arXiv subjects

Yue Pei

Publications and source records attributed to Yue Pei.

4 recordsLinked to original sources

arXiv2026

CT-PrepAgent: Bounded Policy and Controlled Execution for Adaptive CT Data Preparation

Heterogeneous computed tomography (CT) acquisitions and diverse downstream task requirements limit the transferability of fixed data preparation workflows across data sources and tasks. Existing approaches typically rely on manually designed or dataset-specific rules, making it difficult to accommodate changes in acquisition conditions and analytical objectives without manual intervention. Large language model (LLM)-based agents have shown promise for automating medical workflows, yet their potential for adaptive CT data preparation remains largely unexplored. To bridge this gap, we propose CT-PrepAgent, which enables adaptive CT data preparation through a bounded policy and controlled deterministic execution. Deterministic inspection constructs structured data--task profiles, from which a policy decides an eligible DICOM series or predefined preprocessing profile, while the controlled execution flow guards, resolves, executes, and verifies the decision with bounded recovery when enabled and safe quarantine otherwise. Across three public CT segmentation tasks, CT-PrepAgent derived data-task adaptive preprocessing decisions and achieved the highest macro-average Dice. On two private raw-DICOM cohorts, CT-PrepAgent increased verified output yield from 61.7\% to 70.0\% and yielded similar registration metrics on common verified outputs. Controlled fault and replay tests validate bounded recovery, safe quarantine, and policy-free replay under tested fault and drift settings.

cs.AI↗

arXiv2026

Point Tracking Improves World Action Models

Robot policy learning benefits from world-action models that capture environment dynamics, but pixel-level prediction entangles dynamics with nuisance factors such as lighting and texture, making learned representations vulnerable to task-irrelevant visual variation. We propose JOPAT, a JOint Pixel-And-Track World-Action Model that predicts latent visual observations, 2D point tracks with visibility, and actions in a single denoising diffusion transformer. The key insight is that tracks provide an explicit representation of motion that captures long-horizon dynamics and remains robust under occlusion or partial out-of-frame motion, offering greater utility than modeling pixel appearance alone. On LIBERO and real-world LeRobot tasks, JOPAT improves over pixel-based baselines, with the largest gains on long-horizon tasks involving occlusion, object interaction, and off-screen motion.

cs.RO↗

arXiv2026

AntigenLM: Structure-Aware DNA Language Modeling for Influenza

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact, aligned functional units. This structure-aware pretraining enables AntigenLM to capture evolutionary constraints and generalize across tasks. Fine-tuned on time-series hemagglutinin (HA) and neuraminidase (NA) sequences, AntigenLM accurately forecasts future antigenic variants across regions and subtypes, including those unseen during training, outperforming phylogenetic and evolution-based models. It also achieves near-perfect subtype classification. Ablation studies show that disrupting genomic structure through fragmentation or shuffling severely degrades performance, revealing the importance of preserving functional-unit integrity in DNA language modeling. AntigenLM thus provides both a powerful framework for antigen evolution prediction and a general principle for building biologically grounded DNA foundation models.

q-bio.GN↗

arXiv2025

Hybrid Sequence Modeling and Reinforced Verification for Controllable Target-Conditioned Decision Making

Target-conditioned sequence models provide a simple interface for controllable offline decision making, but the requested target return can be an unreliable control signal, especially when the target return lies in underrepresented regions of the dataset. This paper proposes Doctor, a hybrid sequence modeling and reinforced verification framework for controllable target-conditioned offline decision making. Doctor trains a shared masked trajectory Transformer with two complementary objectives: masked trajectory reconstruction for candidate generation and in-sample value learning for action-value verification. At inference time, the model samples multiple nearby target returns, generates candidate actions in parallel, and selects the action whose verified value is closest to the requested target return. We analyze this verifier-guided selection rule and show that its value-level alignment error is bounded by candidate-value coverage around the target return and verifier accuracy. Experiments on D4RL and EpiCare show that Doctor improves target-return alignment under reduced high-return coverage, remains competitive on standard offline return-maximization benchmarks, and enables a single policy to modulate between conservative and aggressive operating points in a simulated clinical decision-making task. These results suggest that reinforced verification can improve the controllability of target-conditioned policies.

cs.LG↗