arXiv subjects

Shuang Ge

Publications and source records attributed to Shuang Ge.

14 recordsLinked to original sources

arXiv2026

Raincheck: Deferred Multimodal Prefill for Efficient Multi-Turn MLLM Inference

Multi-turn conversations with multimodal large language models (MLLMs) reuse input context, but long multimodal inputs increase time to first token (TTFT). Query-aware hard pruning reduces prefill tokens but permanently excludes information that later questions may require. We propose Raincheck, a framework for deferred multimodal prefill that decouples initial token selection from later information availability. An existing pruning method selects tokens for initial prefill; Raincheck preserves and progressively prefills unselected tokens in source order using unused compute capacity during decode. Unfinished prefill continues after answer return during available scheduling gaps. Attention visibility control and affine state mapping enable context updates after generation begins in full-attention and hybrid recurrent models. Prefill-decode fusion reduces repeated weight reads. We evaluate Qwen3-VL-8B and Qwen3.5-9B with 30% initial multimodal-token retention. Across both models and four pruning methods, Raincheck recovers on average 77.7% and 60.4% of the quality lost to matched hard pruning on MultiVerse and ConvBench, respectively. On MultiVerse, the SGLang implementation reduces mean first-turn TTFT by up to 24.1% relative to full prefill, with less than 0.5% increase in mean time per output token (TPOT).

cs.CL↗

arXiv2026

SpecOPD: Branch-Parallel On-Policy Distillation for Speculative Decoding

Speculative decoding (SD) accelerates large language model inference by reducing the sequential cost of token-by-token generation. Advanced SD methods reduce proposal cost with parallel drafters that predict entire blocks in one forward pass, but overall speedup still depends on acceptance length. On-policy distillation (OPD) can push well-trained drafters beyond acceptance-length plateaus, yet conventional pipelines collect supervision through sequential draft-and-verify rollouts. Our key insight is that on-policy supervision need not inherit these dependencies: a draft block can be supervised using only its reference prefix and draft-sampled history. We propose SpecOPD, a branch-parallel OPD framework that parallelizes draft sampling and target supervision across independent branches drawn from the evolving drafter policy at reference anchors. We pack these branches into proposal trees to share target-prefix computation, using tree masks for full attention, branch-consistent indexer groups for sparse attention, and indexed state replay for linear attention to preserve each branch's history. We train the drafter with an E2E-TV surrogate that directly targets acceptance length. Our study spans 8B full-attention (GQA), 27B full-linear (GQA--GDN), and 125B sparse-linear (QSA--GDN) targets, three parallel draft architectures (DFlash, DSpark, and DFlash V2), and four task domains (dialogue, coding, mathematics, and agentic). SpecOPD achieves up to 41.45% higher mean acceptance length, $16.09\times$ supervised-token throughput over sequential-rollout OPD under native configurations, and up to $3.56\times$ generation speedup over autoregressive decoding.

cs.AI↗

arXiv2026

A Multitask Large Reasoning Model for Molecular Science

Artificial intelligence in molecular science must move beyond pattern recognition toward chemically valid and interpretable reasoning. We present a task-adaptive large reasoning model that integrates chemical knowledge through a synergistic multispecialist architecture, chain-of-thought supervision, and molecule-informed reinforcement learning. Task-conditioned routing coordinates prediction and inference specialists across 10 molecular tasks spanning molecular description and generation, nomenclature translation, property prediction, and reaction prediction. The model outperforms more than 20 general-purpose and molecular large language models, improves aggregate performance over the base model by 50.3%, and surpasses the leading molecular multitask baseline on most tasks. Analyses of specialist representations and reasoning pathways reveal task-specific adaptation while retaining interpretable chemical inference. A case study further demonstrates an integrated workflow for central nervous system candidate generation, property screening, molecular interpretation, and retrosynthetic planning. These results demonstrate a versatile multi-task framework for knowledge-guided molecular reasoning and design, with the potential to serve as a core task engine for future molecular science agents.

cs.LG↗

arXiv2026

TailSieve: Partial-Rollout-Guided Tail Routing for LLM Rollouts

Large-scale rollouts have become a core component of modern LLM systems, spanning reinforcement learning (RL) post-training, on-policy distillation (OPD), and sampling-heavy evaluation pipelines. Unlike online serving, which is typically optimized for request-level latency and throughput, a small number of long-tail generations can dominate the end-to-end makespan of an entire rollout step. In practice, rollout requests are often routed uniformly across replicas, which can place extremely long generations inside high-concurrency decoding batches. To address this, we present TailSieve, a partial-rollout-guided framework that jointly controls tail routing and replica allocation for LLM rollouts. In an idealized setting with known completion lengths, we show that makespan-optimal routing in the long-tail regime combines tail isolation with load balancing, and that a simple top-k policy closely approximates this offline optimum. Leveraging the observation that long-tail prompts tend to remain long-tailed across policy updates, TailSieve uses partial rollouts as a training-free signal for identifying candidate tail groups. A hierarchical controller then jointly adapts the number of isolated groups and the replica split between the tail and bulk pools using collected response-work history and a measured concurrency-throughput model. TailSieve achieves up to 1.67x routing-only speedup over uniform group routing. The resulting low-concurrency tail pool further enables route-specialized speculative decoding with MTP or DFlash, achieving up to 2.59x speedup over uniform routing. Selected prompts are regenerated under the current policy, preserving on-policy generation and avoiding additional routing-induced length bias in steady state.

cs.AI↗

arXiv2026

Learning latent progression states from spatial heterogeneity in uterine histopathology

Tumor progression is accompanied by changes in architecture, morphology and microenvironmental organization, yet progression-associated heterogeneity is usually compressed into static diagnostic categories in histopathology. Here we present SpaTIE, a uterus-specific computational pathology framework that learns morphology-aware representations and organizes spatial histopathological heterogeneity into progression-associated tumor states. SpaTIE was developed using 10,426 uterine hematoxylin and eosin whole-slide images and evaluated in TCGA-UCEC and TCGA-UCS cohorts. The learned representations formed morphology manifolds, supported diagnostic, molecular and survival-related prediction tasks, and localized attention to informative tumor regions. Beyond supervised prediction, SpaTIE inferred tumor-state axes from cross-sectional morphology without temporal or molecular supervision. These morphology-derived states were spatially coherent and showed associations with clinicopathological variables and survival outcomes, while not simply recapitulating staging or diagnostic labels. Integrative multi-omics analyses linked the inferred states to DNA methylation, somatic copy-number variation, mutation, RNA-seq and RPPA profiles, highlighting molecular programs related to chromatin regulation, copy-number-associated structural variation, receptor tyrosine kinase signaling, cell adhesion, extracellular-matrix remodeling and metabolic adaptation. Progression-guided virtual perturbation further prioritized molecular features coupled to the morphology-derived state organization. Together, these findings suggest that uterine histopathology contains recoverable progression-associated tumor-state information and establish SpaTIE as a framework for connecting spatial morphology with multi-omics-informed tumor-state discovery.

cs.CV↗

arXiv2026

OmniDelta: Skill-Driven Budget Allocation for Token Compression in OmniLLMs

Emerging Omni-modal Large Language Models (OmniLLMs) enable unified understanding of text, audio, and video, but their long audio-video token sequences introduce substantial memory and inference costs. Existing compression methods mainly focus on selecting important tokens under fixed budgets, leaving the preceding budget-allocation problem underexplored. We show that direct query-to-audio/video similarity is unreliable for inter-modal budget allocation, and that uniform intra-modal budgets can miss key evidence while retaining redundant content. To address these limitations, we propose OmniDelta, a training-free, skill-driven framework that couples intent-aware inter-modal allocation with content-aware intra-modal allocation. OmniDelta first constructs audio and video skill pools to shift the fixed retained-token budget according to query demand, then reallocates modality budgets over audio segments and video frames using local complexity and temporal redundancy. The resulting local budgets can be combined with existing pruning strategies, preserving the total retained-token ratio while changing where the budget is spent. Experiments on four audio-video benchmarks with two Qwen2.5-Omni models show that OmniDelta establishes a new accuracy-efficiency Pareto frontier across pruning ratios. At 25% token retention on Qwen2.5-Omni-7B, OmniDelta reduces GPU memory by 22.0% and achieves a 1.64x end-to-end speedup over full-token inference.

cs.AI↗

arXiv2026

Draft Less, Retrieve More: Hybrid Tree Construction for Speculative Decoding

Speculative decoding (SD) accelerates large language model inference by leveraging a draft-then-verify paradigm. To maximize the acceptance rate, recent methods construct expansive draft trees, which unfortunately incur severe VRAM bandwidth and computational overheads that bottleneck end-to-end speedups. While dynamic-depth pruning can reduce this latency by removing marginal branches, it also discards potentially valid candidates, preventing the acceptance rate from reaching the upper bound of dense trees. In this paper, we identify a critical opportunity in resource allocation: the transition from dense to pruned drafting frees up significant computational budget. To break this Pareto tradeoff, we introduce Graft, a compensation framework that couples pruning and retrieval as mutually reinforcing operations. Pruning supplies sufficient budget for retrieval, while retrieval compensates for pruning-induced coverage loss and recovers accepted length. By employing a sequential `prune-then-graft' mechanism, Graft attaches highly predictive retrieved tokens into positions opened by pruning, filling the topological gaps with near-zero overhead. Graft is entirely training-free and lossless. Comprehensive evaluations show that Graft establishes a new Pareto frontier across practical deployment settings, including short-context generation, long-context generation, and large-scale models. On short-context benchmarks, it achieves up to 5.41$\times$ speedup and improves average speedup over EAGLE-3 by up to 21.8% on the large-scale Qwen3-235B. We also provide a preliminary exploration of applying Graft to the DFlash-style block drafting paradigm, offering initial evidence and insights for extending grafting beyond autoregressive draft trees.

cs.LG↗

arXiv2026

ECHO: Elastic Speculative Decoding with Sparse Gating for High-Concurrency Scenarios

Speculative Decoding promises to accelerate the inference of Large Language Models, yet its efficacy often degrades in production-grade serving. Existing evaluations typically overlook the compute-bound nature of high-concurrency regimes, where verification compute becomes the dominant bottleneck. Consequently, prior methods face a dilemma: static trees incur massive verification waste, while dynamic trees suffer from cumulative misjudgments and kernel incompatibility. To bridge this gap, we introduce ECHO, a high concurrency-oriented framework integrated into SGLang that reformulates speculative execution as a budgeted scheduling problem. Crucially, ECHO employs sparse confidence gating to manage the batch as a unified super-tree, elastically pivoting budget between depth and width to co-optimize the trade-off between reducing global verification steps and maximizing per-step efficiency. Extensive evaluations across diverse model scales-particularly the industrial-grade Qwen3-235B-demonstrate that ECHO consistently outperforms SOTA methods in both low-load and high-load scenarios, achieving up to 5.35x walltime speedup and delivering over 20% relative speedup gain.

cs.DC↗

arXiv2026

When Hidden States Drift: Can KV Caches Rescue Long-Range Speculative Decoding?

Speculative decoding accelerates LLM inference, but SOTA hidden-state-based drafters suffer from long-range decay: draft accuracy degrades as the speculative step increases. Existing work attributes this decay to train-inference mismatch and proposes test-time training (TTT) as a remedy, yet we observe that long-range decay persists even in TTT-trained drafters. We revisit long-range decay from the perspective of context information preservation. In hidden-state reuse, we argue the target hidden state acts as a biased context compression: it aggregates historical token information according to the attention query at the current position, yielding a compact representation optimized for immediate next-token prediction. This compression can suppress information less relevant to the current query but important for later speculative steps. In contrast, the target model's KV cache serves as an explicit context, retaining the complete set of token-wise KV representations. We therefore posit the KV-Reuse Hypothesis: allowing the draft model to reuse the target KV cache can provide richer signals for long-horizon drafting. To test this hypothesis, we introduce KVShot, a diagnostic framework that compares three reuse paradigms: hidden-only, KV-only, and hybrid. Extensive evaluations on Qwen3-8B show that KV-Reuse improves long-range acceptance, although end-to-end speedups remain marginal under current training pipelines. Our analysis identifies two key structural bottlenecks: shallow drafters struggle to estimate target queries accurately, and draft-side KV projections receive sparse gradient signals. These findings suggest that realizing the full potential of KV-aware decoding requires moving beyond TTT toward block-wise training paradigms. By exposing these bottlenecks, KVShot provides a foundational diagnostic testbed and a clear roadmap for designing next-generation inference architectures.

cs.CL↗

arXiv2026

GloPath: An Entity-Centric Foundation Model for Glomerular Lesion Assessment and Clinicopathological Insights

Glomerular pathology is central to the diagnosis and prognosis of renal diseases, yet the heterogeneity of glomerular morphology and fine-grained lesion patterns remain challenging for current AI approaches. We present GloPath, an entity-centric foundation model trained on over one million glomeruli extracted from 14,049 renal biopsy specimens using multi-scale and multi-view self-supervised learning. GloPath addresses two major challenges in nephropathology: glomerular lesion assessment and clinicopathological insights discovery. For lesion assessment, GloPath was benchmarked across three independent cohorts on 52 tasks, including lesion recognition, grading, few-shot classification, and cross-modality diagnosis-outperforming state-of-the-art methods in 42 tasks (80.8%). In the large-scale real-world study, it achieved an ROC-AUC of 91.51% for lesion recognition, demonstrating strong robustness in routine clinical settings. For clinicopathological insights, GloPath systematically revealed statistically significant associations between glomerular morphological parameters and clinical indicators across 224 morphology-clinical variable pairs, demonstrating its capacity to connect tissue-level pathology with patient-level outcomes. Together, these results position GloPath as a scalable and interpretable platform for glomerular lesion assessment and clinicopathological discovery, representing a step toward clinically translatable AI in renal pathology.

cs.CV↗

arXiv2024

Deep Learning in Single-Cell and Spatial Transcriptomics Data Analysis: Advances and Challenges from a Data Science Perspective

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

q-bio.GN↗

arXiv2022

BSM loss: A superior way in modeling aleatory uncertainty of fine_grained classification

Artificial intelligence(AI)-assisted method had received much attention in the risk field such as disease diagnosis. Different from the classification of disease types, it is a fine-grained task to classify the medical images as benign or malignant. However, most research only focuses on improving the diagnostic accuracy and ignores the evaluation of model reliability, which limits its clinical application. For clinical practice, calibration presents major challenges in the low-data regime extremely for over-parametrized models and inherent noises. In particular, we discovered that modeling data-dependent uncertainty is more conducive to confidence calibrations. Compared with test-time augmentation(TTA), we proposed a modified Bootstrapping loss(BS loss) function with Mixup data augmentation strategy that can better calibrate predictive uncertainty and capture data distribution transformation without additional inference time. Our experiments indicated that BS loss with Mixup(BSM) model can halve the Expected Calibration Error(ECE) compared to standard data augmentation, deep ensemble and MC dropout. The correlation between uncertainty and similarity of in-domain data is up to -0.4428 under the BSM model. Additionally, the BSM model is able to perceive the semantic distance of out-of-domain data, demonstrating high potential in real-world clinical practice.

cs.CV↗

arXiv2022

AI assisted method for efficiently generating breast ultrasound screening reports

Background: Ultrasound is one of the preferred choices for early screening of dense breast cancer. Clinically, doctors have to manually write the screening report which is time-consuming and laborious, and it is easy to miss and miswrite. Aim: We proposed a new pipeline to automatically generate AI breast ultrasound screening reports based on ultrasound images, aiming to assist doctors in improving the efficiency of clinical screening and reducing repetitive report writing. Methods: AI was used to efficiently generate personalized breast ultrasound screening preliminary reports, especially for benign and normal cases which account for the majority. Based on the preliminary AI report, doctors then make simple adjustments or corrections to quickly generate the final report. The approach has been trained and tested using a database of 4809 breast tumor instances. Results: Experimental results indicate that this pipeline improves doctors' work efficiency by up to 90%, which greatly reduces repetitive work. Conclusion: Personalized report generation is more widely recognized by doctors in clinical practice compared with non-intelligent reports based on fixed templates or containing options to fill in the blanks.

eess.IV↗

arXiv2022

MIPR:Automatic Annotation of Medical Images with Pixel Rearrangement

Most of the state-of-the-art semantic segmentation reported in recent years is based on fully supervised deep learning in the medical domain. How?ever, the high-quality annotated datasets require intense labor and domain knowledge, consuming enormous time and cost. Previous works that adopt semi?supervised and unsupervised learning are proposed to address the lack of anno?tated data through assisted training with unlabeled data and achieve good perfor?mance. Still, these methods can not directly get the image annotation as doctors do. In this paper, inspired by self-training of semi-supervised learning, we pro?pose a novel approach to solve the lack of annotated data from another angle, called medical image pixel rearrangement (short in MIPR). The MIPR combines image-editing and pseudo-label technology to obtain labeled data. As the number of iterations increases, the edited image is similar to the original image, and the labeled result is similar to the doctor annotation. Therefore, the MIPR is to get labeled pairs of data directly from amounts of unlabled data with pixel rearrange?ment, which is implemented with a designed conditional Generative Adversarial Networks and a segmentation network. Experiments on the ISIC18 show that the effect of the data annotated by our method for segmentation task is is equal to or even better than that of doctors annotations

eess.IV↗