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Yan Cui

Publications and source records attributed to Yan Cui.

At least 19 recordsLinked to original sources
arXiv2026

LM-X: Explainable Vision--Language--Action Modeling via Progress, Event, and Uncertainty Prediction

Large-scale vision--language--action (VLA) policies have advanced generalist robot control, yet most remain stimulus-to-action black boxes: actions are exposed, but their explanatory state is not. They provide no native account of three explanatory signals: task progress, the next semantic transition, or local command reliability. Prior work shows that progress and event structure aid long-horizon control and that uncertainty supports monitoring; however, such capabilities are typically added or extracted only after action pretraining. The field therefore lacks a VLA foundation model whose explanatory state is jointly pretrained with control. Drawing on biological sensorimotor organization, in which outcome-sensitive, event-segmented, and probabilistic predictions structure behavior, we introduce LM-X. LM-X learns three directly supervised online signals: return-to-go (RTG) estimates visible progress and state quality; event-to-go (ETG) predicts the action sequence to the next semantic event; and heteroscedastic action-flow variance reports local command reliability. RTG conditions ETG and both condition action generation; uncertainty is estimated inside the action expert, making explanation part of control rather than a post-hoc description. We pretrain LM-X on more than 20,000 hours of heterogeneous real-robot trajectories, including over 1,000 hours of failed rollouts. A controlled gate favors joint over post-hoc training. LM-X achieves 74.1\% success on 50 randomized-hard RoboTwin2.0 tasks and 73.5\% on seven real-robot tasks, compared with 55.4\% and 50.7\% for GR00T N1.7. Its signals track progress and regression, anticipate event-scale motion, detect high-error actions, and provide advance failure warning. These results establish LM-X as an explainable VLA foundation model that couples transparent predictive state with stronger generalist control.

cs.RO↗
arXiv2026

Matching Matters: A Fair Quality-Efficiency Benchmark for Command-Line Agents

Rapid advances in large language models have improved the task-solving capabilities of command-line-interface (CLI)-based agents, whose CLIs determine how models invoke tools, maintain interaction history, and recover from failures. Consequently, effective matching between CLIs and LLMs has become essential. However, existing agent benchmarks largely emphasize success rate while overlooking practical objectives such as cost and efficiency, as well as the selection of LM-CLI combinations, all of which are critical in real-world deployment. We therefore introduce AgentMeter, a quality-efficiency benchmark with a new metric, the AgentMeter Score (AMS), that jointly characterizes task quality, budget sensitivity, and resource-intensive zero-reward execution, enabling a more complete assessment of deployed LM-CLI pairs. Furthermore, collected task descriptions may inadvertently favor LM-CLI pairs that are particularly compatible with their wording and structure, causing evaluation results to reflect description-specific advantages rather than general task-solving capability. We therefore propose AgentMeter-Opt, a trajectory-grounded optimization framework that constructs pair-adapted, task-preserving description variants to build a fairer evaluation set across LM-CLI pairs. Extensive experiments show that no CLI is universally optimal across language models and that task success, execution cost, and AMS identify different competitive configurations. Results on AgentMeter-Opt further reveal that task-preserving description changes affect LM-CLI pairs unevenly and can alter their relative ordering across valid description conditions. Together, AgentMeter and AgentMeter-Opt provide a practical foundation for fair and deployment-relevant evaluation of command-line agents.

cs.SE↗
arXiv2026

Towards Universal Gene Regulatory Network Inference: Unlocking Generalizable Regulatory Knowledge in Single-cell Foundation Models

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced transcriptomic encoding is widely expected to revolutionize GRN inference. However, we observe that their performance remains far from satisfactory. The primary reason is that the standard reconstruction-based pre-training objectives often fail to explicitly capture latent regulatory signals. To bridge this gap, we first introduce a GRN generalization benchmark designed to evaluate regulatory predictions on unseen genes and datasets, which relies on the zero-shot capabilities of scFMs and is inherently challenging for traditional methods. Furthermore, to unlock the regulatory knowledge within the foundation models, we propose two novel methods, Virtual Value Perturbation and Gradient Trajectory, to distill implicit regulatory information from scFMs into highly generalizable inter-gene features. Extensive experiments demonstrate that our approach significantly outperforms existing methods, establishing a new paradigm for leveraging the potential of scFMs in universal GRN inference.

cs.LG↗
arXiv2026

Linking spatial biology and clinical histology via Haiku

Integrating molecular, morphological, and clinical data is essential for basic and translational biomedical research, yet systematic frameworks for jointly modeling these modalities remain limited. Here we present Haiku, a tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF). It comprises 26.7 million spatial proteomics patches from 3,218 tissue sections across 1,606 patients spanning 11 organ types, with matched hematoxylin and eosin (H&E) histology and clinical metadata aligned in a shared embedding space. Haiku enables three-way cross-modal retrieval, improves downstream classification and clinical prediction tasks over unimodal baselines, and supports zero-shot biomarker inference through fusion retrieval conditioned on clinical metadata-only text descriptions. Across tasks, Haiku outperforms competing approaches, achieving cross-modal retrieval (Recall@50 up to 0.611 versus near-zero baseline), survival prediction (C-index 0.737, +7.91% relative improvement), and zero-shot biomarker inference (mean Pearson correlation 0.718 across 52 biomarkers). Furthermore, we introduce a counterfactual prediction framework in which modifying only clinical metadata while fixing tissue morphology surfaces niche-specific molecular shifts associated with breast cancer stage progression and lung cancer survival outcomes. In a lung adenocarcinoma case study, the counterfactual analysis recovers niche-specific shifts characterized by increased CD8 and granzyme B, reduced PD-L1, and decreased Ki67, broadly consistent with patterns reported for favorable outcomes. We present these counterfactual results as exploratory, hypothesis-generating signals rather than mechanistic claims. These capabilities demonstrate that tri-modal alignment via Haiku enables integrative analysis of spatial biology, bridging molecular measurements with clinical context for biological exploration.

cs.LG↗
arXiv2026

In Search of Lost DNA Sequence Pretraining

DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have overwhelmingly emphasized pretraining scale and custom downstream evaluation datasets, while neglecting some essential components of the pretraining paradigm. In this paper, we reveal three critical yet heretofore overlooked problems in DNA pretraining: inappropriate downstream datasets, inherent flaws in the neighbor-masking strategy, and the lack of detailed discussion on vocabulary. Therefore, we undertake comprehensive investigations and propose principled guidelines, including selection criteria for evaluation datasets, guiding task design, and in-depth vocabulary analysis. Extensive experiments validate the significance of our identified problems and support the rationale behind our recommendations. Finally, we introduce a standardized testbed that enables reproducible and rigorous benchmarking of DNA pretraining methods to advance the development of genomic foundation models.

cs.LG↗
arXiv2026

Revisiting Unknowns: Towards Effective and Efficient Open-Set Active Learning

Open-set active learning (OSAL) aims to identify informative samples for annotation when unlabeled data may contain previously unseen classes-a common challenge in safety-critical and open-world scenarios. Existing approaches typically rely on separately trained open-set detectors, introducing substantial training overhead and overlooking the supervisory value of labeled unknowns for improving known-class learning. In this paper, we propose E$^2$OAL (Effective and Efficient Open-set Active Learning), a unified and detector-free framework that fully exploits labeled unknowns for both stronger supervision and more reliable querying. E$^2$OAL first uncovers the latent class structure of unknowns through label-guided clustering in a frozen contrastively pre-trained feature space, optimized by a structure-aware F1-product objective. To leverage labeled unknowns, it employs a Dirichlet-calibrated auxiliary head that jointly models known and unknown categories, improving both confidence calibration and known-class discrimination. Building on this, a logit-margin purity score estimates the likelihood of known classes to construct a high-purity candidate pool, while an OSAL-specific informativeness metric prioritizes partially ambiguous yet reliable samples. These components together form a flexible two-stage query strategy with adaptive precision control and minimal hyperparameter sensitivity. Extensive experiments across multiple OSAL benchmarks demonstrate that E$^2$OAL consistently surpasses state-of-the-art methods in accuracy, efficiency, and query precision, highlighting its effectiveness and practicality for real-world applications. The code is available at github.com/chenchenzong/E2OAL.

cs.CV↗
arXiv2025

Adaptive Multi-Scale Integration Unlocks Robust Cell Annotation in Histopathology Images

Identifying cell types and subtypes in routine histopathology is fundamental for understanding disease. Existing tile-based models capture nuclear detail but miss the broader tissue context that influences cell identity. Current human annotations are coarse-grained and uneven across studies, making fine-grained, subtype-level classification difficult. In this study, we build a marker-guided dataset from Xenium spatial transcriptomics with single-cell resolution labels for more than two million cells across eight organs and 16 classes to address the lack of high-quality annotations. Leveraging this data resource, we introduce NuClass, a pathologist workflow inspired framework for cell-wise multi-scale integration of nuclear morphology and microenvironmental context. It combines Path local, which focuses on nuclear morphology from 224x224 pixel crops, and Path global, which models the surrounding 1024x1024 pixel neighborhood, through a learnable gating module that balances local and global information. An uncertainty-guided objective directs the global path to prioritize regions where the local path is uncertain, and we provide calibrated confidence estimates and Grad-CAM maps for interpretability. Evaluated on three fully held-out cohorts, NuClass achieves up to 96 percent F1 for its best-performing class, outperforming strong baselines. Our results demonstrate that multi-scale, uncertainty-aware fusion can bridge the gap between slide-level pathological foundation models and reliable, cell-level phenotype prediction.

cs.CV↗
arXiv2025

Gene Incremental Learning for Single-Cell Transcriptomics

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset--single-cell transcriptomics--to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of our method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.

cs.LG↗
arXiv2025

PRISM: Progressive Rain removal with Integrated State-space Modeling

Image deraining is an essential vision technique that removes rain streaks and water droplets, enhancing clarity for critical vision tasks like autonomous driving. However, current single-scale models struggle with fine-grained recovery and global consistency. To address this challenge, we propose Progressive Rain removal with Integrated State-space Modeling (PRISM), a progressive three-stage framework: Coarse Extraction Network (CENet), Frequency Fusion Network (SFNet), and Refine Network (RNet). Specifically, CENet and SFNet utilize a novel Hybrid Attention UNet (HA-UNet) for multi-scale feature aggregation by combining channel attention with windowed spatial transformers. Moreover, we propose Hybrid Domain Mamba (HDMamba) for SFNet to jointly model spatial semantics and wavelet domain characteristics. Finally, RNet recovers the fine-grained structures via an original-resolution subnetwork. Our model learns high-frequency rain characteristics while preserving structural details and maintaining global context, leading to improved image quality. Our method achieves competitive results on multiple datasets against recent deraining methods.

cs.CV↗
arXiv2025

A co-evolving agentic AI system for medical imaging analysis

Agentic AI is rapidly advancing in healthcare and biomedical research. However, in medical image analysis, their performance and adoption remain limited due to the lack of a robust ecosystem, insufficient toolsets, and the absence of real-time interactive expert feedback. Here we present "TissueLab", a co-evolving agentic AI system that allows researchers to ask direct questions, automatically plan and generate explainable workflows, and conduct real-time analyses where experts can visualize intermediate results and refine them. TissueLab integrates tool factories across pathology, radiology, and spatial omics domains. By standardizing inputs, outputs, and capabilities of diverse tools, the system determines when and how to invoke them to address research and clinical questions. Across diverse tasks with clinically meaningful quantifications that inform staging, prognosis, and treatment planning, TissueLab achieves state-of-the-art performance compared with end-to-end vision-language models (VLMs) and other agentic AI systems such as GPT-5. Moreover, TissueLab continuously learns from clinicians, evolving toward improved classifiers and more effective decision strategies. With active learning, it delivers accurate results in unseen disease contexts within minutes, without requiring massive datasets or prolonged retraining. Released as a sustainable open-source ecosystem, TissueLab aims to accelerate computational research and translational adoption in medical imaging while establishing a foundation for the next generation of medical AI.

cs.CV↗
arXiv2025

A Deep SETI Search for Technosignatures in the TRAPPIST-1 System with FAST

The Five-hundred-meter Aperture Spherical Telescope (FAST) is the world's largest single-dish radio telescope, and the search for extraterrestrial intelligence (SETI) is one of its five key science objectives. We conducted a targeted narrowband search toward the TRAPPIST-1 system using FAST. The observations consisted of five independent L-band pointings, each with a 20-minute integration, for a total on-source time of 1.67h. The frequency coverage spanned 1.05--1.45GHz with a spectral resolution of ~7.5Hz. We searched for narrowband drifting signals with Doppler drift rates within +_4Hz/s and a signal-to-noise ratio threshold of S/N>10 in two orthogonal linear polarizations separately.Based on the system parameters adopted in this work, we estimate a minimum detectable equivalent isotropic radiated power of 2.04x10^10W, placing one of the most stringent constraints to date on persistent or high-duty-cycle narrowband transmitters in this system. No credible technosignature candidates were identified within the searched parameter space. Nevertheless,TRAPPIST-1 remains a compelling target for future SETI efforts. We plan to extend our search to other signal types, such as periodic or transient transmitters, and to carry out broader surveys of nearby exoplanetary systems with FAST.

astro-ph.IM↗
arXiv2025

Efficient Speculative Decoding for Llama at Scale: Challenges and Solutions

Speculative decoding is a standard method for accelerating the inference speed of large language models. However, scaling it for production environments poses several engineering challenges, including efficiently implementing different operations (e.g., tree attention and multi-round speculative decoding) on GPU. In this paper, we detail the training and inference optimization techniques that we have implemented to enable EAGLE-based speculative decoding at a production scale for Llama models. With these changes, we achieve a new state-of-the-art inference latency for Llama models. For example, Llama4 Maverick decodes at a speed of about 4 ms per token (with a batch size of one) on 8 NVIDIA H100 GPUs, which is 10% faster than the previously best known method. Furthermore, for EAGLE-based speculative decoding, our optimizations enable us to achieve a speed-up for large batch sizes between 1.4x and 2.0x at production scale.

cs.CL↗
arXiv2025

Toward Efficient Spiking Transformers: Synapse Pruning Meets Synergistic Learning-Based Compensation

As a foundational architecture of artificial intelligence models, Transformer has been recently adapted to spiking neural networks with promising performance across various tasks. However, existing spiking Transformer(ST)-based models require a substantial number of parameters and incur high computational costs, thus limiting their deployment in resource-constrained environments. To address these challenges, we propose combining synapse pruning with a synergistic learning-based compensation strategy to derive lightweight ST-based models. Specifically, two types of tailored pruning strategies are introduced to reduce redundancy in the weight matrices of ST blocks: an unstructured $\mathrm{L_{1}P}$ method to induce sparse representations, and a structured DSP method to induce low-rank representations. In addition, we propose an enhanced spiking neuron model, termed the synergistic leaky integrate-and-fire (sLIF) neuron, to effectively compensate for model pruning through synergistic learning between synaptic and intrinsic plasticity mechanisms. Extensive experiments on benchmark datasets demonstrate that the proposed methods significantly reduce model size and computational overhead while maintaining competitive performance. These results validate the effectiveness of the proposed pruning and compensation strategies in constructing efficient and high-performing ST-based models.

cs.LG↗
arXiv2025

CellForge: Agentic Design of Virtual Cell Models

Virtual cell modeling aims to predict cellular responses to diverse perturbations but faces challenges from biological complexity, multimodal data heterogeneity, and the need for interdisciplinary expertise. We introduce CellForge, a multi-agent framework that autonomously designs and synthesizes neural network architectures tailored to specific single-cell datasets and perturbation tasks. Given raw multi-omics data and task descriptions, CellForge discovers candidate architectures through collaborative reasoning among specialized agents, then generates executable implementations. Our core contribution is the framework itself: showing that multi-agent collaboration mechanisms - rather than manual human design or single-LLM prompting - can autonomously produce executable, high-quality computational methods. This approach goes beyond conventional hyperparameter tuning by enabling entirely new architectural components such as trajectory-aware encoders and perturbation diffusion modules to emerge from agentic deliberation. We evaluate CellForge on six datasets spanning gene knockouts, drug treatments, and cytokine stimulations across multiple modalities (scRNA-seq, scATAC-seq, CITE-seq). The results demonstrate that the models generated by CellForge are highly competitive with established baselines, while revealing systematic patterns of architectural innovation. CellForge highlights the scientific value of multi-agent frameworks: collaboration among specialized agents enables genuine methodological innovation and executable solutions that single agents or human experts cannot achieve. This represents a paradigm shift toward autonomous scientific method development in computational biology. Code is available at https://github.com/gersteinlab/CellForge.

cs.LG↗
arXiv2025

Graph Neural Networks as a Substitute for Transformers in Single-Cell Transcriptomics

Graph Neural Networks (GNNs) and Transformers share significant similarities in their encoding strategies for interacting with features from nodes of interest, where Transformers use query-key scores and GNNs use edges. Compared to GNNs, which are unable to encode relative positions, Transformers leverage dynamic attention capabilities to better represent relative relationships, thereby becoming the standard backbones in large-scale sequential pre-training. However, the subtle difference prompts us to consider: if positions are no longer crucial, could we substitute Transformers with Graph Neural Networks in some fields such as Single-Cell Transcriptomics? In this paper, we first explore the similarities and differences between GNNs and Transformers, specifically in terms of relative positions. Additionally, we design a synthetic example to illustrate their equivalence where there are no relative positions between tokens in the sample. Finally, we conduct extensive experiments on a large-scale position-agnostic dataset-single-cell transcriptomics-finding that GNNs achieve competitive performance compared to Transformers while consuming fewer computation resources. These findings provide novel insights for researchers in the field of single-cell transcriptomics, challenging the prevailing notion that the Transformer is always the optimum choice.

cs.LG↗
arXiv2025

ST-FlowNet: An Efficient Spiking Neural Network for Event-Based Optical Flow Estimation

Spiking Neural Networks (SNNs) have emerged as a promising tool for event-based optical flow estimation tasks due to their ability to leverage spatio-temporal information and low-power capabilities. However, the performance of SNN models is often constrained, limiting their application in real-world scenarios. In this work, we address this gap by proposing a novel neural network architecture, ST-FlowNet, specifically tailored for optical flow estimation from event-based data. The ST-FlowNet architecture integrates ConvGRU modules to facilitate cross-modal feature augmentation and temporal alignment of the predicted optical flow, improving the network's ability to capture complex motion dynamics. Additionally, to overcome the challenges associated with training SNNs, we introduce a novel approach to derive SNN models from pre-trained artificial neural networks (ANNs) through ANN-to-SNN conversion or our proposed BISNN method. Notably, the BISNN method alleviates the complexities involved in biological parameter selection, further enhancing the robustness of SNNs in optical flow estimation tasks. Extensive evaluations on three benchmark event-based datasets demonstrate that the SNN-based ST-FlowNet model outperforms state-of-the-art methods, delivering superior performance in accurate optical flow estimation across a diverse range of dynamic visual scenes. Furthermore, the inherent energy efficiency of SNN models is highlighted, establishing a compelling advantage for their practical deployment. Overall, our work presents a novel framework for optical flow estimation using SNNs and event-based data, contributing to the advancement of neuromorphic vision applications.

cs.CV↗
arXiv2025

Multibeam SETI Observations toward Nearby M dwarfs with FAST

The search for extraterrestrial intelligence (SETI) targeted searches aim to observe specific areas and objects to find possible technosignatures. Many SETI researches have focused on nearby stars and their planets in recent years. In this paper, we report a targeted SETI observations using the most sensitive L-band Five-hundred-meter Aperture Spherical radio Telescope (FAST) toward three nearby M dwarfs, all of which have been discovered exoplanet candidates. The minimum equivalent isotropic radiant power of the lower limit from the three sources we can detect is $6.19 \times 10^{8}$ W, which is well within the reach of current human technology. Applying the multibeam coincidence matching (MBCM) blind search mode, we search for narrowband drifting signals across 1.05-1.45 GHz in each of the two orthogonal linear polarization directions. An unusual signal at 1312.50 MHz detected from the observation toward AD Leo originally piqued our interest. However, we finally eliminate the possibility of an extraterrestrial origin based on much evidence, such as the polarization, frequency, and beam coverage characteristics.

astro-ph.IM↗