arXiv subjects

Chunfeng Song

Publications and source records attributed to Chunfeng Song.

33 records · Page 2Linked to original sources

arXiv2025

SciReasoner: Laying the Scientific Reasoning Ground Across Disciplines

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

cs.CL↗

arXiv2025

SynBrain: Enhancing Visual-to-fMRI Synthesis via Probabilistic Representation Learning

Deciphering how visual stimuli are transformed into cortical responses is a fundamental challenge in computational neuroscience. This visual-to-neural mapping is inherently a one-to-many relationship, as identical visual inputs reliably evoke variable hemodynamic responses across trials, contexts, and subjects. However, existing deterministic methods struggle to simultaneously model this biological variability while capturing the underlying functional consistency that encodes stimulus information. To address these limitations, we propose SynBrain, a generative framework that simulates the transformation from visual semantics to neural responses in a probabilistic and biologically interpretable manner. SynBrain introduces two key components: (i) BrainVAE models neural representations as continuous probability distributions via probabilistic learning while maintaining functional consistency through visual semantic constraints; (ii) A Semantic-to-Neural Mapper acts as a semantic transmission pathway, projecting visual semantics into the neural response manifold to facilitate high-fidelity fMRI synthesis. Experimental results demonstrate that SynBrain surpasses state-of-the-art methods in subject-specific visual-to-fMRI encoding performance. Furthermore, SynBrain adapts efficiently to new subjects with few-shot data and synthesizes high-quality fMRI signals that are effective in improving data-limited fMRI-to-image decoding performance. Beyond that, SynBrain reveals functional consistency across trials and subjects, with synthesized signals capturing interpretable patterns shaped by biological neural variability. Our code is available at https://github.com/MichaelMaiii/SynBrain.

cs.LG↗

arXiv2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

cs.LG↗

arXiv2025

Think Twice to See More: Iterative Visual Reasoning in Medical VLMs

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

cs.CV↗

arXiv2025

Neuro-3D: Towards 3D Visual Decoding from EEG Signals

Human's perception of the visual world is shaped by the stereo processing of 3D information. Understanding how the brain perceives and processes 3D visual stimuli in the real world has been a longstanding endeavor in neuroscience. Towards this goal, we introduce a new neuroscience task: decoding 3D visual perception from EEG signals, a neuroimaging technique that enables real-time monitoring of neural dynamics enriched with complex visual cues. To provide the essential benchmark, we first present EEG-3D, a pioneering dataset featuring multimodal analysis data and extensive EEG recordings from 12 subjects viewing 72 categories of 3D objects rendered in both videos and images. Furthermore, we propose Neuro-3D, a 3D visual decoding framework based on EEG signals. This framework adaptively integrates EEG features derived from static and dynamic stimuli to learn complementary and robust neural representations, which are subsequently utilized to recover both the shape and color of 3D objects through the proposed diffusion-based colored point cloud decoder. To the best of our knowledge, we are the first to explore EEG-based 3D visual decoding. Experiments indicate that Neuro-3D not only reconstructs colored 3D objects with high fidelity, but also learns effective neural representations that enable insightful brain region analysis. The dataset and associated code will be made publicly available.

cs.CV↗

arXiv2025

AdaBrain-Bench: Benchmarking Brain Foundation Models for Brain-Computer Interface Applications

Non-invasive Brain-Computer Interfaces (BCI) offer a safe and accessible means of connecting the human brain to external devices, with broad applications in home and clinical settings to enhance human capabilities. However, the high noise level and limited task-specific data in non-invasive signals constrain decoding capabilities. Recently, the adoption of self-supervised pre-training is transforming the landscape of non-invasive BCI research, enabling the development of brain foundation models to capture generic neural representations from large-scale unlabeled electroencephalography (EEG) signals with substantial noises. However, despite these advances, the field currently lacks comprehensive, practical and extensible benchmarks to assess the utility of the public foundation models across diverse BCI tasks, hindering their widespread adoption. To address this challenge, we present AdaBrain-Bench, a large-scale standardized benchmark to systematically evaluate brain foundation models in widespread non-invasive BCI tasks. AdaBrain-Bench encompasses a diverse collection of representative BCI decoding datasets spanning 7 key applications. It introduces a streamlined task adaptation pipeline integrated with multi-dimensional evaluation metrics and a set of adaptation tools. The benchmark delivers an inclusive framework for assessing generalizability of brain foundation models across key transfer settings, including cross-subject, multi-subject, and few-shot scenarios. We leverage AdaBrain-Bench to evaluate a suite of publicly available brain foundation models and offer insights into practices for selecting appropriate models in various scenarios. We make our benchmark pipeline available to enable reproducible research and external use, offering a continuously evolving platform to foster progress toward robust and generalized neural decoding solutions.

cs.LG↗

arXiv2025

CSBrain: A Cross-scale Spatiotemporal Brain Foundation Model for EEG Decoding

Understanding and decoding brain activity from electroencephalography (EEG) signals is a fundamental challenge in neuroscience and AI, with applications in cognition, emotion recognition, diagnosis, and brain-computer interfaces. While recent EEG foundation models advance generalized decoding via unified architectures and large-scale pretraining, they adopt a scale-agnostic dense modeling paradigm inherited from NLP and vision. This design neglects a core property of neural activity: cross-scale spatiotemporal structure. EEG task patterns span a wide range of temporal and spatial scales, from short bursts to slow rhythms, and from localized cortical responses to distributed interactions. Ignoring this diversity leads to suboptimal representations and weak generalization. We propose CSBrain, a Cross-scale Spatiotemporal Brain foundation model for generalized EEG decoding. CSBrain introduces: (i) Cross-scale Spatiotemporal Tokenization (CST), which aggregates multi-scale features from localized temporal windows and anatomical brain regions into compact scale-aware tokens; and (ii) Structured Sparse Attention (SSA), which captures cross-window and cross-region dependencies, enhancing scale diversity while removing spurious correlations. CST and SSA are alternately stacked to progressively integrate multi-scale dependencies. Experiments on 11 EEG tasks across 16 datasets show that CSBrain consistently outperforms task-specific and foundation model baselines. These results establish cross-scale modeling as a key inductive bias and position CSBrain as a robust backbone for future brain-AI research.

cs.HC↗

arXiv2025

Neural Representational Consistency Emerges from Probabilistic Neural-Behavioral Representation Alignment

Individual brains exhibit striking structural and physiological heterogeneity, yet neural circuits can generate remarkably consistent functional properties across individuals, an apparent paradox in neuroscience. While recent studies have observed preserved neural representations in motor cortex through manual alignment across subjects, the zero-shot validation of such preservation and its generalization to more cortices remain unexplored. Here we present PNBA (Probabilistic Neural-Behavioral Representation Alignment), a new framework that leverages probabilistic modeling to address hierarchical variability across trials, sessions, and subjects, with generative constraints preventing representation degeneration. By establishing reliable cross-modal representational alignment, PNBA reveals robust preserved neural representations in monkey primary motor cortex (M1) and dorsal premotor cortex (PMd) through zero-shot validation. We further establish similar representational preservation in mouse primary visual cortex (V1), reflecting a general neural basis. These findings resolve the paradox of neural heterogeneity by establishing zero-shot preserved neural representations across cortices and species, enriching neural coding insights and enabling zero-shot behavior decoding.

q-bio.NC↗

arXiv2025

MindAligner: Explicit Brain Functional Alignment for Cross-Subject Visual Decoding from Limited fMRI Data

Brain decoding aims to reconstruct visual perception of human subject from fMRI signals, which is crucial for understanding brain's perception mechanisms. Existing methods are confined to the single-subject paradigm due to substantial brain variability, which leads to weak generalization across individuals and incurs high training costs, exacerbated by limited availability of fMRI data. To address these challenges, we propose MindAligner, an explicit functional alignment framework for cross-subject brain decoding from limited fMRI data. The proposed MindAligner enjoys several merits. First, we learn a Brain Transfer Matrix (BTM) that projects the brain signals of an arbitrary new subject to one of the known subjects, enabling seamless use of pre-trained decoding models. Second, to facilitate reliable BTM learning, a Brain Functional Alignment module is proposed to perform soft cross-subject brain alignment under different visual stimuli with a multi-level brain alignment loss, uncovering fine-grained functional correspondences with high interpretability. Experiments indicate that MindAligner not only outperforms existing methods in visual decoding under data-limited conditions, but also provides valuable neuroscience insights in cross-subject functional analysis. The code will be made publicly available.

cs.CV↗

arXiv2024

Multi-Modal Latent Variables for Cross-Individual Primary Visual Cortex Modeling and Analysis

Elucidating the functional mechanisms of the primary visual cortex (V1) remains a fundamental challenge in systems neuroscience. Current computational models face two critical limitations, namely the challenge of cross-modal integration between partial neural recordings and complex visual stimuli, and the inherent variability in neural characteristics across individuals, including differences in neuron populations and firing patterns. To address these challenges, we present a multi-modal identifiable variational autoencoder (miVAE) that employs a two-level disentanglement strategy to map neural activity and visual stimuli into a unified latent space. This framework enables robust identification of cross-modal correlations through refined latent space modeling. We complement this with a novel score-based attribution analysis that traces latent variables back to their origins in the source data space. Evaluation on a large-scale mouse V1 dataset demonstrates that our method achieves state-of-the-art performance in cross-individual latent representation and alignment, without requiring subject-specific fine-tuning, and exhibits improved performance with increasing data size. Significantly, our attribution algorithm successfully identifies distinct neuronal subpopulations characterized by unique temporal patterns and stimulus discrimination properties, while simultaneously revealing stimulus regions that show specific sensitivity to edge features and luminance variations. This scalable framework offers promising applications not only for advancing V1 research but also for broader investigations in neuroscience.

q-bio.NC↗

arXiv2024

Toward Understanding BERT-Like Pre-Training for DNA Foundation Models

With the success of large-scale pre-training in language tasks, there is an increasing trend of applying it to the domain of life sciences. In particular, pre-training methods based on DNA sequences have received increasing attention because of their potential to capture general information about genes. However, existing pre-training methods for DNA sequences largely rely on direct adoptions of BERT pre-training from NLP, lacking a comprehensive understanding and a specifically tailored approach. To address this research gap, we provide the first empirical study with three insightful observations. Based on the empirical study, we notice that overlapping tokenizer can benefit the fine-tuning of downstream tasks but leads to inadequate pre-training with fast convergence. To unleash the pre-training potential, we introduce a novel approach called RandomMask, which gradually increases the task difficulty of BERT-like pre-training by continuously expanding its mask boundary, forcing the model to learn more knowledge. RandomMask is simple but effective, achieving state-of-the-art performance across 6 downstream tasks. RandomMask achieves a staggering 68.16\% in Matthew's correlation coefficient for Epigenetic Mark Prediction, a groundbreaking increase of 19.85\% over the baseline and a remarkable 3.69\% improvement over the previous state-of-the-art result.

cs.AI↗

arXiv2022

The Devil Is in the Details: Window-based Attention for Image Compression

Learned image compression methods have exhibited superior rate-distortion performance than classical image compression standards. Most existing learned image compression models are based on Convolutional Neural Networks (CNNs). Despite great contributions, a main drawback of CNN based model is that its structure is not designed for capturing local redundancy, especially the non-repetitive textures, which severely affects the reconstruction quality. Therefore, how to make full use of both global structure and local texture becomes the core problem for learning-based image compression. Inspired by recent progresses of Vision Transformer (ViT) and Swin Transformer, we found that combining the local-aware attention mechanism with the global-related feature learning could meet the expectation in image compression. In this paper, we first extensively study the effects of multiple kinds of attention mechanisms for local features learning, then introduce a more straightforward yet effective window-based local attention block. The proposed window-based attention is very flexible which could work as a plug-and-play component to enhance CNN and Transformer models. Moreover, we propose a novel Symmetrical TransFormer (STF) framework with absolute transformer blocks in the down-sampling encoder and up-sampling decoder. Extensive experimental evaluations have shown that the proposed method is effective and outperforms the state-of-the-art methods. The code is publicly available at https://github.com/Googolxx/STF.

eess.IV↗

arXiv2020

CIAN: Cross-Image Affinity Net for Weakly Supervised Semantic Segmentation

Weakly supervised semantic segmentation with only image-level labels saves large human effort to annotate pixel-level labels. Cutting-edge approaches rely on various innovative constraints and heuristic rules to generate the masks for every single image. Although great progress has been achieved by these methods, they treat each image independently and do not take account of the relationships across different images. In this paper, however, we argue that the cross-image relationship is vital for weakly supervised segmentation. Because it connects related regions across images, where supplementary representations can be propagated to obtain more consistent and integral regions. To leverage this information, we propose an end-to-end cross-image affinity module, which exploits pixel-level cross-image relationships with only image-level labels. By means of this, our approach achieves 64.3% and 65.3% mIoU on Pascal VOC 2012 validation and test set respectively, which is a new state-of-the-art result by only using image-level labels for weakly supervised semantic segmentation, demonstrating the superiority of our approach.

cs.CV↗

arXiv2019

Box-driven Class-wise Region Masking and Filling Rate Guided Loss for Weakly Supervised Semantic Segmentation

Semantic segmentation has achieved huge progress via adopting deep Fully Convolutional Networks (FCN). However, the performance of FCN based models severely rely on the amounts of pixel-level annotations which are expensive and time-consuming. To address this problem, it is a good choice to learn to segment with weak supervision from bounding boxes. How to make full use of the class-level and region-level supervisions from bounding boxes is the critical challenge for the weakly supervised learning task. In this paper, we first introduce a box-driven class-wise masking model (BCM) to remove irrelevant regions of each class. Moreover, based on the pixel-level segment proposal generated from the bounding box supervision, we could calculate the mean filling rates of each class to serve as an important prior cue, then we propose a filling rate guided adaptive loss (FR-Loss) to help the model ignore the wrongly labeled pixels in proposals. Unlike previous methods directly training models with the fixed individual segment proposals, our method can adjust the model learning with global statistical information. Thus it can help reduce the negative impacts from wrongly labeled proposals. We evaluate the proposed method on the challenging PASCAL VOC 2012 benchmark and compare with other methods. Extensive experimental results show that the proposed method is effective and achieves the state-of-the-art results.

cs.CV↗

arXiv2019

Air Quality Measurement Based on Double-Channel Convolutional Neural Network Ensemble Learning

Environmental air quality affects people's life, obtaining real-time and accurate environmental air quality has a profound guiding significance for the development of social activities. At present, environmental air quality measurement mainly adopts the method that setting air quality detector at specific monitoring points in cities and timing sampling analysis, which is easy to be restricted by time and space factors. Some air quality measurement algorithms related to deep learning mostly adopt a single convolutional neural network to train the whole image, which will ignore the difference of different parts of the image. In this paper, we propose a method for air quality measurement based on double-channel convolutional neural network ensemble learning to solve the problem of feature extraction for different parts of environmental images. Our method mainly includes two aspects: ensemble learning of double-channel convolutional neural network and self-learning weighted feature fusion. We constructed a double-channel convolutional neural network, used each channel to train different parts of the environment images for feature extraction. We propose a feature weight self-learning method, which weights and concatenates the extracted feature vectors, and uses the fused feature vectors to measure air quality. Our method can be applied to the two tasks of air quality grade measurement and air quality index (AQI) measurement. Moreover, we build an environmental image dataset of random time and location condition. The experiments show that our method can achieve nearly 82% accuracy and a small mean absolute error (MAE) on our test dataset. At the same time, through comparative experiment, we proved that our proposed method gained considerable improvement in performance compared with single channel convolutional neural network air quality measurements.

cs.CV↗