arXiv subjects

Jiyao Liu

Publications and source records attributed to Jiyao Liu.

35 records · Page 2Linked to original sources

arXiv2025

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

cs.AI↗

arXiv2025

GOOD: Training-Free Guided Diffusion Sampling for Out-of-Distribution Detection

Recent advancements have explored text-to-image diffusion models for synthesizing out-of-distribution (OOD) samples, substantially enhancing the performance of OOD detection. However, existing approaches typically rely on perturbing text-conditioned embeddings, resulting in semantic instability and insufficient shift diversity, which limit generalization to realistic OOD. To address these challenges, we propose GOOD, a novel and flexible framework that directly guides diffusion sampling trajectories towards OOD regions using off-the-shelf in-distribution (ID) classifiers. GOOD incorporates dual-level guidance: (1) Image-level guidance based on the gradient of log partition to reduce input likelihood, drives samples toward low-density regions in pixel space. (2) Feature-level guidance, derived from k-NN distance in the classifier's latent space, promotes sampling in feature-sparse regions. Hence, this dual-guidance design enables more controllable and diverse OOD sample generation. Additionally, we introduce a unified OOD score that adaptively combines image and feature discrepancies, enhancing detection robustness. We perform thorough quantitative and qualitative analyses to evaluate the effectiveness of GOOD, demonstrating that training with samples generated by GOOD can notably enhance OOD detection performance.

cs.CV↗

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

MedQ-Bench: Evaluating and Exploring Medical Image Quality Assessment Abilities in MLLMs

Medical Image Quality Assessment (IQA) serves as the first-mile safety gate for clinical AI, yet existing approaches remain constrained by scalar, score-based metrics and fail to reflect the descriptive, human-like reasoning process central to expert evaluation. To address this gap, we introduce MedQ-Bench, a comprehensive benchmark that establishes a perception-reasoning paradigm for language-based evaluation of medical image quality with Multi-modal Large Language Models (MLLMs). MedQ-Bench defines two complementary tasks: (1) MedQ-Perception, which probes low-level perceptual capability via human-curated questions on fundamental visual attributes; and (2) MedQ-Reasoning, encompassing both no-reference and comparison reasoning tasks, aligning model evaluation with human-like reasoning on image quality. The benchmark spans five imaging modalities and over forty quality attributes, totaling 2,600 perceptual queries and 708 reasoning assessments, covering diverse image sources including authentic clinical acquisitions, images with simulated degradations via physics-based reconstructions, and AI-generated images. To evaluate reasoning ability, we propose a multi-dimensional judging protocol that assesses model outputs along four complementary axes. We further conduct rigorous human-AI alignment validation by comparing LLM-based judgement with radiologists. Our evaluation of 14 state-of-the-art MLLMs demonstrates that models exhibit preliminary but unstable perceptual and reasoning skills, with insufficient accuracy for reliable clinical use. These findings highlight the need for targeted optimization of MLLMs in medical IQA. We hope that MedQ-Bench will catalyze further exploration and unlock the untapped potential of MLLMs for medical image quality evaluation.

cs.CV↗

arXiv2025

Intern-S1: A Scientific Multimodal Foundation Model

In recent years, a plethora of open-source foundation models have emerged, achieving remarkable progress in some widely attended fields, with performance being quite close to that of closed-source models. However, in high-value but more challenging scientific professional fields, either the fields still rely on expert models, or the progress of general foundation models lags significantly compared to those in popular areas, far from sufficient for transforming scientific research and leaving substantial gap between open-source models and closed-source models in these scientific domains. To mitigate this gap and explore a step further toward Artificial General Intelligence (AGI), we introduce Intern-S1, a specialized generalist equipped with general understanding and reasoning capabilities with expertise to analyze multiple science modal data. Intern-S1 is a multimodal Mixture-of-Experts (MoE) model with 28 billion activated parameters and 241 billion total parameters, continually pre-trained on 5T tokens, including over 2.5T tokens from scientific domains. In the post-training stage, Intern-S1 undergoes offline and then online reinforcement learning (RL) in InternBootCamp, where we propose Mixture-of-Rewards (MoR) to synergize the RL training on more than 1000 tasks simultaneously. Through integrated innovations in algorithms, data, and training systems, Intern-S1 achieved top-tier performance in online RL training. On comprehensive evaluation benchmarks, Intern-S1 demonstrates competitive performance on general reasoning tasks among open-source models and significantly outperforms open-source models in scientific domains, surpassing closed-source state-of-the-art models in professional tasks, such as molecular synthesis planning, reaction condition prediction, predicting thermodynamic stabilities for crystals. Our models are available at https://huggingface.co/internlm/Intern-S1.

cs.LG↗

arXiv2025

THE-Tree: Can Tracing Historical Evolution Enhance Scientific Verification and Reasoning?

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce \textbf{THE-Tree} (\textbf{T}echnology \textbf{H}istory \textbf{E}volution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

cs.AI↗

arXiv2025

RetinaLogos: Fine-Grained Synthesis of High-Resolution Retinal Images Through Captions

The scarcity of high-quality, labelled retinal imaging data, which presents a significant challenge in the development of machine learning models for ophthalmology, hinders progress in the field. Existing methods for synthesising Colour Fundus Photographs (CFPs) largely rely on predefined disease labels, which restricts their ability to generate images that reflect fine-grained anatomical variations, subtle disease stages, and diverse pathological features beyond coarse class categories. To overcome these challenges, we first introduce an innovative pipeline that creates a large-scale, captioned retinal dataset comprising 1.4 million entries, called RetinaLogos-1400k. Specifically, RetinaLogos-1400k uses the visual language model(VLM) to describe retinal conditions and key structures, such as optic disc configuration, vascular distribution, nerve fibre layers, and pathological features. Building on this dataset, we employ a novel three-step training framework, RetinaLogos, which enables fine-grained semantic control over retinal images and accurately captures different stages of disease progression, subtle anatomical variations, and specific lesion types. Through extensive experiments, our method demonstrates superior performance across multiple datasets, with 62.07% of text-driven synthetic CFPs indistinguishable from real ones by ophthalmologists. Moreover, the synthetic data improves accuracy by 5%-10% in diabetic retinopathy grading and glaucoma detection. Codes are available at https://github.com/uni-medical/retina-text2cfp.

eess.IV↗

arXiv2025

MedAide: Information Fusion and Anatomy of Medical Intents via LLM-based Agent Collaboration

In healthcare intelligence, the ability to fuse heterogeneous, multi-intent information from diverse clinical sources is fundamental to building reliable decision-making systems. Large Language Model (LLM)-driven information interaction systems currently showing potential promise in the healthcare domain. Nevertheless, they often suffer from information redundancy and coupling when dealing with complex medical intents, leading to severe hallucinations and performance bottlenecks. To this end, we propose MedAide, an LLM-based medical multi-agent collaboration framework designed to enable intent-aware information fusion and coordinated reasoning across specialized healthcare domains. Specifically, we introduce a regularization-guided module that combines syntactic constraints with retrieval augmented generation to decompose complex queries into structured representations, facilitating fine-grained clinical information fusion and intent resolution. Additionally, a dynamic intent prototype matching module is proposed to utilize dynamic prototype representation with a semantic similarity matching mechanism to achieve adaptive recognition and updating of the agent's intent in multi-round healthcare dialogues. Ultimately, we design a rotation agent collaboration mechanism that introduces dynamic role rotation and decision-level information fusion across specialized medical agents. Extensive experiments are conducted on four medical benchmarks with composite intents. Experimental results from automated metrics and expert doctor evaluations show that MedAide outperforms current LLMs and improves their medical proficiency and strategic reasoning.

cs.CL↗

arXiv2025

MedGround-R1: Advancing Medical Image Grounding via Spatial-Semantic Rewarded Group Relative Policy Optimization

Medical Image Grounding (MIG), which involves localizing specific regions in medical images based on textual descriptions, requires models to not only perceive regions but also deduce spatial relationships of these regions. Existing Vision-Language Models (VLMs) for MIG often rely on Supervised Fine-Tuning (SFT) with large amounts of Chain-of-Thought (CoT) reasoning annotations, which are expensive and time-consuming to acquire. Recently, DeepSeek-R1 demonstrated that Large Language Models (LLMs) can acquire reasoning abilities through Group Relative Policy Optimization (GRPO) without requiring CoT annotations. In this paper, we adapt the GRPO reinforcement learning framework to VLMs for Medical Image Grounding. We propose the Spatial-Semantic Rewarded Group Relative Policy Optimization to train the model without CoT reasoning annotations. Specifically, we introduce Spatial-Semantic Rewards, which combine spatial accuracy reward and semantic consistency reward to provide nuanced feedback for both spatially positive and negative completions. Additionally, we propose to use the Chain-of-Box template, which integrates visual information of referring bounding boxes into the reasoning process, enabling the model to explicitly reason about spatial regions during intermediate steps. Experiments on three datasets MS-CXR, ChestX-ray8, and M3D-RefSeg demonstrate that our method achieves state-of-the-art performance in Medical Image Grounding. Ablation studies further validate the effectiveness of each component in our approach. Code, checkpoints, and datasets are available at https://github.com/bio-mlhui/MedGround-R1

cs.LG↗

arXiv2025

Multi-modal MRI Translation via Evidential Regression and Distribution Calibration

Multi-modal Magnetic Resonance Imaging (MRI) translation leverages information from source MRI sequences to generate target modalities, enabling comprehensive diagnosis while overcoming the limitations of acquiring all sequences. While existing deep-learning-based multi-modal MRI translation methods have shown promising potential, they still face two key challenges: 1) lack of reliable uncertainty quantification for synthesized images, and 2) limited robustness when deployed across different medical centers. To address these challenges, we propose a novel framework that reformulates multi-modal MRI translation as a multi-modal evidential regression problem with distribution calibration. Our approach incorporates two key components: 1) an evidential regression module that estimates uncertainties from different source modalities and an explicit distribution mixture strategy for transparent multi-modal fusion, and 2) a distribution calibration mechanism that adapts to source-target mapping shifts to ensure consistent performance across different medical centers. Extensive experiments on three datasets from the BraTS2023 challenge demonstrate that our framework achieves superior performance and robustness across domains.

eess.IV↗

arXiv2025

GMAI-VL-R1: Harnessing Reinforcement Learning for Multimodal Medical Reasoning

Recent advances in general medical AI have made significant strides, but existing models often lack the reasoning capabilities needed for complex medical decision-making. This paper presents GMAI-VL-R1, a multimodal medical reasoning model enhanced by reinforcement learning (RL) to improve its reasoning abilities. Through iterative training, GMAI-VL-R1 optimizes decision-making, significantly boosting diagnostic accuracy and clinical support. We also develop a reasoning data synthesis method, generating step-by-step reasoning data via rejection sampling, which further enhances the model's generalization. Experimental results show that after RL training, GMAI-VL-R1 excels in tasks such as medical image diagnosis and visual question answering. While the model demonstrates basic memorization with supervised fine-tuning, RL is crucial for true generalization. Our work establishes new evaluation benchmarks and paves the way for future advancements in medical reasoning models. Code, data, and model will be released at \href{https://github.com/uni-medical/GMAI-VL-R1}{this link}.

cs.CV↗

arXiv2025

Adaptive Data Augmentation with NaturalSpeech3 for Far-field Speaker Verification

The scarcity of speaker-annotated far-field speech presents a significant challenge in developing high-performance far-field speaker verification (SV) systems. While data augmentation using large-scale near-field speech has been a common strategy to address this limitation, the mismatch in acoustic environments between near-field and far-field speech significantly hinders the improvement of far-field SV effectiveness. In this paper, we propose an adaptive speech augmentation approach leveraging NaturalSpeech3, a pre-trained foundation text-to-speech (TTS) model, to convert near-field speech into far-field speech by incorporating far-field acoustic ambient noise for data augmentation. Specifically, we utilize FACodec from NaturalSpeech3 to decompose the speech waveform into distinct embedding subspaces-content, prosody, speaker, and residual (acoustic details) embeddings-and reconstruct the speech waveform from these disentangled representations. In our method, the prosody, content, and residual embeddings of far-field speech are combined with speaker embeddings from near-field speech to generate augmented pseudo far-field speech that maintains the speaker identity from the out-domain near-field speech while preserving the acoustic environment of the in-domain far-field speech. This approach not only serves as an effective strategy for augmenting training data for far-field speaker verification but also extends to cross-data augmentation for enrollment and test speech in evaluation trials.Experimental results on FFSVC demonstrate that the adaptive data augmentation method significantly outperforms traditional approaches, such as random noise addition and reverberation, as well as other competitive data augmentation strategies.

cs.SD↗

arXiv2025

Subject Disentanglement Neural Network for Speech Envelope Reconstruction from EEG

Reconstructing speech envelopes from EEG signals is essential for exploring neural mechanisms underlying speech perception. Yet, EEG variability across subjects and physiological artifacts complicate accurate reconstruction. To address this problem, we introduce Subject Disentangling Neural Network (SDN-Net), which disentangles subject identity information from reconstructed speech envelopes to enhance cross-subject reconstruction accuracy. SDN-Net integrates three key components: MLA-Codec, MPN-MI, and CTA-MTDNN. The MLA-Codec, a fully convolutional neural network, decodes EEG signals into speech envelopes. The CTA-MTDNN module, a multi-scale time-delay neural network with channel and temporal attention, extracts subject identity features from EEG signals. Lastly, the MPN-MI module, a mutual information estimator with a multi-layer perceptron, supervises the removal of subject identity information from the reconstructed speech envelope. Experiments on the Auditory EEG Decoding Dataset demonstrate that SDN-Net achieves superior performance in inner- and cross-subject speech envelope reconstruction compared to recent state-of-the-art methods.

eess.SP↗

arXiv2023

Relate auditory speech to EEG by shallow-deep attention-based network

Electroencephalography (EEG) plays a vital role in detecting how brain responses to different stimulus. In this paper, we propose a novel Shallow-Deep Attention-based Network (SDANet) to classify the correct auditory stimulus evoking the EEG signal. It adopts the Attention-based Correlation Module (ACM) to discover the connection between auditory speech and EEG from global aspect, and the Shallow-Deep Similarity Classification Module (SDSCM) to decide the classification result via the embeddings learned from the shallow and deep layers. Moreover, various training strategies and data augmentation are used to boost the model robustness. Experiments are conducted on the dataset provided by Auditory EEG challenge (ICASSP Signal Processing Grand Challenge 2023). Results show that the proposed model has a significant gain over the baseline on the match-mismatch track.

cs.SD↗

arXiv2022

Orientation recognition and correction of Cardiac MRI with deep neural network

In this paper, the problem of orientation correction in cardiac MRI images is investigated and a framework for orientation recognition via deep neural networks is proposed. For multi-modality MRI, we introduce a transfer learning strategy to transfer our proposed model from single modality to multi-modality. We embed the proposed network into the orientation correction command-line tool, which can implement orientation correction on 2D DICOM and 3D NIFTI images. Our source code, network models and tools are available at https://github.com/Jy-stdio/MSCMR_orient/

eess.IV↗

arXiv2022

Spatial-temporal Transformers for EEG Emotion Recognition

Electroencephalography (EEG) is a popular and effective tool for emotion recognition. However, the propagation mechanisms of EEG in the human brain and its intrinsic correlation with emotions are still obscure to researchers. This work proposes four variant transformer frameworks~(spatial attention, temporal attention, sequential spatial-temporal attention and simultaneous spatial-temporal attention) for EEG emotion recognition to explore the relationship between emotion and spatial-temporal EEG features. Specifically, spatial attention and temporal attention are to learn the topological structure information and time-varying EEG characteristics for emotion recognition respectively. Sequential spatial-temporal attention does the spatial attention within a one-second segment and temporal attention within one sample sequentially to explore the influence degree of emotional stimulation on EEG signals of diverse EEG electrodes in the same temporal segment. The simultaneous spatial-temporal attention, whose spatial and temporal attention are performed simultaneously, is used to model the relationship between different spatial features in different time segments. The experimental results demonstrate that simultaneous spatial-temporal attention leads to the best emotion recognition accuracy among the design choices, indicating modeling the correlation of spatial and temporal features of EEG signals is significant to emotion recognition.

cs.RO↗

arXiv2021

Positional-Spectral-Temporal Attention in 3D Convolutional Neural Networks for EEG Emotion Recognition

Recognizing the feelings of human beings plays a critical role in our daily communication. Neuroscience has demonstrated that different emotion states present different degrees of activation in different brain regions, EEG frequency bands and temporal stamps. In this paper, we propose a novel structure to explore the informative EEG features for emotion recognition. The proposed module, denoted by PST-Attention, consists of Positional, Spectral and Temporal Attention modules to explore more discriminative EEG features. Specifically, the Positional Attention module is to capture the activate regions stimulated by different emotions in the spatial dimension. The Spectral and Temporal Attention modules assign the weights of different frequency bands and temporal slices respectively. Our method is adaptive as well as efficient which can be fit into 3D Convolutional Neural Networks (3D-CNN) as a plug-in module. We conduct experiments on two real-world datasets. 3D-CNN combined with our module achieves promising results and demonstrate that the PST-Attention is able to capture stable patterns for emotion recognition from EEG.

eess.SP↗