arXiv subjects

Runkai Zhao

Publications and source records attributed to Runkai Zhao.

18 recordsLinked to original sources

arXiv2026

EasyBCI Agent: Towards Universal Neural Data Preprocessing for Brain-Computer Interfaces

Brain-computer interfaces translate neural activity into device commands, yet their performance hinges on preprocessing that remains manual, expert-dependent and poorly reproducible. Large language model agents can automate scientific coding, but existing systems lack the modality coverage, raw-data isolation, experience accumulation and domain oversight that neural preprocessing requires. We introduce EasyBCI, a two-phase LLM agent that plans and executes preprocessing pipelines for six signal types. A Plan Agent profiles each recording into a text-only Data Fingerprint that never exposes raw data to the model and selects a literature-grounded operator sequence. An Execution Agent generates, runs and self-corrects code until quality criteria are met, while a quality-gated experience system retains validated strategies as reusable skills. A domain expert intervenes at two decision gates, retaining human judgement where undetected error can invalidate downstream analyses. Evaluation on EEG with a fixed linear classifier shows that all five EasyBCI backbones preserve more task-relevant separability than the manual pipeline. Under same-backbone comparison, EasyBCI outperforms general-purpose coding agents on both label schemes for four of five configurations. EasyBCI extends to five additional modalities spanning nearly three orders of magnitude in sampling rate, producing complete reproducible pipelines with recorded decision provenance. These results indicate that domain-specific orchestration can bring auditable preprocessing within reach of laboratories lacking dedicated expertise, illustrating design principles applicable to AI agents in other scientific domains.

q-bio.QM↗

arXiv2026

SciDataSailor: Deep Scientific Data Exploring

Scientific datasets are commonly organized as hierarchical repositories containing heterogeneous and interdependent files, making their inspection, integration, and analysis labor-intensive and reliant on domain expertise. Although large language model (LLM) agents have advanced substantially in planning, reasoning, and tool use, existing research has largely overlooked their ability to interact with real scientific data assets through executable environments. We introduce Deep Scientific Data Exploration, an agentic task paradigm in which agents navigate repositories, interpret heterogeneous files and schemas, execute analyses, integrate cross-file evidence, and produce conclusions grounded in executed observations. To operationalize this paradigm, we present SciDataSailor, a framework for synthesizing tool-interactive trajectories by balancing broad exploration with targeted exploitation. SciDataSailor instantiates trajectory synthesis as Monte Carlo Tree Search (MCTS) with four task-specific mechanisms: difficulty-stratified exploration seeds, dual-feedback first-play urgency, hierarchical strategy-to-tool action generation, and entropy-guided branching. Using this framework, we construct SciDataSailor-SFT-2K for supervised fine-tuning and SciDataSailor-Bench for evaluation, with the latter comprising 627 meta-information summarization tasks and 586 scientific question-answering tasks across 27 datasets spanning the life, earth, and physical sciences.

cs.AI↗

arXiv2026

Timestep Rescheduling in Diffusion Inversion

Diffusion inversion, which maps images back to the Gaussian latent space of a diffusion model, is a critical task for image reconstruction and editing. While DDIM enables fast deterministic inversion, it inherently introduces deviations that accumulate into noticeable inversion errors. Existing methods often address this by solving a fixed-point problem but largely overlook how the selection of the diffusion timestep in the noise scheduler influences inversion fidelity. In this work, we reveal that the deviation scale in diffusion inversion is strongly dependent on the timestep size, and exhibits a parabolic trend, with larger errors concentrated at both small and large timesteps. Based on this finding, we propose a simple yet effective nonuniform timestep scheduler that integrates a global rescaling with a local dynamic programming based rescheduling, enabling a strategic allocation of computational effort that minimizes the overall inversion error and preserves higher inversion accuracy. Our method serves as an off-the-shelf enhancement for existing inversion techniques and requires no extra parameters or computational overhead. Through extensive experiments, we verify that integrating our scheduler consistently boosts the performance of existing inversion methods, achieving superior results in image reconstruction and editing.

cs.CV↗

arXiv2026

NeuroSeg Meets DINOv3: Transferring 2D Self-Supervised Visual Priors to 3D Neuron Segmentation via DINOv3 Initialization

2D visual foundation models, such as DINOv3, a self-supervised model trained on large-scale natural images, have demonstrated strong zero-shot generalization, capturing both rich global context and fine-grained structural cues. However, an analogous 3D foundation model for downstream volumetric neuroimaging remains lacking, largely due to the challenges of 3D image acquisition and the scarcity of high-quality annotations. To address this gap, we propose to adapt the 2D visual representations learned by DINOv3 to a 3D biomedical segmentation model, enabling more data-efficient and morphologically faithful neuronal reconstruction. Specifically, we design an inflation-based adaptation strategy that inflates 2D filters into 3D operators, preserving semantic priors from DINOv3 while adapting to 3D neuronal volume patches. In addition, we introduce a topology-aware skeleton loss to explicitly enforce structural fidelity of graph-based neuronal arbor reconstruction. Extensive experiments on four neuronal imaging datasets, including two from BigNeuron and two public datasets, NeuroFly and CWMBS, demonstrate consistent improvements in reconstruction accuracy over SoTA methods, with average gains of 2.9% in Entire Structure Average, 2.8% in Different Structure Average, and 3.8% in Percentage of Different Structure. Code: https://github.com/yy0007/NeurINO.

cs.CV↗

arXiv2026

VirPro: Visual-referred Probabilistic Prompt Learning for Weakly-Supervised Monocular 3D Detection

Monocular 3D object detection typically relies on pseudo-labeling techniques to reduce dependency on real-world annotations. Recent advances demonstrate that deterministic linguistic cues can serve as effective auxiliary weak supervision signals, providing complementary semantic context. However, hand-crafted textual descriptions struggle to capture the inherent visual diversity of individuals across scenes, limiting the model's ability to learn scene-aware representations. To address this challenge, we propose Visual-referred Probabilistic Prompt Learning (VirPro), an adaptive multi-modal pretraining paradigm that can be seamlessly integrated into diverse weakly supervised monocular 3D detection frameworks. Specifically, we generate a diverse set of learnable, instance-conditioned prompts across scenes and store them in an Adaptive Prompt Bank (APB). Subsequently, we introduce Multi-Gaussian Prompt Modeling (MGPM), which incorporates scene-based visual features into the corresponding textual embeddings, allowing the text prompts to express visual uncertainties. Then, from the fused vision-language embeddings, we decode a prompt-targeted Gaussian, from which we derive a unified object-level prompt embedding for each instance. RoI-level contrastive matching is employed to enforce modality alignment, bringing embeddings of co-occurring objects within the same scene closer in the latent space, thus enhancing semantic coherence. Extensive experiments on the KITTI benchmark demonstrate that integrating our pretraining paradigm consistently yields substantial performance gains, achieving up to a 4.8% average precision improvement than the baseline. Code is available at https://github.com/AustinLCP/VirPro.

cs.CV↗

arXiv2026

SciDataCopilot: An Agentic Data Preparation Framework for AGI-driven Scientific Discovery

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30$\times$ speedup in data preparation.

cs.DB↗

arXiv2026

BrainVista: Modeling Naturalistic Brain Dynamics as Multimodal Next-Token Prediction

Naturalistic fMRI characterizes the brain as a dynamic predictive engine driven by continuous sensory streams. However, modeling the causal forward evolution in realistic neural simulation is impeded by the timescale mismatch between multimodal inputs and the complex topology of cortical networks. To address these challenges, we introduce BrainVista, a multimodal autoregressive framework designed to model the causal evolution of brain states. BrainVista incorporates Network-wise Tokenizers to disentangle system-specific dynamics and a Spatial Mixer Head that captures inter-network information flow without compromising functional boundaries. Furthermore, we propose a novel Stimulus-to-Brain (S2B) masking mechanism to synchronize high-frequency sensory stimuli with hemodynamically filtered signals, enabling strict, history-only causal conditioning. We validate our framework on Algonauts 2025, CineBrain, and HAD, achieving state-of-the-art fMRI encoding performance. In long-horizon rollout settings, our model yields substantial improvements over baselines, increasing pattern correlation by 36.0\% and 33.3\% on relative to the strongest baseline Algonauts 2025 and CineBrain, respectively.

q-bio.NC↗

arXiv2025

Improving Multimodal Brain Encoding Model with Dynamic Subject-awareness Routing

Naturalistic fMRI encoding must handle multimodal inputs, shifting fusion styles, and pronounced inter-subject variability. We introduce AFIRE (Agnostic Framework for Multimodal fMRI Response Encoding), an agnostic interface that standardizes time-aligned post-fusion tokens from varied encoders, and MIND, a plug-and-play Mixture-of-Experts decoder with a subject-aware dynamic gating. Trained end-to-end for whole-brain prediction, AFIRE decouples the decoder from upstream fusion, while MIND combines token-dependent Top-K sparse routing with a subject prior to personalize expert usage without sacrificing generality. Experiments across multiple multimodal backbones and subjects show consistent improvements over strong baselines, enhanced cross-subject generalization, and interpretable expert patterns that correlate with content type. The framework offers a simple attachment point for new encoders and datasets, enabling robust, plug-and-improve performance for naturalistic neuroimaging studies.

cs.AI↗

arXiv2025

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

cs.CL↗

arXiv2025

DistillDrive: End-to-End Multi-Mode Autonomous Driving Distillation by Isomorphic Hetero-Source Planning Model

End-to-end autonomous driving has been recently seen rapid development, exerting a profound influence on both industry and academia. However, the existing work places excessive focus on ego-vehicle status as their sole learning objectives and lacks of planning-oriented understanding, which limits the robustness of the overall decision-making prcocess. In this work, we introduce DistillDrive, an end-to-end knowledge distillation-based autonomous driving model that leverages diversified instance imitation to enhance multi-mode motion feature learning. Specifically, we employ a planning model based on structured scene representations as the teacher model, leveraging its diversified planning instances as multi-objective learning targets for the end-to-end model. Moreover, we incorporate reinforcement learning to enhance the optimization of state-to-decision mappings, while utilizing generative modeling to construct planning-oriented instances, fostering intricate interactions within the latent space. We validate our model on the nuScenes and NAVSIM datasets, achieving a 50\% reduction in collision rate and a 3-point improvement in closed-loop performance compared to the baseline model. Code and model are publicly available at https://github.com/YuruiAI/DistillDrive

cs.RO↗

arXiv2025

Stealthy Patch-Wise Backdoor Attack in 3D Point Cloud via Curvature Awareness

Backdoor attacks pose a severe threat to deep neural networks (DNNs) by implanting hidden backdoors that can be activated with predefined triggers to manipulate model behaviors maliciously. Recent studies have extended backdoor attacks to 3D point clouds, but most existing triggers are sample-wise and often cause visible geometric artifacts or high optimization cost. To address these limitations, we propose the Stealthy Patch-Wise Backdoor Attack (SPBA), a patch-wise backdoor attack framework for 3D point clouds. Specifically, SPBA decomposes a point cloud into local patches, where each patch is formed by a Farthest Point Sampling (FPS) center and its K-nearest neighbors (KNN). Candidate patches are ranked using a patch imperceptibility score derived from local curvature variation, and a unified spectral trigger is injected into the selected patches by perturbing only the coordinates of existing points while preserving the original point cardinality. Extensive experiments on ModelNet40 and ShapeNetPart further demonstrate that SPBA achieves state-of-the-art stealthiness among prior methods and reduces spectral-trigger computation by 98.43% relative to a sample-wise spectral baseline, while maintaining competitive attack performance. These results support localized spectral design as an effective and efficient approach to stealthy backdoor attacks in 3D point cloud models. Code is available at https://github.com/HazardFY/SPBA.

cs.CV↗

arXiv2025

CA-W3D: Leveraging Context-Aware Knowledge for Weakly Supervised Monocular 3D Detection

Weakly supervised monocular 3D detection, while less annotation-intensive, often struggles to capture the global context required for reliable 3D reasoning. Conventional label-efficient methods focus on object-centric features, neglecting contextual semantic relationships that are critical in complex scenes. In this work, we propose a Context-Aware Weak Supervision for Monocular 3D object detection, namely CA-W3D, to address this limitation in a two-stage training paradigm. Specifically, we first introduce a pre-training stage employing Region-wise Object Contrastive Matching (ROCM), which aligns regional object embeddings derived from a trainable monocular 3D encoder and a frozen open-vocabulary 2D visual grounding model. This alignment encourages the monocular encoder to discriminate scene-specific attributes and acquire richer contextual knowledge. In the second stage, we incorporate a pseudo-label training process with a Dual-to-One Distillation (D2OD) mechanism, which effectively transfers contextual priors into the monocular encoder while preserving spatial fidelity and maintaining computational efficiency during inference. Extensive experiments conducted on the public KITTI benchmark demonstrate the effectiveness of our approach, surpassing the SoTA method over all metrics, highlighting the importance of contextual-aware knowledge in weakly-supervised monocular 3D detection.

cs.CV↗

arXiv2024

DINeuro: Distilling Knowledge from 2D Natural Images via Deformable Tubular Transferring Strategy for 3D Neuron Reconstruction

Reconstructing neuron morphology from 3D light microscope imaging data is critical to aid neuroscientists in analyzing brain networks and neuroanatomy. With the boost from deep learning techniques, a variety of learning-based segmentation models have been developed to enhance the signal-to-noise ratio of raw neuron images as a pre-processing step in the reconstruction workflow. However, most existing models directly encode the latent representative features of volumetric neuron data but neglect their intrinsic morphological knowledge. To address this limitation, we design a novel framework that distills the prior knowledge from a 2D Vision Transformer pre-trained on extensive 2D natural images to facilitate neuronal morphological learning of our 3D Vision Transformer. To bridge the knowledge gap between the 2D natural image and 3D microscopic morphologic domains, we propose a deformable tubular transferring strategy that adapts the pre-trained 2D natural knowledge to the inherent tubular characteristics of neuronal structure in the latent embedding space. The experimental results on the Janelia dataset of the BigNeuron project demonstrate that our method achieves a segmentation performance improvement of 4.53% in mean Dice and 3.56% in mean 95% Hausdorff distance.

eess.IV↗

arXiv2024

Unleashing the Potential of Mamba: Boosting a LiDAR 3D Sparse Detector by Using Cross-Model Knowledge Distillation

The LiDAR 3D object detector that balances accuracy and speed is crucial for achieving real-time perception in autonomous driving. However, many existing LiDAR detection models rely on complex feature transformations, leading to poor real-time performance and high resource consumption, which limits their practical effectiveness. In this work, we propose a Faster LiDAR 3D object detection framework that Adaptively aligns Sparse voxels to enable efficient heterogeneous knowledge Distillation, called FASD. We aim to distill the Transformer's sequence modeling capability into Mamba models, significantly boosting accuracy through knowledge transfer. Specifically, we first design a cross-model knowledge distillation architecture to convey the global contextual understanding capabilities of the Transformer to Mamba. The Transformer-based teacher model employs a scale-adaptive attention mechanism to enhance multi-scale fusion. In contrast, the Mamba-based student model leverages feature alignment through spatial alignment adapters, supervised with latent-space features and span-head logit distributions, leading to improved performance and efficiency. We evaluated FASD on the Waymo and nuScenes datasets, achieving up to a 2x reduction in FLOPs and a 4x reduction in memory consumption, while improving baseline performance by 1-2 percentage points and maintaining high deployment efficiency.

cs.CV↗

arXiv2024

Future Does Matter: Boosting 3D Object Detection with Temporal Motion Estimation in Point Cloud Sequences

Accurate and robust LiDAR 3D object detection is essential for comprehensive scene understanding in autonomous driving. Despite its importance, LiDAR detection performance is limited by inherent constraints of point cloud data, particularly under conditions of extended distances and occlusions. Recently, temporal aggregation has been proven to significantly enhance detection accuracy by fusing multi-frame viewpoint information and enriching the spatial representation of objects. In this work, we introduce a novel LiDAR 3D object detection framework, namely LiSTM, to facilitate spatial-temporal feature learning with cross-frame motion forecasting information. We aim to improve the spatial-temporal interpretation capabilities of the LiDAR detector by incorporating a dynamic prior, generated from a non-learnable motion estimation model. Specifically, Motion-Guided Feature Aggregation (MGFA) is proposed to utilize the object trajectory from previous and future motion states to model spatial-temporal correlations into gaussian heatmap over a driving sequence. This motion-based heatmap then guides the temporal feature fusion, enriching the proposed object features. Moreover, we design a Dual Correlation Weighting Module (DCWM) that effectively facilitates the interaction between past and prospective frames through scene- and channel-wise feature abstraction. In the end, a cascade cross-attention-based decoder is employed to refine the 3D prediction. We have conducted experiments on the Waymo and nuScenes datasets to demonstrate that the proposed framework achieves superior 3D detection performance with effective spatial-temporal feature learning.

cs.CV↗

arXiv2024

Boosting 3D Neuron Segmentation with 2D Vision Transformer Pre-trained on Natural Images

Neuron reconstruction, one of the fundamental tasks in neuroscience, rebuilds neuronal morphology from 3D light microscope imaging data. It plays a critical role in analyzing the structure-function relationship of neurons in the nervous system. However, due to the scarcity of neuron datasets and high-quality SWC annotations, it is still challenging to develop robust segmentation methods for single neuron reconstruction. To address this limitation, we aim to distill the consensus knowledge from massive natural image data to aid the segmentation model in learning the complex neuron structures. Specifically, in this work, we propose a novel training paradigm that leverages a 2D Vision Transformer model pre-trained on large-scale natural images to initialize our Transformer-based 3D neuron segmentation model with a tailored 2D-to-3D weight transferring strategy. Our method builds a knowledge sharing connection between the abundant natural and the scarce neuron image domains to improve the 3D neuron segmentation ability in a data-efficiency manner. Evaluated on a popular benchmark, BigNeuron, our method enhances neuron segmentation performance by 8.71% over the model trained from scratch with the same amount of training samples.

cs.CV↗

arXiv2024

Advancements in 3D Lane Detection Using LiDAR Point Clouds: From Data Collection to Model Development

Advanced Driver-Assistance Systems (ADAS) have successfully integrated learning-based techniques into vehicle perception and decision-making. However, their application in 3D lane detection for effective driving environment perception is hindered by the lack of comprehensive LiDAR datasets. The sparse nature of LiDAR point cloud data prevents an efficient manual annotation process. To solve this problem, we present LiSV-3DLane, a large-scale 3D lane dataset that comprises 20k frames of surround-view LiDAR point clouds with enriched semantic annotation. Unlike existing datasets confined to a frontal perspective, LiSV-3DLane provides a full 360-degree spatial panorama around the ego vehicle, capturing complex lane patterns in both urban and highway environments. We leverage the geometric traits of lane lines and the intrinsic spatial attributes of LiDAR data to design a simple yet effective automatic annotation pipeline for generating finer lane labels. To propel future research, we propose a novel LiDAR-based 3D lane detection model, LiLaDet, incorporating the spatial geometry learning of the LiDAR point cloud into Bird's Eye View (BEV) based lane identification. Experimental results indicate that LiLaDet outperforms existing camera- and LiDAR-based approaches in the 3D lane detection task on the K-Lane dataset and our LiSV-3DLane.

cs.CV↗

arXiv2022

PointNeuron: 3D Neuron Reconstruction via Geometry and Topology Learning of Point Clouds

Digital neuron reconstruction from 3D microscopy images is an essential technique for investigating brain connectomics and neuron morphology. Existing reconstruction frameworks use convolution-based segmentation networks to partition the neuron from noisy backgrounds before applying the tracing algorithm. The tracing results are sensitive to the raw image quality and segmentation accuracy. In this paper, we propose a novel framework for 3D neuron reconstruction. Our key idea is to use the geometric representation power of the point cloud to better explore the intrinsic structural information of neurons. Our proposed framework adopts one graph convolutional network to predict the neural skeleton points and another one to produce the connectivity of these points. We finally generate the target SWC file through the interpretation of the predicted point coordinates, radius, and connections. Evaluated on the Janelia-Fly dataset from the BigNeuron project, we show that our framework achieves competitive neuron reconstruction performance. Our geometry and topology learning of point clouds could further benefit 3D medical image analysis, such as cardiac surface reconstruction. Our code is available at https://github.com/RunkaiZhao/PointNeuron.

cs.CV↗