arXiv subjects

Rui Xiao

Publications and source records attributed to Rui Xiao.

At least 19 recordsLinked to original sources

arXiv2026

Deploying DeepSeek 175B Locally on a Single Consumer-Grade RTX 4060 Laptop with 32GB RAM for 200k-Scale Protein-Ligand Virtual Screening

Recent advances in large language models (LLMs) have demonstrated exceptional performance in protein-ligand interaction prediction, but state-of-the-art pipelines for large-scale virtual screening almost exclusively rely on high-end GPU clusters with hundreds of gigabytes of memory, creating prohibitive hardware barriers for small academic teams. In this work, we present a fully local low-resource framework that deploys the 175-billion-parameter DeepSeek 175B LLM on a single consumer-grade RTX 4060 laptop equipped with 32GB system RAM and 8GB VRAM, completing a full 200k-scale protein-ligand virtual screening workflow across 20 distinct protein targets. Our implementation achieves 100x throughput of an 8-card A100 cluster baseline under identical task configurations within 72 hours, with an average binding affinity prediction error of 0.88 kcal/mol across all targets, satisfying the 1.0 kcal/mol chemical accuracy requirement for preclinical drug discovery. Systematic runtime profiling reveals that heterogeneous memory management overhead accounts for 72% of total execution time, while accuracy loss introduced by model optimization contributes less than 10% to total prediction error. This work validates the engineering feasibility of running industrial-scale trillion-parameter LLM-driven biomedical computing tasks on consumer hardware, establishing a new low-barrier paradigm for AI-powered early stage drug discovery.

cs.LG↗

arXiv2026

Identity-Aware U-Net: Fine-grained Cell Segmentation via Identity-Aware Representation Learning

Precise segmentation of objects with highly similar shapes remains a challenging problem in dense prediction, especially in scenarios with ambiguous boundaries, overlapping instances, and weak inter-instance visual differences. While conventional segmentation models are effective at localizing object regions, they often lack the discriminative capacity required to reliably distinguish a target object from morphologically similar distractors. In this work, we study fine-grained object segmentation from an identity-aware perspective and propose Identity-Aware U-Net (IAU-Net), a unified framework that jointly models spatial localization and instance discrimination. Built upon a U-Net-style encoder-decoder architecture, our method augments the segmentation backbone with an auxiliary embedding branch that learns discriminative identity representations from high-level features, while the main branch predicts pixel-accurate masks. To enhance robustness in distinguishing objects with near-identical contours or textures, we further incorporate triplet-based metric learning, which pulls target-consistent embeddings together and separates them from hard negatives with similar morphology. This design enables the model to move beyond category-level segmentation and acquire a stronger capability for precise discrimination among visually similar objects. Experiments on benchmarks including cell segmentation demonstrate promising results, particularly in challenging cases involving similar contours, dense layouts, and ambiguous boundaries.

cs.CV↗

arXiv2026

FINER: MLLMs Hallucinate under Fine-grained Negative Queries

Multimodal large language models (MLLMs) struggle with hallucinations, particularly with fine-grained queries, a challenge underrepresented by existing benchmarks that focus on coarse image-related questions. We introduce FIne-grained NEgative queRies (FINER), alongside two benchmarks: FINER-CompreCap and FINER-DOCCI. Using FINER, we analyze hallucinations across four settings: multi-object, multi-attribute, multi-relation, and ``what'' questions. Our benchmarks reveal that MLLMs hallucinate when fine-grained mismatches co-occur with genuinely present elements in the image. To address this, we propose FINER-Tuning, leveraging Direct Preference Optimization (DPO) on FINER-inspired data. Finetuning four frontier MLLMs with FINER-Tuning yields up to 24.2\% gains (InternVL3.5-14B) on hallucinations from our benchmarks, while simultaneously improving performance on eight existing hallucination suites, and enhancing general multimodal capabilities across six benchmarks. Code, benchmark, and models are available at \href{https://explainableml.github.io/finer-project/}{https://explainableml.github.io/finer-project/}.

cs.CV↗

arXiv2025

Training-free Uncertainty Guidance for Complex Visual Tasks with MLLMs

Multimodal Large Language Models (MLLMs) often struggle with fine-grained perception, such as identifying small objects in high-resolution images or detecting key moments in long videos. Existing methods typically rely on complex, task-specific fine-tuning, which reduces generalizability and increases system complexity. In this work, we propose an effective, training-free framework that uses an MLLM's intrinsic uncertainty as proactive guidance. Our core insight is that a model's uncertainty decreases when provided with relevant visual information. We introduce a unified mechanism that scores candidate visual inputs by response uncertainty, enabling the model to autonomously focus on the most informative data. We apply this simple principle to three challenging visual tasks: Visual Search, Long Video Understanding, and Temporal Grounding, allowing off-the-shelf MLLMs to achieve performance competitive with specialized, fine-tuned systems. Our results demonstrate that leveraging intrinsic uncertainty is a powerful strategy for improving fine-grained multimodal performance.

cs.CV↗

arXiv2025

CAME-AB: Cross-Modality Attention with Mixture-of-Experts for Antibody Binding Site Prediction

Antibody binding site prediction plays a pivotal role in computational immunology and therapeutic antibody design. Existing sequence or structure methods rely on single-view features and fail to identify antibody-specific binding sites on the antigens. In this paper, we propose \textbf{CAME-AB}, a novel Cross-modality Attention framework with a Mixture-of-Experts (MoE) backbone for robust antibody binding site prediction. CAME-AB integrates five biologically grounded modalities, including raw amino acid encodings, BLOSUM substitution profiles, pretrained language model embeddings, structure-aware features, and GCN-refined biochemical graphs, into a unified multimodal representation. To enhance adaptive cross-modal reasoning, we propose an \emph{adaptive modality fusion} module that learns to dynamically weight each modality based on its global relevance and input-specific contribution. A Transformer encoder combined with an MoE module further promotes feature specialization and capacity expansion. We additionally incorporate a supervised contrastive learning objective to explicitly shape the latent space geometry, encouraging intra-class compactness and inter-class separability. To improve optimization stability and generalization, we apply stochastic weight averaging during training. Extensive experiments on benchmark antibody-antigen datasets demonstrate that CAME-AB consistently outperforms strong baselines on multiple metrics, including Precision, Recall, F1-score, AUC-ROC, and MCC. Ablation studies further validate the effectiveness of each architectural component and the benefit of multimodal feature integration. The model implementation details and the codes are available on https://anonymous.4open.science/r/CAME-AB-C525

cs.LG↗

arXiv2025

A statistical theory for polymer elasticity: from molecular kinematics to continuum behavior

Predicting the macroscopic mechanical behavior of polymeric materials from the micro-structural features has remained a challenge for decades. Existing theoretical models often fail to accurately capture the experimental data, due to non-physical assumptions that link the molecule kinematics with the macroscopic deformation. In this work, we construct a novel Hamiltonian for chain segments enabling a unified statistical description of both individual macromolecular chains and continuum polymer networks. The chain kinematics, including the stretch and orientation properties, are retrieved by the thermodynamic observables without phenomenological assumptions. The theory shows that the chain stretch is specified by a simple relation via its current spatial direction and the continuum Eulerian logarithmic strain, while the probability of a chain in this spatial direction is governed by the new Hamiltonian of a single segment. The model shows a significantly improved prediction on the hyperelastic response of elastomers, relying on minimal, physically-grounded parameters.

cond-mat.soft↗

arXiv2024

Conformable Convolution for Topologically Aware Learning of Complex Anatomical Structures

While conventional computer vision emphasizes pixel-level and feature-based objectives, medical image analysis of intricate biological structures necessitates explicit representation of their complex topological properties. Despite their successes, deep learning models often struggle to accurately capture the connectivity and continuity of fine, sometimes pixel-thin, yet critical structures due to their reliance on implicit learning from data. Such shortcomings can significantly impact the reliability of analysis results and hinder clinical decision-making. To address this challenge, we introduce Conformable Convolution, a novel convolutional layer designed to explicitly enforce topological consistency. Conformable Convolution learns adaptive kernel offsets that preferentially focus on regions of high topological significance within an image. This prioritization is guided by our proposed Topological Posterior Generator (TPG) module, which leverages persistent homology. The TPG module identifies key topological features and guides the convolutional layers by applying persistent homology to feature maps transformed into cubical complexes. Our proposed modules are architecture-agnostic, enabling them to be integrated seamlessly into various architectures. We showcase the effectiveness of our framework in the segmentation task, where preserving the interconnectedness of structures is critical. Experimental results on three diverse datasets demonstrate that our framework effectively preserves the topology in the segmentation downstream task, both quantitatively and qualitatively.

eess.IV↗

arXiv2024

Molly: Making Large Language Model Agents Solve Python Problem More Logically

Applying large language models (LLMs) as teaching assists has attracted much attention as an integral part of intelligent education, particularly in computing courses. To reduce the gap between the LLMs and the computer programming education expert, fine-tuning and retrieval augmented generation (RAG) are the two mainstream methods in existing researches. However, fine-tuning for specific tasks is resource-intensive and may diminish the model`s generalization capabilities. RAG can perform well on reducing the illusion of LLMs, but the generation of irrelevant factual content during reasoning can cause significant confusion for learners. To address these problems, we introduce the Molly agent, focusing on solving the proposed problem encountered by learners when learning Python programming language. Our agent automatically parse the learners' questioning intent through a scenario-based interaction, enabling precise retrieval of relevant documents from the constructed knowledge base. At generation stage, the agent reflect on the generated responses to ensure that they not only align with factual content but also effectively answer the user's queries. Extensive experimentation on a constructed Chinese Python QA dataset shows the effectiveness of the Molly agent, indicating an enhancement in its performance for providing useful responses to Python questions.

cs.CL↗

arXiv2024

FLAIR: VLM with Fine-grained Language-informed Image Representations

CLIP has shown impressive results in aligning images and texts at scale. However, its ability to capture detailed visual features remains limited because CLIP matches images and texts at a global level. To address this issue, we propose FLAIR, Fine-grained Language-informed Image Representations, an approach that utilizes long and detailed image descriptions to learn localized image embeddings. By sampling diverse sub-captions that describe fine-grained details about an image, we train our vision-language model to produce not only global embeddings but also text-specific image representations. Our model introduces text-conditioned attention pooling on top of local image tokens to produce fine-grained image representations that excel at retrieving detailed image content. We achieve state-of-the-art performance on both, existing multimodal retrieval benchmarks, as well as, our newly introduced fine-grained retrieval task which evaluates vision-language models' ability to retrieve partial image content. Furthermore, our experiments demonstrate the effectiveness of FLAIR trained on 30M image-text pairs in capturing fine-grained visual information, including zero-shot semantic segmentation, outperforming models trained on billions of pairs. Code is available at https://github.com/ExplainableML/flair .

cs.CV↗

arXiv2024

COSMOS: Cross-Modality Self-Distillation for Vision Language Pre-training

Vision-Language Models (VLMs) trained with contrastive loss have achieved significant advancements in various vision and language tasks. However, the global nature of the contrastive loss makes VLMs focus predominantly on foreground objects, neglecting other crucial information in the image, which limits their effectiveness in downstream tasks. To address these challenges, we propose COSMOS: CrOSs-MOdality Self-distillation for vision-language pre-training that integrates a novel text-cropping strategy and cross-attention module into a self-supervised learning framework. We create global and local views of images and texts (i.e., multi-modal augmentations), which are essential for self-distillation in VLMs. We further introduce a cross-attention module, enabling COSMOS to learn comprehensive cross-modal representations optimized via a cross-modality self-distillation loss. COSMOS consistently outperforms previous strong baselines on various zero-shot downstream tasks, including retrieval, classification, and semantic segmentation. Additionally, it surpasses CLIP-based models trained on larger datasets in visual perception and contextual understanding tasks. Code is available at https://github.com/ExplainableML/cosmos.

cs.CV↗

arXiv2024

Accurate Explanation Model for Image Classifiers using Class Association Embedding

Image classification is a primary task in data analysis where explainable models are crucially demanded in various applications. Although amounts of methods have been proposed to obtain explainable knowledge from the black-box classifiers, these approaches lack the efficiency of extracting global knowledge regarding the classification task, thus is vulnerable to local traps and often leads to poor accuracy. In this study, we propose a generative explanation model that combines the advantages of global and local knowledge for explaining image classifiers. We develop a representation learning method called class association embedding (CAE), which encodes each sample into a pair of separated class-associated and individual codes. Recombining the individual code of a given sample with altered class-associated code leads to a synthetic real-looking sample with preserved individual characters but modified class-associated features and possibly flipped class assignments. A building-block coherency feature extraction algorithm is proposed that efficiently separates class-associated features from individual ones. The extracted feature space forms a low-dimensional manifold that visualizes the classification decision patterns. Explanation on each individual sample can be then achieved in a counter-factual generation manner which continuously modifies the sample in one direction, by shifting its class-associated code along a guided path, until its classification outcome is changed. We compare our method with state-of-the-art ones on explaining image classification tasks in the form of saliency maps, demonstrating that our method achieves higher accuracies. The code is available at https://github.com/xrt11/XAI-CODE.

cs.CV↗

arXiv2024

QACP: An Annotated Question Answering Dataset for Assisting Chinese Python Programming Learners

In online learning platforms, particularly in rapidly growing computer programming courses, addressing the thousands of students' learning queries requires considerable human cost. The creation of intelligent assistant large language models (LLMs) tailored for programming education necessitates distinct data support. However, in real application scenarios, the data resources for training such LLMs are relatively scarce. Therefore, to address the data scarcity in intelligent educational systems for programming, this paper proposes a new Chinese question-and-answer dataset for Python learners. To ensure the authenticity and reliability of the sources of the questions, we collected questions from actual student questions and categorized them according to various dimensions such as the type of questions and the type of learners. This annotation principle is designed to enhance the effectiveness and quality of online programming education, providing a solid data foundation for developing the programming teaching assists (TA). Furthermore, we conducted comprehensive evaluations of various LLMs proficient in processing and generating Chinese content, highlighting the potential limitations of general LLMs as intelligent teaching assistants in computer programming courses.

cs.CL↗

arXiv2023

Effective electrical manipulation of topological antiferromagnet by orbital Hall effect

Electrical control of the non-trivial topology in Weyl antiferromagnet is of great interests to develop next-generation spintronic devices. Recent works suggest that spin Hall effect can switch the topological antiferromagnetic order. However, the switching efficiency remains relatively low. Here, we demonstrate effective manipulation of antiferromagnetic order in Weyl semimetal Mn3Sn by orbital Hall effect originated from metal Mn or oxide CuOx. While Mn3Sn is proven to be able to convert orbit current to spin current by itself, we find that inserting a heavy metal layer like Pt with proper thickness can effectively reduce the critical switching current density by one order of magnitude. In addition, we show that the memristor-like switching behavior of Mn3Sn can mimic the potentiation and depression processes of a synapse with high linearity, which is beneficial for constructing artificial neural network with high accuracy. Our work paves an alternative way to manipulate topological antiferromagnetic order and may inspire more high-performance antiferromagnetic functional devices.

cond-mat.mtrl-sci↗

arXiv2023

Active Globally Explainable Learning for Medical Images via Class Association Embedding and Cyclic Adversarial Generation

Explainability poses a major challenge to artificial intelligence (AI) techniques. Current studies on explainable AI (XAI) lack the efficiency of extracting global knowledge about the learning task, thus suffer deficiencies such as imprecise saliency, context-aware absence and vague meaning. In this paper, we propose the class association embedding (CAE) approach to address these issues. We employ an encoder-decoder architecture to embed sample features and separate them into class-related and individual-related style vectors simultaneously. Recombining the individual-style code of a given sample with the class-style code of another leads to a synthetic sample with preserved individual characters but changed class assignment, following a cyclic adversarial learning strategy. Class association embedding distills the global class-related features of all instances into a unified domain with well separation between classes. The transition rules between different classes can be then extracted and further employed to individual instances. We then propose an active XAI framework which manipulates the class-style vector of a certain sample along guided paths towards the counter-classes, resulting in a series of counter-example synthetic samples with identical individual characters. Comparing these counterfactual samples with the original ones provides a global, intuitive illustration to the nature of the classification tasks. We adopt the framework on medical image classification tasks, which show that more precise saliency maps with powerful context-aware representation can be achieved compared with existing methods. Moreover, the disease pathology can be directly visualized via traversing the paths in the class-style space.

cs.CV↗

arXiv2023

SCOPE: Structural Continuity Preservation for Medical Image Segmentation

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

cs.CV↗

arXiv2021

A Customized NoC Architecture to Enable Highly Localized Computing-On-the-Move DNN Dataflow

The ever-increasing computation complexity of fastgrowing Deep Neural Networks (DNNs) has requested new computing paradigms to overcome the memory wall in conventional Von Neumann computing architectures. The emerging Computing-In-Memory (CIM) architecture has been a promising candidate to accelerate neural network computing. However, data movement between CIM arrays may still dominate the total power consumption in conventional designs. This paper proposes a flexible CIM processor architecture named Domino and "Computing-On-the-Move" (COM) dataflow, to enable stream computing and local data access to significantly reduce data movement energy. Meanwhile, Domino employs customized distributed instruction scheduling within Network-on-Chip (NoC) to implement inter-memory computing and attain mapping flexibility. The evaluation with prevailing DNN models shows that Domino achieves 1.77-to-2.37$\times$ power efficiency over several state-of-the-art CIM accelerators and improves the throughput by 1.28-to-13.16$\times$.

cs.AR↗

arXiv2021

Domino: A Tailored Network-on-Chip Architecture to Enable Highly Localized Inter- and Intra-Memory DNN Computing

The ever-increasing computation complexity of fast-growing Deep Neural Networks (DNNs) has requested new computing paradigms to overcome the memory wall in conventional Von Neumann computing architectures. The emerging Computing-In-Memory (CIM) architecture has been a promising candidate to accelerate neural network computing. However, the data movement between CIM arrays may still dominate the total power consumption in conventional designs. This paper proposes a flexible CIM processor architecture named Domino to enable stream computing and local data access to significantly reduce the data movement energy. Meanwhile, Domino employs tailored distributed instruction scheduling within Network-on-Chip (NoC) to implement inter-memory-computing and attain mapping flexibility. The evaluation with prevailing CNN models shows that Domino achieves 1.15-to-9.49$\times$ power efficiency over several state-of-the-art CIM accelerators and improves the throughput by 1.57-to-12.96$\times$.

cs.AR↗

arXiv2021

A Low Power In-Memory Multiplication andAccumulation Array with Modified Radix-4 Inputand Canonical Signed Digit Weights

A mass of data transfer between the processing and storage units has been the leading bottleneck in modern Von-Neuman computing systems, especially when used for Artificial Intelligence (AI) tasks. Computing-in-Memory (CIM) has shown great potential to reduce both latency and power consumption. However, the conventional analog CIM schemes are suffering from reliability issues, which may significantly degenerate the accuracy of the computation. Recently, CIM schemes with digitized input data and weights have been proposed for high reliable computing. However, the properties of the digital memory and input data are not fully utilized. This paper presents a novel low power CIM scheme to further reduce the power consumption by using a Modified Radix-4 (M-RD4) booth algorithm at the input and a Modified Canonical Signed Digit (M-CSD) for the network weights. The simulation results show that M-Rd4 and M-CSD reduce the ratio of $1\times1$ by 78.5\% on LeNet and 80.2\% on AlexNet, and improve the computing efficiency by 41.6\% in average. The computing-power rate at the fixed-point 8-bit is 60.68 TOPS/s/W.

cs.AR↗