arXiv subjects

Siyuan Yan

Publications and source records attributed to Siyuan Yan.

At least 19 recordsLinked to original sources

arXiv2026

Latent Ordinal Evidence, Misaligned Outputs: Inference-Time Ordinal Lens Alignment for Multimodal LLMs

Multimodal LLMs apply the language model interface to visual inputs, where ordinal regression tasks such as age estimation, image quality assessment, and disease grading require autoregressive decisions over ordered class labels. We ask whether MLLMs reliably convert internal ordinal evidence into ordered digit-token outputs. Across four ordinal benchmarks and four MLLM backbones, ordinal labels are linearly recoverable from hidden states with Spearman correlation up to 0.938, and a task-designed prompt further sharpens this structure. Yet native digit-token outputs weakly expose it: the unembedding matrix filters the ordinal direction, and the digit-token row space retains below 1.15% across all 16 model-dataset combinations, with a 16 to 77 absolute-point accuracy gap between linear-probe and native outputs. We introduce Ordinal Lens Alignment (OLA), a frozen-backbone inference-time method that trains lightweight W_S-anchored lenses on mid-to-deep decoder layers, fuses them into an ordinal distribution, and corrects only digit-token logits at generation. OLA outperforms the SOTA LoRA-tuned OrderChain baseline in most settings while keeping the MLLM frozen, surpasses discriminative ordinal baselines in most cells, and improves over an offline lens in every setting.

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arXiv2026

NeRD: Neuro-Symbolic Rule Distillation for Efficient Ontology-Grounded Chain-of-Thought in Medical Image Diagnosis

Interpretability is essential for trustworthy medical image diagnosis. However, existing concept-driven interpretable methods have key limitations: Concept Bottleneck Models (CBMs) require scoring all predefined concepts at inference time and for manual intervention, imposing a substantial burden on clinicians, while rationale-based generative approaches often select concepts by class discriminability, which can drift from diagnostic ontologies. To address these issues, we propose Neuro-Symbolic Rule Distillation (NeRD), a framework that produces efficient, ontology-grounded reasoning chains that are sufficient yet non-redundant, without manually crafting diagnostic rules. Experiments on two skin datasets demonstrate strong diagnostic performance and interpretability, and blinded expert evaluation confirms the clinical plausibility of NeRD rationales. Our method further enables a first expert-in-the-loop study for Multimodal Chain-of-Thought-based diagnosis, achieving efficient and effective concept-level intervention.

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arXiv2026

DermAgent: A Self-Reflective Agentic System for Dermatological Image Analysis with Multi-Tool Reasoning and Traceable Decision-Making

Dermatological diagnosis requires integrating fine-grained visual perception with expert clinical knowledge. Although Multimodal Large Language Models (MLLMs) facilitate interactive medical image analysis, their application in dermatology is hindered by insufficient domain-specific grounding and hallucinations. To address these issues, we propose DermAgent, a collaborative multi-tool agent that orchestrates seven specialized vision and language modules within a Plan-Execute-Reflect framework. DermAgent delivers stepwise, traceable diagnostic reasoning through three core components. First, it employs complementary visual perception tools for comprehensive morphological description, dermoscopic concept annotation, and disease diagnosis. Second, to overcome the lack of domain prior, a dual-modality retrieval module anchors every prediction in external evidence by cross-referencing 413,210 diagnosed image cases and 3,199 clinical guideline chunks. To further mitigate hallucinations, a deterministic critic module conducts strict post-hoc auditing via confidence, coverage, and conflict gates, automatically detecting inter-source disagreements to trigger targeted self-correction. Extensive experiments on five dermatology benchmarks demonstrate that DermAgent consistently outperforms state-of-the-art MLLMs and medical agent baselines across zero-shot fine-grained disease diagnosis, concept annotation, and clinical captioning tasks, exceeding GPT-4o by 17.6% in skin disease diagnostic accuracy and 3.15% in captioning ROUGE-L. Our code is available at https://github.com/YizeezLiu/DermAgent.

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arXiv2026

A Vision-Language Foundation Model for Zero-shot Clinical Collaboration and Automated Concept Discovery in Dermatology

Medical foundation models have shown promise in controlled benchmarks, yet widespread deployment remains hindered by reliance on task-specific fine-tuning. Here, we introduce DermFM-Zero, a dermatology vision-language foundation model trained via masked latent modelling and contrastive learning on over 4 million multimodal data points. We evaluated DermFM-Zero across 20 benchmarks spanning zero-shot diagnosis and multimodal retrieval, achieving state-of-the-art performance without task-specific adaptation. We further evaluated its zero-shot capabilities in three multinational reader studies involving over 1,100 clinicians. In primary care settings, AI assistance enabled general practitioners to nearly double their differential diagnostic accuracy across 98 skin conditions. In specialist settings, the model significantly outperformed board-certified dermatologists in multimodal skin cancer assessment. In collaborative workflows, AI assistance enabled non-experts to surpass unassisted experts while improving management appropriateness. Finally, we show that DermFM-Zero's latent representations are interpretable: sparse autoencoders unsupervisedly disentangle clinically meaningful concepts that outperform predefined-vocabulary approaches and enable targeted suppression of artifact-induced biases, enhancing robustness without retraining. These findings demonstrate that a foundation model can provide effective, safe, and transparent zero-shot clinical decision support.

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arXiv2026

DermoGPT: Open Weights and Open Data for Morphology-Grounded Dermatological Reasoning MLLMs

Multimodal Large Language Models (MLLMs) show promise for medical applications, yet progress in dermatology lags due to limited training data, narrow task coverage, and lack of clinically-grounded supervision that mirrors expert diagnostic workflows. We present a comprehensive framework to address these gaps. First, we introduce DermoInstruct, a large-scale morphology-anchored instruction corpus comprising 211,243 images and 772,675 trajectories across five task formats, capturing the complete diagnostic pipeline from morphological observation and clinical reasoning to final diagnosis. Second, we establish DermoBench, a rigorous benchmark evaluating 11 tasks across four clinical axes: Morphology, Diagnosis, Reasoning, and Fairness, including a challenging subset of 3,600 expert-verified open-ended instances and human performance baselines. Third, we develop DermoGPT, a dermatology reasoning MLLM trained via supervised fine-tuning followed by our Morphologically-Anchored Visual-Inference-Consistent (MAVIC) reinforcement learning objective, which enforces consistency between visual observations and diagnostic conclusions. At inference, we deploy Confidence-Consistency Test-time adaptation (CCT) for robust predictions. Experiments show DermoGPT significantly outperforms 16 representative baselines across all axes, achieving state-of-the-art performance while substantially narrowing the human-AI gap. DermoInstruct, DermoBench and DermoGPT will be made publicly available at https://github.com/mendicant04/DermoGPT upon acceptance.

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arXiv2025

Multi-Aspect Knowledge-Enhanced Medical Vision-Language Pretraining with Multi-Agent Data Generation

Vision-language pretraining (VLP) has emerged as a powerful paradigm in medical image analysis, enabling representation learning from large-scale image-text pairs without relying on expensive manual annotations. However, existing methods often struggle with the noise inherent in web-collected data and the complexity of unstructured long medical texts. To address these challenges, we propose a novel VLP framework integrating a Multi-Agent data GENeration (MAGEN) system and Ontology-based Multi-Aspect Knowledge-Enhanced (O-MAKE) pretraining. First, MAGEN enhances data quality by synthesizing knowledge-enriched descriptions via a foundation model-assisted captioning and retrieval-based verification pipeline. Second, O-MAKE addresses the difficulty of learning from long, unstructured texts by decomposing them into distinct knowledge aspects. This facilitates fine-grained alignment at both global and patch levels, while explicitly modeling medical concept relationships through ontology-guided mechanisms. We validate our framework in the field of dermatology, where comprehensive experiments demonstrate the effectiveness of each component. Our approach achieves state-of-the-art zero-shot performance on disease classification and cross-modal retrieval tasks across eight datasets. Our code and the augmented dataset Derm1M-AgentAug, comprising over 400k skin-image-text pairs, will be released at https://github.com/SiyuanYan1/Derm1M.

cs.CV↗

arXiv2025

Trustworthy and Fair SkinGPT-R1 for Democratizing Dermatological Reasoning across Diverse Ethnicities

The clinical translation of dermatological AI is hindered by opaque reasoning and systematic performance disparities across skin tones. Here we present SkinGPT-R1, a multimodal large language model that integrates chain-of-thought diagnostic reasoning with a fairness-aware mixture-of-experts architecture for interpretable and equitable skin disease diagnosis. Through parameter-efficient adaptation of a frozen reasoning backbone, SkinGPT-R1 generates structured diagnostic reports comprising visual findings, differential reasoning, and final diagnosis. Across seven external datasets spanning diverse pathologies and imaging conditions, SkinGPT-R1 achieves state-of-the-art accuracy on six benchmarks, including 82.50\% on a challenging 40-class long-tail classification task (+19.30\% over leading baselines). Blinded evaluation by five board-certified dermatologists on 1,000 phenotypically balanced cases yields a mean score of 3.6 out of 5, with the highest ratings in safety (3.8) and reasoning coherence (3.6), indicating that the generated rationales are clinically safe, logically grounded, and suitable for supporting diagnostic decision-making. Critically, SkinGPT-R1 mitigates algorithmic bias across the full Fitzpatrick spectrum, achieving a robust worst-group performance of 41.40\% on the Fitz17k benchmark and a five-fold relative improvement in lower-bound accuracy on the DDI dataset compared to standard multimodal baselines. These results establish a framework for trustworthy, fair, and explainable AI-assisted dermatological diagnosis.

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arXiv2025

Adamas: Hadamard Sparse Attention for Efficient Long-Context Inference

Large language models (LLMs) now support context windows of hundreds of thousands to millions of tokens, enabling applications such as long-document summarization, large-scale code synthesis, multi-document question answering and persistent multi-turn dialogue. However, such extended contexts exacerbate the quadratic cost of self-attention, leading to severe latency in autoregressive decoding. Existing sparse attention methods alleviate these costs but rely on heuristic patterns that struggle to recall critical key-value (KV) pairs for each query, resulting in accuracy degradation. We introduce Adamas, a lightweight yet highly accurate sparse attention mechanism designed for long-context inference. Adamas applies the Hadamard transform, bucketization and 2-bit compression to produce compact representations, and leverages Manhattan-distance estimation for efficient top-k selections. Experiments show that Adamas matches the accuracy of full attention with only a 64-token budget, achieves near-lossless performance at 128, and supports up to 8x higher sparsity than prior state-of-the-art (SOTA) methods while delivering up to 4.4x self-attention and 1.5x end-to-end speedups on 32K-length sequences. Remarkably, Adamas attains comparable or even lower perplexity than full attention, underscoring its effectiveness in maintaining accuracy under aggressive sparsity.

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arXiv2025

WISE: Weak-Supervision-Guided Step-by-Step Explanations for Multimodal LLMs in Image Classification

Multimodal Large Language Models (MLLMs) have shown promise in visual-textual reasoning, with Multimodal Chain-of-Thought (MCoT) prompting significantly enhancing interpretability. However, existing MCoT methods rely on rationale-rich datasets and largely focus on inter-object reasoning, overlooking the intra-object understanding crucial for image classification. To address this gap, we propose WISE, a Weak-supervision-guided Step-by-step Explanation method that augments any image classification dataset with MCoTs by reformulating the concept-based representations from Concept Bottleneck Models (CBMs) into concise, interpretable reasoning chains under weak supervision. Experiments across ten datasets show that our generated MCoTs not only improve interpretability by 37% but also lead to gains in classification accuracy when used to fine-tune MLLMs. Our work bridges concept-based interpretability and generative MCoT reasoning, providing a generalizable framework for enhancing MLLMs in fine-grained visual understanding.

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arXiv2025

Dr.V: A Hierarchical Perception-Temporal-Cognition Framework to Diagnose Video Hallucination by Fine-grained Spatial-Temporal Grounding

Recent advancements in large video models (LVMs) have significantly enhance video understanding. However, these models continue to suffer from hallucinations, producing content that conflicts with input videos. To address this issue, we propose Dr.V, a hierarchical framework covering perceptive, temporal, and cognitive levels to diagnose video hallucination by fine-grained spatial-temporal grounding. Dr.V comprises of two key components: a benchmark dataset Dr.V-Bench and a satellite video agent Dr.V-Agent. Dr.V-Bench includes 10k instances drawn from 4,974 videos spanning diverse tasks, each enriched with detailed spatial-temporal annotation. Dr.V-Agent detects hallucinations in LVMs by systematically applying fine-grained spatial-temporal grounding at the perceptive and temporal levels, followed by cognitive level reasoning. This step-by-step pipeline mirrors human-like video comprehension and effectively identifies hallucinations. Extensive experiments demonstrate that Dr.V-Agent is effective in diagnosing hallucination while enhancing interpretability and reliability, offering a practical blueprint for robust video understanding in real-world scenarios. All our data and code are available at https://github.com/Eurekaleo/Dr.V.

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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.

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arXiv2025

Controllable Skin Synthesis via Lesion-Focused Vector Autoregression Model

Skin images from real-world clinical practice are often limited, resulting in a shortage of training data for deep-learning models. While many studies have explored skin image synthesis, existing methods often generate low-quality images and lack control over the lesion's location and type. To address these limitations, we present LF-VAR, a model leveraging quantified lesion measurement scores and lesion type labels to guide the clinically relevant and controllable synthesis of skin images. It enables controlled skin synthesis with specific lesion characteristics based on language prompts. We train a multiscale lesion-focused Vector Quantised Variational Auto-Encoder (VQVAE) to encode images into discrete latent representations for structured tokenization. Then, a Visual AutoRegressive (VAR) Transformer trained on tokenized representations facilitates image synthesis. Lesion measurement from the lesion region and types as conditional embeddings are integrated to enhance synthesis fidelity. Our method achieves the best overall FID score (average 0.74) among seven lesion types, improving upon the previous state-of-the-art (SOTA) by 6.3%. The study highlights our controllable skin synthesis model's effectiveness in generating high-fidelity, clinically relevant synthetic skin images. Our framework code is available at https://github.com/echosun1996/LF-VAR.

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arXiv2025

MAKE: Multi-Aspect Knowledge-Enhanced Vision-Language Pretraining for Zero-shot Dermatological Assessment

Dermatological diagnosis represents a complex multimodal challenge that requires integrating visual features with specialized clinical knowledge. While vision-language pretraining (VLP) has advanced medical AI, its effectiveness in dermatology is limited by text length constraints and the lack of structured texts. In this paper, we introduce MAKE, a Multi-Aspect Knowledge-Enhanced vision-language pretraining framework for zero-shot dermatological tasks. Recognizing that comprehensive dermatological descriptions require multiple knowledge aspects that exceed standard text constraints, our framework introduces: (1) a multi-aspect contrastive learning strategy that decomposes clinical narratives into knowledge-enhanced sub-texts through large language models, (2) a fine-grained alignment mechanism that connects subcaptions with diagnostically relevant image features, and (3) a diagnosis-guided weighting scheme that adaptively prioritizes different sub-captions based on clinical significance prior. Through pretraining on 403,563 dermatological image-text pairs collected from education resources, MAKE significantly outperforms state-of-the-art VLP models on eight datasets across zero-shot skin disease classification, concept annotation, and cross-modal retrieval tasks. Our code will be made publicly available at https: //github.com/SiyuanYan1/MAKE.

cs.CV↗

arXiv2025

Scaling Laws for Speculative Decoding

The escalating demand for efficient decoding in large language models (LLMs) is particularly critical for reasoning-intensive architectures like OpenAI-o3 and DeepSeek-R1, which depend on extended chain-of-thought reasoning. This study investigates speculative decoding techniques through dense LLM architectures to establish foundational insights for accelerating reasoning tasks. While speculative decoding methods leveraging parallel draft-verification cycles have emerged as promising acceleration techniques, the scaling laws governing decoding efficiency remain under-explored compared to conventional backbone LLMs developed through Pretraining->SFT->RLHF training paradigms. In this work, we discover Log-linear Scaling Laws (Theorem 1.1, 1.2 and 1.3) governing draft model acceptance rate (or decoding speed) across three dimensions: pretraining token volume, draft model capacity, and decoding batch size. Building on these laws, we achieve Scylla, which coordinates multi-dimensional scaling for popular LLMs (Llama2/3, Qwen2.5). Empirical validation shows Scylla achieves 1.5-2.2 higher acceptance rate than EAGLE2 and 0.3 higher than EAGLE3 at temperature T = 0, with peak performance gains on summarization and QA tasks (Figure 2). Industrial inference engine deployments demonstrate 2X decoding throughput improvements over EAGLE2 (Table 5), validating the transformative potential of systematic scaling for efficient LLM inference. Code will be released later.

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arXiv2025

Derm1M: A Million-scale Vision-Language Dataset Aligned with Clinical Ontology Knowledge for Dermatology

The emergence of vision-language models has transformed medical AI, enabling unprecedented advances in diagnostic capability and clinical applications. However, progress in dermatology has lagged behind other medical domains due to the lack of standard image-text pairs. Existing dermatological datasets are limited in both scale and depth, offering only single-label annotations across a narrow range of diseases instead of rich textual descriptions, and lacking the crucial clinical context needed for real-world applications. To address these limitations, we present Derm1M, the first large-scale vision-language dataset for dermatology, comprising 1,029,761 image-text pairs. Built from diverse educational resources and structured around a standard ontology collaboratively developed by experts, Derm1M provides comprehensive coverage for over 390 skin conditions across four hierarchical levels and 130 clinical concepts with rich contextual information such as medical history, symptoms, and skin tone. To demonstrate Derm1M potential in advancing both AI research and clinical application, we pretrained a series of CLIP-like models, collectively called DermLIP, on this dataset. The DermLIP family significantly outperforms state-of-the-art foundation models on eight diverse datasets across multiple tasks, including zero-shot skin disease classification, clinical and artifacts concept identification, few-shot/full-shot learning, and cross-modal retrieval. Our dataset and code will be publicly available at https://github.com/SiyuanYan1/Derm1M upon acceptance.

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arXiv2024

OphCLIP: Hierarchical Retrieval-Augmented Learning for Ophthalmic Surgical Video-Language Pretraining

Surgical practice involves complex visual interpretation, procedural skills, and advanced medical knowledge, making surgical vision-language pretraining (VLP) particularly challenging due to this complexity and the limited availability of annotated data. To address the gap, we propose OphCLIP, a hierarchical retrieval-augmented vision-language pretraining framework specifically designed for ophthalmic surgical workflow understanding. OphCLIP leverages the OphVL dataset we constructed, a large-scale and comprehensive collection of over 375K hierarchically structured video-text pairs with tens of thousands of different combinations of attributes (surgeries, phases/operations/actions, instruments, medications, as well as more advanced aspects like the causes of eye diseases, surgical objectives, and postoperative recovery recommendations, etc). These hierarchical video-text correspondences enable OphCLIP to learn both fine-grained and long-term visual representations by aligning short video clips with detailed narrative descriptions and full videos with structured titles, capturing intricate surgical details and high-level procedural insights, respectively. Our OphCLIP also designs a retrieval-augmented pretraining framework to leverage the underexplored large-scale silent surgical procedure videos, automatically retrieving semantically relevant content to enhance the representation learning of narrative videos. Evaluation across 11 datasets for phase recognition and multi-instrument identification shows OphCLIP's robust generalization and superior performance.

cs.CV↗

arXiv2024

A Multimodal Vision Foundation Model for Clinical Dermatology

Diagnosing and treating skin diseases require advanced visual skills across domains and the ability to synthesize information from multiple imaging modalities. While current deep learning models excel at specific tasks like skin cancer diagnosis from dermoscopic images, they struggle to meet the complex, multimodal requirements of clinical practice. Here, we introduce PanDerm, a multimodal dermatology foundation model pretrained through self-supervised learning on over 2 million real-world skin disease images from 11 clinical institutions across 4 imaging modalities. We evaluated PanDerm on 28 diverse benchmarks, including skin cancer screening, risk stratification, differential diagnosis of common and rare skin conditions, lesion segmentation, longitudinal monitoring, and metastasis prediction and prognosis. PanDerm achieved state-of-the-art performance across all evaluated tasks, often outperforming existing models when using only 10% of labeled data. We conducted three reader studies to assess PanDerm's potential clinical utility. PanDerm outperformed clinicians by 10.2% in early-stage melanoma detection through longitudinal analysis, improved clinicians' skin cancer diagnostic accuracy by 11% on dermoscopy images, and enhanced non-dermatologist healthcare providers' differential diagnosis by 16.5% across 128 skin conditions on clinical photographs. These results demonstrate PanDerm's potential to improve patient care across diverse clinical scenarios and serve as a model for developing multimodal foundation models in other medical specialties, potentially accelerating the integration of AI support in healthcare. The code can be found at https://github.com/SiyuanYan1/PanDerm.

cs.CV↗

arXiv2024

MONICA: Benchmarking on Long-tailed Medical Image Classification

Long-tailed learning is considered to be an extremely challenging problem in data imbalance learning. It aims to train well-generalized models from a large number of images that follow a long-tailed class distribution. In the medical field, many diagnostic imaging exams such as dermoscopy and chest radiography yield a long-tailed distribution of complex clinical findings. Recently, long-tailed learning in medical image analysis has garnered significant attention. However, the field currently lacks a unified, strictly formulated, and comprehensive benchmark, which often leads to unfair comparisons and inconclusive results. To help the community improve the evaluation and advance, we build a unified, well-structured codebase called Medical OpeN-source Long-taIled ClassifiCAtion (MONICA), which implements over 30 methods developed in relevant fields and evaluated on 12 long-tailed medical datasets covering 6 medical domains. Our work provides valuable practical guidance and insights for the field, offering detailed analysis and discussion on the effectiveness of individual components within the inbuilt state-of-the-art methodologies. We hope this codebase serves as a comprehensive and reproducible benchmark, encouraging further advancements in long-tailed medical image learning. The codebase is publicly available on https://github.com/PyJulie/MONICA.

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