arXiv subjects

Keyi Li

Publications and source records attributed to Keyi Li.

11 recordsLinked to original sources

arXiv2026

Bioinfoysis Technical Report

Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.

cs.AI↗

arXiv2026

Density-Reweighted Entropic Optimal Transport: Decoupling Geometry from Sampling Density

Dataset alignment is a central step in data analysis across science and engineering, where the goal is to match observations between datasets. Entropic Optimal Transport (EOT) offers a computationally tractable framework for this task by encoding cross-dataset affinities in a transport plan. However, when two datasets are sampled from geometrically similar low-dimensional structures with substantially different sampling densities, the EOT plan may match points by relative sampling density rather than geometric proximity, yielding geometrically misleading correspondences. To address this issue, we propose a density-reweighted EOT framework in which the influence of sampling density on the transport plan can be discounted to a desired degree, ranging from standard EOT to alignment driven purely by underlying geometry. Under suitable regularity conditions, we establish convergence of the reweighted EOT plan to a family of population-level plans whose dependence on sampling density is made explicit. Through simulations, we show that our approach recovers geometrically faithful correspondences, improving over related EOT-based frameworks when datasets exhibit substantial sampling density disparity.

stat.ML↗

arXiv2026

Standard-quantum-limit-surpassing vector polarimetry using Rydberg atoms in an SU(1,1) interferometer

Vector polarimetry is an important application frontier for Rydberg-atom-based sensing. While prior research has largely concentrated on developing novel measurement schemes, high-sensitivity vector polarimetry remains an open question. Here we propose a theoretical framework for high-sensitivity detection of radio-frequency (RF) electric field polarization direction, which is particularly suitable for weak-field detection. Under a static magnetic field, the asymmetry in coupling between the Zeeman sublevels of the Rydberg atom and the RF field's polarization components enables the polarization angles to be determined from the atomic absorption index, which is retrieved via homodyne detection by incorporating the Rydberg atom system into an SU(1,1) interferometer. We derive the sensitivity of the polarization angles along with the corresponding standard quantum limit (SQL) and quantum Cram\'{e}r--Rao bound (QCRB). Our results demonstrate a sensitivity surpassing the SQL across wide angular ranges using either dual coherent states or a coherent state combined with a squeezed vacuum state as input. Significantly, the optimal sensitivity reaches below \SI{e-6}{\degree}, with sensitivities better than \SI{e-3}{\degree} maintained over most of the angular domain. This work establishes a foundation for high-precision vector polarimetry, thereby advancing the development of Rydberg-atom-based quantum sensing and contributing to a deeper understanding of light--matter interactions.

quant-ph↗

arXiv2025

GRASPing Anatomy to Improve Pathology Segmentation

Radiologists rely on anatomical understanding to accurately delineate pathologies, yet most current deep learning approaches use pure pattern recognition and ignore the anatomical context in which pathologies develop. To narrow this gap, we introduce GRASP (Guided Representation Alignment for the Segmentation of Pathologies), a modular plug-and-play framework that enhances pathology segmentation models by leveraging existing anatomy segmentation models through pseudolabel integration and feature alignment. Unlike previous approaches that obtain anatomical knowledge via auxiliary training, GRASP integrates into standard pathology optimization regimes without retraining anatomical components. We evaluate GRASP on two PET/CT datasets, conduct systematic ablation studies, and investigate the framework's inner workings. We find that GRASP consistently achieves top rankings across multiple evaluation metrics and diverse architectures. The framework's dual anatomy injection strategy, combining anatomical pseudo-labels as input channels with transformer-guided anatomical feature fusion, effectively incorporates anatomical context.

cs.CV↗

arXiv2025

Euclidean Distance Deflation Under High-Dimensional Heteroskedastic Noise

Pairwise Euclidean distance calculation is a fundamental step in many machine learning and data analysis algorithms. In real-world applications, however, these distances are frequently distorted by heteroskedastic noise$\unicode{x2014}$a prevalent form of inhomogeneous corruption characterized by variable noise magnitudes across data observations. Such noise inflates the computed distances in a nontrivial way, leading to misrepresentations of the underlying data geometry. In this work, we address the tasks of estimating the noise magnitudes per observation and correcting the pairwise Euclidean distances under heteroskedastic noise. Perhaps surprisingly, we show that in general high-dimensional settings and without assuming prior knowledge on the clean data structure or noise distribution, both tasks can be performed reliably, even when the noise levels vary considerably. Specifically, we develop a principled, hyperparameter-free approach that jointly estimates the noise magnitudes and corrects the distances. We provide theoretical guarantees for our approach, establishing probabilistic bounds on the estimation errors of both noise magnitudes and distances. These bounds, measured in the normalized $\ell_1$ norm, converge to zero at polynomial rates as both feature dimension and dataset size increase. Experiments on synthetic datasets demonstrate that our method accurately estimates distances in challenging regimes, significantly improving the robustness of subsequent distance-based computations. Notably, when applied to single-cell RNA sequencing data, our method yields noise magnitude estimates consistent with an established prototypical model, enabling accurate nearest neighbor identification that is fundamental to many downstream analyses.

stat.ML↗

arXiv2025

Accelerating Diffusion Transformer via Increment-Calibrated Caching with Channel-Aware Singular Value Decomposition

Diffusion transformer (DiT) models have achieved remarkable success in image generation, thanks for their exceptional generative capabilities and scalability. Nonetheless, the iterative nature of diffusion models (DMs) results in high computation complexity, posing challenges for deployment. Although existing cache-based acceleration methods try to utilize the inherent temporal similarity to skip redundant computations of DiT, the lack of correction may induce potential quality degradation. In this paper, we propose increment-calibrated caching, a training-free method for DiT acceleration, where the calibration parameters are generated from the pre-trained model itself with low-rank approximation. To deal with the possible correction failure arising from outlier activations, we introduce channel-aware Singular Value Decomposition (SVD), which further strengthens the calibration effect. Experimental results show that our method always achieve better performance than existing naive caching methods with a similar computation resource budget. When compared with 35-step DDIM, our method eliminates more than 45% computation and improves IS by 12 at the cost of less than 0.06 FID increase. Code is available at https://github.com/ccccczzy/icc.

cs.CV↗

arXiv2025

Advancing AI Research Assistants with Expert-Involved Learning

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

cs.AI↗

arXiv2024

Every Component Counts: Rethinking the Measure of Success for Medical Semantic Segmentation in Multi-Instance Segmentation Tasks

We present Connected-Component~(CC)-Metrics, a novel semantic segmentation evaluation protocol, targeted to align existing semantic segmentation metrics to a multi-instance detection scenario in which each connected component matters. We motivate this setup in the common medical scenario of semantic metastases segmentation in a full-body PET/CT. We show how existing semantic segmentation metrics suffer from a bias towards larger connected components contradicting the clinical assessment of scans in which tumor size and clinical relevance are uncorrelated. To rebalance existing segmentation metrics, we propose to evaluate them on a per-component basis thus giving each tumor the same weight irrespective of its size. To match predictions to ground-truth segments, we employ a proximity-based matching criterion, evaluating common metrics locally at the component of interest. Using this approach, we break free of biases introduced by large metastasis for overlap-based metrics such as Dice or Surface Dice. CC-Metrics also improves distance-based metrics such as Hausdorff Distances which are uninformative for small changes that do not influence the maximum or 95th percentile, and avoids pitfalls introduced by directly combining counting-based metrics with overlap-based metrics as it is done in Panoptic Quality.

cs.CV↗

arXiv2024

MaskMatch: Boosting Semi-Supervised Learning Through Mask Autoencoder-Driven Feature Learning

Conventional methods in semi-supervised learning (SSL) often face challenges related to limited data utilization, mainly due to their reliance on threshold-based techniques for selecting high-confidence unlabeled data during training. Various efforts (e.g., FreeMatch) have been made to enhance data utilization by tweaking the thresholds, yet none have managed to use 100% of the available data. To overcome this limitation and improve SSL performance, we introduce \algo, a novel algorithm that fully utilizes unlabeled data to boost semi-supervised learning. \algo integrates a self-supervised learning strategy, i.e., Masked Autoencoder (MAE), that uses all available data to enforce the visual representation learning. This enables the SSL algorithm to leverage all available data, including samples typically filtered out by traditional methods. In addition, we propose a synthetic data training approach to further increase data utilization and improve generalization. These innovations lead \algo to achieve state-of-the-art results on challenging datasets. For instance, on CIFAR-100 with 2 labels per class, STL-10 with 4 labels per class, and Euro-SAT with 2 labels per class, \algo achieves low error rates of 18.71%, 9.47%, and 3.07%, respectively. The code will be made publicly available.

cs.CV↗

arXiv2022

Exploring Runtime Decision Support for Trauma Resuscitation

AI-based recommender systems have been successfully applied in many domains (e.g., e-commerce, feeds ranking). Medical experts believe that incorporating such methods into a clinical decision support system may help reduce medical team errors and improve patient outcomes during treatment processes (e.g., trauma resuscitation, surgical processes). Limited research, however, has been done to develop automatic data-driven treatment decision support. We explored the feasibility of building a treatment recommender system to provide runtime next-minute activity predictions. The system uses patient context (e.g., demographics and vital signs) and process context (e.g., activities) to continuously predict activities that will be performed in the next minute. We evaluated our system on a pre-recorded dataset of trauma resuscitation and conducted an ablation study on different model variants. The best model achieved an average F1-score of 0.67 for 61 activity types. We include medical team feedback and discuss the future work.

cs.AI↗

arXiv2022

Generating Privacy-Preserving Process Data with Deep Generative Models

Process data with confidential information cannot be shared directly in public, which hinders the research in process data mining and analytics. Data encryption methods have been studied to protect the data, but they still may be decrypted, which leads to individual identification. We experimented with different models of representation learning and used the learned model to generate synthetic process data. We introduced an adversarial generative network for process data generation (ProcessGAN) with two Transformer networks for the generator and the discriminator. We evaluated ProcessGAN and traditional models on six real-world datasets, of which two are public and four are collected in medical domains. We used statistical metrics and supervised learning scores to evaluate the synthetic data. We also used process mining to discover workflows for the authentic and synthetic datasets and had medical experts evaluate the clinical applicability of the synthetic workflows. We found that ProcessGAN outperformed traditional sequential models when trained on small authentic datasets of complex processes. ProcessGAN better represented the long-range dependencies between the activities, which is important for complicated processes such as the medical processes. Traditional sequential models performed better when trained on large data of simple processes. We conclude that ProcessGAN can generate a large amount of sharable synthetic process data indistinguishable from authentic data.

cs.LG↗