables online DRL learning from temporal transitions, substantially enhancing decision-making in dynamic scenarios. To facilitate scalable training of Transqer with diverse data, an efficient simulation platform E-Sparrow, along with a data augmentation technique leveraging symmetric invariance, are developed. Comparative evaluations against state-of-the-art methods, alongside assessments of generalizability, scalability, and real-time performance, were conducted to validate the effectiveness of ColorDynamic. Results indicate that our approach achieves a success rate exceeding 90% while exhibiting real-time capacity (1.2-1.3 ms per planning). Additionally, ablation studies were performed to corroborate the contributions of individual components. Building on this, the OkayPlan-ColorDynamic (OPCD) navigation system is presented, with simulated and real-world experiments demonstrating its superiority and applicability in complex scenarios. The codebase and experimental demonstrations have been open-sourced on our website to facilitate reproducibility and further research.

cs.RO

Mapping effective connectivity by virtually perturbing a surrogate brain

Effective connectivity (EC), indicative of the causal interactions between brain regions, is fundamental to understanding information processing in the brain. Traditional approaches, which infer EC from neural responses to stimulations, are not suited for mapping whole-brain EC in humans due to being invasive and having limited spatial coverage of stimulations. To address this gap, we present Neural Perturbational Inference (NPI), a data-driven framework designed to map EC across the entire brain. NPI employs an artificial neural network trained to learn large-scale neural dynamics as a computational surrogate of the brain. NPI maps EC by perturbing each region of the surrogate brain and observing the resulting responses in all other regions. NPI captures the directionality, strength, and excitatory/inhibitory properties of brain-wide EC. Our validation of NPI, using models having ground-truth EC, shows its superiority over Granger causality and dynamic causal modeling. Applying NPI to resting-state fMRI data from diverse datasets reveals consistent and structurally supported EC. Further validation using a cortico-cortical evoked potentials dataset reveals a significant correlation between NPI-inferred EC and real stimulation propagation pathways. By transitioning from correlational to causal understandings of brain functionality, NPI marks a stride in decoding the brain's functional architecture and facilitating both neuroscience research and clinical applications.

q-bio.NC

Suppressing seizure via optimal electrical stimulation to the hub of epileptic brain network

The electrical stimulation to the seizure onset zone (SOZ) serves as an efficient approach to seizure suppression. Recently, seizure dynamics have gained widespread attendance in its network propagation mechanisms. Compared with the direct stimulation to SOZ, other brain network-level approaches that can effectively suppress epileptic seizures remain under-explored. In this study, we introduce a platform equipped with a system identification module and a control strategy module, to validate the effectiveness of the hub of the epileptic brain network in suppressing seizure. The identified surrogate dynamics show high predictive performance in reconstructing neural dynamics which enables the model predictive framework to achieve accurate neural stimulation. The electrical stimulation on the hub of the epileptic brain network shows remarkable performance as the direct stimulation of SOZ in suppressing seizure dynamics. Underpinned by network control theory, our platform offers a general tool for the validation of neural stimulation.

q-bio.NC

Uncovering cognitive taskonomy through transfer learning in masked autoencoder-based fMRI reconstruction

Data reconstruction is a widely used pre-training task to learn the generalized features for many downstream tasks. Although reconstruction tasks have been applied to neural signal completion and denoising, neural signal reconstruction is less studied. Here, we employ the masked autoencoder (MAE) model to reconstruct functional magnetic resonance imaging (fMRI) data, and utilize a transfer learning framework to obtain the cognitive taskonomy, a matrix to quantify the similarity between cognitive tasks. Our experimental results demonstrate that the MAE model effectively captures the temporal dynamics patterns and interactions within the brain regions, enabling robust cross-subject fMRI signal reconstruction. The cognitive taskonomy derived from the transfer learning framework reveals the relationships among cognitive tasks, highlighting subtask correlations within motor tasks and similarities between emotion, social, and gambling tasks. Our study suggests that the fMRI reconstruction with MAE model can uncover the latent representation and the obtained taskonomy offers guidance for selecting source tasks in neural decoding tasks for improving the decoding performance on target tasks.

q-bio.NC

Controlling network-coupled neural dynamics with nonlinear network control theory

This paper addresses the problem of controlling the temporal dynamics of complex nonlinear network-coupled dynamical systems, specifically in terms of neurodynamics. Based on the Lyapunov direct method, we derive a control strategy with theoretical guarantees of controllability. To verify the performance of the derived control strategy, we perform numerical experiments on two nonlinear network-coupled dynamical systems that emulate phase synchronization and neural population dynamics. The results demonstrate the feasibility and effectiveness of our control strategy.

eess.SY

Reverse engineering the brain input: Network control theory to identify cognitive task-related control nodes

The human brain receives complex inputs when performing cognitive tasks, which range from external inputs via the senses to internal inputs from other brain regions. However, the explicit inputs to the brain during a cognitive task remain unclear. Here, we present an input identification framework for reverse engineering the control nodes and the corresponding inputs to the brain. The framework is verified with synthetic data generated by a predefined linear system, indicating it can robustly reconstruct data and recover the inputs. Then we apply the framework to the real motor-task fMRI data from 200 human subjects. Our results show that the model with sparse inputs can reconstruct neural dynamics in motor tasks ($EV=0.779$) and the identified 28 control nodes largely overlap with the motor system. Underpinned by network control theory, our framework offers a general tool for understanding brain inputs.

q-bio.NC

Deep learning acceleration of iterative model-based light fluence correction for photoacoustic tomography

Photoacoustic tomography (PAT) is a promising imaging technique that can visualize the distribution of chromophores within biological tissue. However, the accuracy of PAT imaging is compromised by light fluence (LF), which hinders the quantification of light absorbers. Currently, model-based iterative methods are used for LF correction, but they require significant computational resources due to repeated LF estimation based on differential light transport models. To improve LF correction efficiency, we propose to use Fourier neural operator (FNO), a neural network specially designed for solving differential equations, to learn the forward projection of light transport in PAT. Trained using paired finite-element-based LF simulation data, our FNO model replaces the traditional computational heavy LF estimator during iterative correction, such that the correction procedure is significantly accelerated. Simulation and experimental results demonstrate that our method achieves comparable LF correction quality to traditional iterative methods while reducing the correction time by over 30 times.

eess.IV

Network analysis on cortical morphometry in first-episode schizophrenia

First-episode schizophrenia (FES) results in abnormality of brain connectivity at different levels. Despite some successful findings on functional and structural connectivity of FES, relatively few studies have been focused on morphological connectivity, which may provide a potential biomarker for FES. In this study, we aim to investigate cortical morphological connectivity in FES. T1-weighted magnetic resonance image data from 92 FES patients and 106 healthy controls (HCs) are analyzed.We parcellate brain into 68 cortical regions, calculate the averaged thickness and surface area of each region, construct undirected networks by correlating cortical thickness or surface area measures across 68 regions for each group, and finally compute a variety of network-related topology characteristics. Our experimental results show that both the cortical thickness network and the surface area network in two groups are small-world networks; that is, those networks have high clustering coefficients and low characteristic path lengths. At certain network sparsity levels, both the cortical thickness network and the surface area network of FES have significantly lower clustering coefficients and local efficiencies than those of HC, indicating FES-related abnormalities in local connectivity and small-worldness. These abnormalities mainly involve the frontal, parietal, and temporal lobes. Further regional analyses confirm significant group differences in the node betweenness of the posterior cingulate gyrus for both the cortical thickness network and the surface area network. Our work supports that cortical morphological connectivity, which is constructed based on correlations across subjects' cortical thickness, may serve as a tool to study topological abnormalities in neurological disorders.

q-bio.NC

Explainable fMRI-based Brain Decoding via Spatial Temporal-pyramid Graph Convolutional Network

Brain decoding, aiming to identify the brain states using neural activity, is important for cognitive neuroscience and neural engineering. However, existing machine learning methods for fMRI-based brain decoding either suffer from low classification performance or poor explainability. Here, we address this issue by proposing a biologically inspired architecture, Spatial Temporal-pyramid Graph Convolutional Network (STpGCN), to capture the spatial-temporal graph representation of functional brain activities. By designing multi-scale spatial-temporal pathways and bottom-up pathways that mimic the information process and temporal integration in the brain, STpGCN is capable of explicitly utilizing the multi-scale temporal dependency of brain activities via graph, thereby achieving high brain decoding performance. Additionally, we propose a sensitivity analysis method called BrainNetX to better explain the decoding results by automatically annotating task-related brain regions from the brain-network standpoint. We conduct extensive experiments on fMRI data under 23 cognitive tasks from Human Connectome Project (HCP) S1200. The results show that STpGCN significantly improves brain decoding performance compared to competing baseline models; BrainNetX successfully annotates task-relevant brain regions. Post hoc analysis based on these regions further validates that the hierarchical structure in STpGCN significantly contributes to the explainability, robustness and generalization of the model. Our methods not only provide insights into information representation in the brain under multiple cognitive tasks but also indicate a bright future for fMRI-based brain decoding.

q-bio.NC

Online Learning Koopman operator for closed-loop electrical neurostimulation in epilepsy

Electrical neuromodulation as a palliative treatment has been increasingly used in the control of epilepsy. However, current neuromodulations commonly implement predetermined actuation strategies and lack the capability of self-adaptively adjusting stimulation inputs. In this work, rooted in optimal control theory, we propose a Koopman-MPC framework for real-time closed-loop electrical neuromodulation in epilepsy, which integrates i) a deep Koopman operator based dynamical model to predict the temporal evolution of epileptic EEG with an approximate finite-dimensional linear dynamics and ii) a model predictive control (MPC) module to design optimal seizure suppression strategies. The Koopman operator based linear dynamical model is embedded in the latent state space of the autoencoder neural network, in which we can approximate and update the Koopman operator online. The linear dynamical property of the Koopman operator ensures the convexity of the optimization problem for subsequent MPC control. The proposed deep Koopman operator model shows greater predictive capability than the baseline models (e.g., vector autoregressive model, kernel based method and recurrent neural network (RNN)) in both synthetic and real epileptic EEG data. Moreover, compared with the RNN-MPC framework, our Koopman-MPC framework can suppress seizure dynamics with better computational efficiency in both the Jansen-Rit model and the Epileptor model. Koopman-MPC framework opens a new window for model-based closed-loop neuromodulation and sheds light on nonlinear neurodynamics and feedback control policies.

eess.SY

Partial Least Square Regression via Three-factor SVD-type Manifold Optimization for EEG Decoding

Partial least square regression (PLSR) is a widely-used statistical model to reveal the linear relationships of latent factors that comes from the independent variables and dependent variables. However, traditional methods to solve PLSR models are usually based on the Euclidean space, and easily getting stuck into a local minimum. To this end, we propose a new method to solve the partial least square regression, named PLSR via optimization on bi-Grassmann manifold (PLSRbiGr). Specifically, we first leverage the three-factor SVD-type decomposition of the cross-covariance matrix defined on the bi-Grassmann manifold, converting the orthogonal constrained optimization problem into an unconstrained optimization problem on bi-Grassmann manifold, and then incorporate the Riemannian preconditioning of matrix scaling to regulate the Riemannian metric in each iteration. PLSRbiGr is validated with a variety of experiments for decoding EEG signals at motor imagery (MI) and steady-state visual evoked potential (SSVEP) task. Experimental results demonstrate that PLSRbiGr outperforms competing algorithms in multiple EEG decoding tasks, which will greatly facilitate small sample data learning.

cs.LG

Kuramoto model based analysis reveals oxytocin effects on brain network dynamics

The oxytocin effects on large-scale brain networks such as Default Mode Network (DMN) and Frontoparietal Network (FPN) have been largely studied using fMRI data. However, these studies are mainly based on the statistical correlation or Bayesian causality inference, lacking interpretability at physical and neuroscience level. Here, we propose a physics-based framework of Kuramoto model to investigate oxytocin effects on the phase dynamic neural coupling in DMN and FPN. Testing on fMRI data of 59 participants administrated with either oxytocin or placebo, we demonstrate that oxytocin changes the topology of brain communities in DMN and FPN, leading to higher synchronization in the FPN and lower synchronization in the DMN, as well as a higher variance of the coupling strength within the DMN and more flexible coupling patterns across time. These results together indicate that oxytocin may increase the ability to overcome the corresponding internal oscillation dispersion and support the flexibility in neural synchrony in various social contexts, providing new evidence for explaining the oxytocin modulated social behaviors. Our proposed Kuramoto model-based framework can be a potential tool in network neuroscience and offers physical and neural insights into phase dynamics of the brain.

q-bio.NC