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Yuan Cheng

Publications and source records attributed to Yuan Cheng.

At least 73 records · Page 4Linked to original sources

Efficient Network Automatic Relevance Determination

We propose Network Automatic Relevance Determination (NARD), an extension of ARD for linearly probabilistic models, to simultaneously model sparse relationships between inputs $X \in \mathbb R^{d \times N}$ and outputs $Y \in \mathbb R^{m \times N}$, while capturing the correlation structure among the $Y$. NARD employs a matrix normal prior which contains a sparsity-inducing parameter to identify and discard irrelevant features, thereby promoting sparsity in the model. Algorithmically, it iteratively updates both the precision matrix and the relationship between $Y$ and the refined inputs. To mitigate the computational inefficiencies of the $\mathcal O(m^3 + d^3)$ cost per iteration, we introduce Sequential NARD, which evaluates features sequentially, and a Surrogate Function Method, leveraging an efficient approximation of the marginal likelihood and simplifying the calculation of determinant and inverse of an intermediate matrix. Combining the Sequential update with the Surrogate Function method further reduces computational costs. The computational complexity per iteration for these three methods is reduced to $\mathcal O(m^3+p^3)$, $\mathcal O(m^3 + d^2)$, $\mathcal O(m^3+p^2)$, respectively, where $p \ll d$ is the final number of features in the model. Our methods demonstrate significant improvements in computational efficiency with comparable performance on both synthetic and real-world datasets.

cs.AI↗

Exploiting Layer Normalization Fine-tuning in Visual Transformer Foundation Models for Classification

LayerNorm is pivotal in Vision Transformers (ViTs), yet its fine-tuning dynamics under data scarcity and domain shifts remain underexplored. This paper shows that shifts in LayerNorm parameters after fine-tuning (LayerNorm shifts) are indicative of the transitions between source and target domains; its efficacy is contingent upon the degree to which the target training samples accurately represent the target domain, as quantified by our proposed Fine-tuning Shift Ratio ($FSR$). Building on this, we propose a simple yet effective rescaling mechanism using a scalar $λ$ that is negatively correlated to $FSR$ to align learned LayerNorm shifts with those ideal shifts achieved under fully representative data, combined with a cyclic framework that further enhances the LayerNorm fine-tuning. Extensive experiments across natural and pathological images, in both in-distribution (ID) and out-of-distribution (OOD) settings, and various target training sample regimes validate our framework. Notably, OOD tasks tend to yield lower $FSR$ and higher $λ$ in comparison to ID cases, especially with scarce data, indicating under-represented target training samples. Moreover, ViTFs fine-tuned on pathological data behave more like ID settings, favoring conservative LayerNorm updates. Our findings illuminate the underexplored dynamics of LayerNorm in transfer learning and provide practical strategies for LayerNorm fine-tuning.

cs.CV↗

Towards a Universal 3D Medical Multi-modality Generalization via Learning Personalized Invariant Representation

Variations in medical imaging modalities and individual anatomical differences pose challenges to cross-modality generalization in multi-modal tasks. Existing methods often concentrate exclusively on common anatomical patterns, thereby neglecting individual differences and consequently limiting their generalization performance. This paper emphasizes the critical role of learning individual-level invariance, i.e., personalized representation $\mathbb{X}_h$, to enhance multi-modality generalization under both homogeneous and heterogeneous settings. It reveals that mappings from individual biological profile to different medical modalities remain static across the population, which is implied in the personalization process. We propose a two-stage approach: pre-training with invariant representation $\mathbb{X}_h$ for personalization, then fine-tuning for diverse downstream tasks. We provide both theoretical and empirical evidence demonstrating the feasibility and advantages of personalization, showing that our approach yields greater generalizability and transferability across diverse multi-modal medical tasks compared to methods lacking personalization. Extensive experiments further validate that our approach significantly enhances performance in various generalization scenarios.

cs.CV↗

Widespread remote introgression in the grass genomes

Genetic transfers are pervasive across both prokaryotes and eukaryotes, encompassing canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, here defined as remote introgression (RI), has remained poorly explored in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for RI event detection, and apply it to a comprehensive dataset of 122 grass genomes. Our analysis identifies 622 RI events originating from 543 distinct homologous genes, revealing distinct characteristics among grass subfamilies. Specifically, the subfamily Pooideae exhibits the highest number of introgressed genes while Bambusoideae contains the lowest. Comparisons among accepted genes, their donor copies and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation, with significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in a Chloridoideae species Cleistogenes songorica, which is potentially associated with its exceptional drought tolerance. Furthermore, we provide compelling evidence that RI has contributed to the origin and diversification of biosynthetic gene clusters of gramine, a defensive alkaloid chemical, across grass species. Collectively, our study establishes a robust method for RI detection and highlights its critical role in adaptive evolution.

q-bio.PE↗

PAST: A multimodal single-cell foundation model for histopathology and spatial transcriptomics in cancer

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

q-bio.QM↗

Structure-aware Semantic Discrepancy and Consistency for 3D Medical Image Self-supervised Learning

3D medical image self-supervised learning (mSSL) holds great promise for medical analysis. Effectively supporting broader applications requires considering anatomical structure variations in location, scale, and morphology, which are crucial for capturing meaningful distinctions. However, previous mSSL methods partition images with fixed-size patches, often ignoring the structure variations. In this work, we introduce a novel perspective on 3D medical images with the goal of learning structure-aware representations. We assume that patches within the same structure share the same semantics (semantic consistency) while those from different structures exhibit distinct semantics (semantic discrepancy). Based on this assumption, we propose an mSSL framework named $S^2DC$, achieving Structure-aware Semantic Discrepancy and Consistency in two steps. First, $S^2DC$ enforces distinct representations for different patches to increase semantic discrepancy by leveraging an optimal transport strategy. Second, $S^2DC$ advances semantic consistency at the structural level based on neighborhood similarity distribution. By bridging patch-level and structure-level representations, $S^2DC$ achieves structure-aware representations. Thoroughly evaluated across 10 datasets, 4 tasks, and 3 modalities, our proposed method consistently outperforms the state-of-the-art methods in mSSL.

cs.CV↗

Fast on the Easy, Deep on the Hard: Efficient Reasoning via Powered Length Penalty

Large language models (LLMs) have demonstrated significant advancements in reasoning capabilities, performing well on various challenging benchmarks. Techniques like Chain-of-Thought prompting have been introduced to further improve reasoning. However, these approaches frequently generate longer outputs, which in turn increase computational latency. Although some methods use reinforcement learning to shorten reasoning, they often apply uniform penalties without considering the problem's complexity, leading to suboptimal outcomes. In this study, we seek to enhance the efficiency of LLM reasoning by promoting conciseness for simpler problems while preserving sufficient reasoning for more complex ones for accuracy, thus improving the model's overall performance. Specifically, we manage the model's reasoning efficiency by dividing the reward function and including a novel penalty for output length. Our approach has yielded impressive outcomes in benchmark evaluations across three datasets: GSM8K, MATH500, and AIME2024. For the comparatively simpler datasets GSM8K and MATH500, our method has effectively shortened output lengths while preserving or enhancing accuracy. On the more demanding AIME2024 dataset, our approach has resulted in improved accuracy.

cs.CL↗

SD-MAD: Sign-Driven Few-shot Multi-Anomaly Detection in Medical Images

Medical anomaly detection (AD) is crucial for early clinical intervention, yet it faces challenges due to limited access to high-quality medical imaging data, caused by privacy concerns and data silos. Few-shot learning has emerged as a promising approach to alleviate these limitations by leveraging the large-scale prior knowledge embedded in vision-language models (VLMs). Recent advancements in few-shot medical AD have treated normal and abnormal cases as a one-class classification problem, often overlooking the distinction among multiple anomaly categories. Thus, in this paper, we propose a framework tailored for few-shot medical anomaly detection in the scenario where the identification of multiple anomaly categories is required. To capture the detailed radiological signs of medical anomaly categories, our framework incorporates diverse textual descriptions for each category generated by a Large-Language model, under the assumption that different anomalies in medical images may share common radiological signs in each category. Specifically, we introduce SD-MAD, a two-stage Sign-Driven few-shot Multi-Anomaly Detection framework: (i) Radiological signs are aligned with anomaly categories by amplifying inter-anomaly discrepancy; (ii) Aligned signs are selected further to mitigate the effect of the under-fitting and uncertain-sample issue caused by limited medical data, employing an automatic sign selection strategy at inference. Moreover, we propose three protocols to comprehensively quantify the performance of multi-anomaly detection. Extensive experiments illustrate the effectiveness of our method.

cs.CV↗

BBAL: A Bidirectional Block Floating Point-Based Quantisation Accelerator for Large Language Models

Large language models (LLMs), with their billions of parameters, pose substantial challenges for deployment on edge devices, straining both memory capacity and computational resources. Block Floating Point (BFP) quantisation reduces memory and computational overhead by converting high-overhead floating point operations into low-bit fixed point operations. However, BFP requires aligning all data to the maximum exponent, which causes loss of small and moderate values, resulting in quantisation error and degradation in the accuracy of LLMs. To address this issue, we propose a Bidirectional Block Floating Point (BBFP) data format, which reduces the probability of selecting the maximum as shared exponent, thereby reducing quantisation error. By utilizing the features in BBFP, we present a full-stack Bidirectional Block Floating Point-Based Quantisation Accelerator for LLMs (BBAL), primarily comprising a processing element array based on BBFP, paired with proposed cost-effective nonlinear computation unit. Experimental results show BBAL achieves a 22% improvement in accuracy compared to an outlier-aware accelerator at similar efficiency, and a 40% efficiency improvement over a BFP-based accelerator at similar accuracy.

cs.AR↗

Serial Low-rank Adaptation of Vision Transformer

Fine-tuning large pre-trained vision foundation models in a parameter-efficient manner is critical for downstream vision tasks, considering the practical constraints of computational and storage costs. Low-rank adaptation (LoRA) is a well-established technique in this domain, achieving impressive efficiency by reducing the parameter space to a low-rank form. However, developing more advanced low-rank adaptation methods to reduce parameters and memory requirements remains a significant challenge in resource-constrained application scenarios. In this study, we consider on top of the commonly used vision transformer and propose Serial LoRA, a novel LoRA variant that introduces a shared low-rank matrix serially composite with the attention mechanism. Such a design extracts the underlying commonality of parameters in adaptation, significantly reducing redundancy. Notably, Serial LoRA uses only 1/4 parameters of LoRA but achieves comparable performance in most cases. We conduct extensive experiments on a range of vision foundation models with the transformer structure, and the results confirm consistent superiority of our method.

cs.CV↗

NVR: Vector Runahead on NPUs for Sparse Memory Access

Deep Neural Networks are increasingly leveraging sparsity to reduce the scaling up of model parameter size. However, reducing wall-clock time through sparsity and pruning remains challenging due to irregular memory access patterns, leading to frequent cache misses. In this paper, we present NPU Vector Runahead (NVR), a prefetching mechanism tailored for NPUs to address cache miss problems in sparse DNN workloads. Rather than optimising memory patterns with high overhead and poor portability, NVR adapts runahead execution to the unique architecture of NPUs. NVR provides a general micro-architectural solution for sparse DNN workloads without requiring compiler or algorithmic support, operating as a decoupled, speculative, lightweight hardware sub-thread alongside the NPU, with minimal hardware overhead (under 5%). NVR achieves an average 90% reduction in cache misses compared to SOTA prefetching in general-purpose processors, delivering 4x average speedup on sparse workloads versus NPUs without prefetching. Moreover, we investigate the advantages of incorporating a small cache (16KB) into the NPU combined with NVR. Our evaluation shows that expanding this modest cache delivers 5x higher performance benefits than increasing the L2 cache size by the same amount.

cs.AR↗

SemiSAM+: Rethinking Semi-Supervised Medical Image Segmentation in the Era of Foundation Models

Deep learning-based medical image segmentation typically requires large amount of labeled data for training, making it less applicable in clinical settings due to high annotation cost. Semi-supervised learning (SSL) has emerged as an appealing strategy due to its less dependence on acquiring abundant annotations from experts compared to fully supervised methods. Beyond existing model-centric advancements of SSL by designing novel regularization strategies, we anticipate a paradigmatic shift due to the emergence of promptable segmentation foundation models with universal segmentation capabilities using positional prompts represented by Segment Anything Model (SAM). In this paper, we present SemiSAM+, a foundation model-driven SSL framework to efficiently learn from limited labeled data for medical image segmentation. SemiSAM+ consists of one or multiple promptable foundation models as generalist models, and a trainable task-specific segmentation model as specialist model. For a given new segmentation task, the training is based on the specialist-generalist collaborative learning procedure, where the trainable specialist model delivers positional prompts to interact with the frozen generalist models to acquire pseudo-labels, and then the generalist model output provides the specialist model with informative and efficient supervision which benefits the automatic segmentation and prompt generation in turn. Extensive experiments on two public datasets and one in-house clinical dataset demonstrate that SemiSAM+ achieves significant performance improvement, especially under extremely limited annotation scenarios, and shows strong efficiency as a plug-and-play strategy that can be easily adapted to different specialist and generalist models.

eess.IV↗

Pushing the Limits of BFP on Narrow Precision LLM Inference

The substantial computational and memory demands of Large Language Models (LLMs) hinder their deployment. Block Floating Point (BFP) has proven effective in accelerating linear operations, a cornerstone of LLM workloads. However, as sequence lengths grow, nonlinear operations, such as Attention, increasingly become performance bottlenecks due to their quadratic computational complexity. These nonlinear operations are predominantly executed using inefficient floating-point formats, which renders the system challenging to optimize software efficiency and hardware overhead. In this paper, we delve into the limitations and potential of applying BFP to nonlinear operations. Given our findings, we introduce a hardware-software co-design framework (DB-Attn), including: (i) DBFP, an advanced BFP version, overcomes nonlinear operation challenges with a pivot-focus strategy for diverse data and an adaptive grouping strategy for flexible exponent sharing. (ii) DH-LUT, a novel lookup table algorithm dedicated to accelerating nonlinear operations with DBFP format. (iii) An RTL-level DBFP-based engine is implemented to support DB-Attn, applicable to FPGA and ASIC. Results show that DB-Attn provides significant performance improvements with negligible accuracy loss, achieving 74% GPU speedup on Softmax of LLaMA and 10x low overhead performance improvement over SOTA designs.

cs.AR↗

OstQuant: Refining Large Language Model Quantization with Orthogonal and Scaling Transformations for Better Distribution Fitting

Post-training quantization (PTQ) has emerged as a widely adopted technique for compressing and accelerating Large Language Models (LLMs). The major challenge in LLM quantization is that uneven and heavy-tailed data distributions can expand the quantization range, thereby reducing bit precision for most values. Recent methods attempt to eliminate outliers and balance inter-channel differences by employing linear transformations; however, they remain heuristic and are often overlook optimizing the data distribution across the entire quantization space.In this paper, we introduce Quantization Space Utilization Rate (QSUR), a novel metric that effectively assesses the quantizability of transformed data by measuring the space utilization of the data in the quantization space. We complement QSUR with mathematical derivations that examine the effects and limitations of various transformations, guiding our development of Orthogonal and Scaling Transformation-based Quantization (OSTQuant). OSQuant employs a learnable equivalent transformation, consisting of an orthogonal transformation and a scaling transformation, to optimize the distributions of weights and activations across the entire quantization space. Futhermore, we propose the KL-Top loss function, designed to mitigate noise during optimization while retaining richer semantic information within the limited calibration data imposed by PTQ. OSTQuant outperforms existing work on various LLMs and benchmarks. In the W4-only setting, it retains 99.5\% of the floating-point accuracy. In the more challenging W4A4KV4 configuration, OSTQuant reduces the performance gap by 32\% on the LLaMA-3-8B model compared to state-of-the-art methods. \href{https://github.com/BrotherHappy/OSTQuant}{https://github.com/BrotherHappy/OSTQuant}.

cs.LG↗

Aneumo: A Large-Scale Comprehensive Synthetic Dataset of Aneurysm Hemodynamics

Intracranial aneurysm (IA) is a common cerebrovascular disease that is usually asymptomatic but may cause severe subarachnoid hemorrhage (SAH) if ruptured. Although clinical practice is usually based on individual factors and morphological features of the aneurysm, its pathophysiology and hemodynamic mechanisms remain controversial. To address the limitations of current research, this study constructed a comprehensive hemodynamic dataset of intracranial aneurysms. The dataset is based on 466 real aneurysm models, and 10,000 synthetic models were generated by resection and deformation operations, including 466 aneurysm-free models and 9,534 deformed aneurysm models. The dataset also provides medical image-like segmentation mask files to support insightful analysis. In addition, the dataset contains hemodynamic data measured at eight steady-state flow rates (0.001 to 0.004 kg/s), including critical parameters such as flow velocity, pressure, and wall shear stress, providing a valuable resource for investigating aneurysm pathogenesis and clinical prediction. This dataset will help advance the understanding of the pathologic features and hemodynamic mechanisms of intracranial aneurysms and support in-depth research in related fields. Dataset hosted at https://github.com/Xigui-Li/Aneumo.

cs.CV↗

An Open Quantum Chemistry Property Database of 120 Kilo Molecules with 20 Million Conformers

Artificial intelligence is revolutionizing computational chemistry, bringing unprecedented innovation and efficiency to the field. To further advance research and expedite progress, we introduce the Quantum Open Organic Molecular (QO2Mol) database -- a large-scale quantum chemistry dataset designed for professional and transformative research in organic molecular sciences under an open-source license. The database comprises 120,000 organic molecules and approximately 20 million conformers, encompassing 10 different elements (C, H, O, N, S, P, F, Cl, Br, I), with heavy atom counts exceeding 40. Utilizing the high-precision B3LYP/def2-SVP quantum mechanical level, each conformation was meticulously computed for quantum mechanical properties, including potential energy and forces. These molecules are derived from fragments of compounds in ChEMBL, ensuring their structural relevance to real-world compounds. Its extensive coverage of molecular structures and diverse elemental composition enables comprehensive studies of structure-property relationships, enhancing the accuracy and applicability of machine learning models in predicting molecular behaviors. The QO2Mol database and benchmark codes are available at https://github.com/saiscn/QO2Mol/ .

physics.chem-ph↗

SemiSAM: Enhancing Semi-Supervised Medical Image Segmentation via SAM-Assisted Consistency Regularization

Semi-supervised learning has attracted much attention due to its less dependence on acquiring abundant annotations from experts compared to fully supervised methods, which is especially important for medical image segmentation which typically requires intensive pixel/voxel-wise labeling by domain experts. Although semi-supervised methods can improve the performance by utilizing unlabeled data, there are still gaps between fully supervised methods under extremely limited annotation scenarios. In this paper, we propose a simple yet efficient strategy to explore the usage of the Segment Anything Model (SAM) for enhancing semi-supervised medical image segmentation. Concretely, the segmentation model trained with domain knowledge provides information for localization and generating input prompts to the SAM. Then the generated pseudo-labels of SAM are utilized as additional supervision to assist in the learning procedure of the semi-supervised framework. Extensive experiments demonstrate that SemiSAM significantly improves the performance of existing semi-supervised frameworks when only one or a few labeled images are available and shows strong efficiency as a plug-and-play strategy for semi-supervised medical image segmentation.

cs.CV↗

CogniDual Framework: Self-Training Large Language Models within a Dual-System Theoretical Framework for Improving Cognitive Tasks

Cognitive psychology investigates perception, attention, memory, language, problem-solving, decision-making, and reasoning. Kahneman's dual-system theory elucidates the human decision-making process, distinguishing between the rapid, intuitive System 1 and the deliberative, rational System 2. Recent advancements have positioned large language Models (LLMs) as formidable tools nearing human-level proficiency in various cognitive tasks. Nonetheless, the presence of a dual-system framework analogous to human cognition in LLMs remains unexplored. This study introduces the \textbf{CogniDual Framework for LLMs} (CFLLMs), designed to assess whether LLMs can, through self-training, evolve from deliberate deduction to intuitive responses, thereby emulating the human process of acquiring and mastering new information. Our findings reveal the cognitive mechanisms behind LLMs' response generation, enhancing our understanding of their capabilities in cognitive psychology. Practically, self-trained models can provide faster responses to certain queries, reducing computational demands during inference.

cs.CL↗