arXiv subjects

Siyuan Ma

Publications and source records attributed to Siyuan Ma.

At least 19 recordsLinked to original sources

arXiv2026

Effect-Size Estimation and Confounding-Aware Permutations for PERMANOVA

Motivation: PERMANOVA is widely used to test associations between covariates and high-dimensional data with arbitrary distributions, such as ecology, metabolomics, or microbial community profiling. In these contexts, its effect size measure (R2) is generally used to indicate how much the high-dimensional measurement covaries with respect to a separate, univariate measure. However, as we show, this conventional effect size is inflated under the null, resulting in values that do not accurately reflect the conventional expectation of "variance explained." Furthermore, standard permutation schemes yield inflated false positives in the presence of non-independent samples, such as repeated measure designs. Results: We introduce confounding-aware permutation schemes for both invariant and variant covariates. We additionally develop a causally-grounded, distance-based effect-size estimator derived from the Hájek average treatment effect estimator, providing interpretable effect sizes in the units of the chosen dissimilarity metric. Simulations using microbiome profiles demonstrate that these approaches control false positives while maintaining power, outperforming standard PERMANOVA implementations. Availability and Implementation: An R implementation is freely available in the permaBrioche module of the bioBakery ecosystem https://huttenhower.sph.harvard.edu/permabrioche. Contact: chuttenh@hsph.harvard.edu

stat.ME↗

arXiv2026

AskGLP1: A Knowledge Graph LLM Agent for Exploring GLP-1 Experience from Online Patient Narratives

GLP-1 medications are increasingly used for weight management, and many people share their experiences online. These narratives show why people take the drugs and what they experience, but they remain unstructured and disconnected from formal pharmacovigilance. We therefore present AskGLP1, a system that transforms online patient narratives into a knowledge graph (KG) and answers questions about medication experiences. Through an LLM-assisted pipeline grounded in the MedDRA terminology, AskGLP1 screens nearly 8.5 million Reddit posts for medication experiences and distills 163,135 of them, with 2,506 WebMD reviews, into a KG of 385,790 drug-side-effect and drug-purpose relations. We find that GLP-1 experiences are source- and drug-specific. Online narratives share the most common gastrointestinal symptoms with FAERS, but they foreground everyday burdens such as fatigue and food aversion, whereas FAERS reports more often include injection-site reactions and selected serious diagnoses such as pancreatitis. We further find that posts report less nausea and vomiting for tirzepatide than for semaglutide, more fatigue for Wegovy than Ozempic and for Zepbound than Mounjaro. Evaluations show that the agent answers with verifiable evidence and declines requests for medical advice. Our findings reveal gaps between what FAERS captures and what people report online, and they call for patient-centered approaches to pharmacovigilance. Code, prompts, and evaluation questions are available at https://github.com/ZhaoqianXue/AskGLP1.

cs.CL↗

arXiv2026

RoboJudge: Multimodal Language Models as Judges for Embodied Video Generation

Video generation models are promising foundations for embodied world models, but only if their generated rollouts are physically valid and faithful to task instructions. Multimodal large language models (MLLMs) are increasingly used to judge these properties, yet their agreement with human judgments on embodied videos has not been systematically evaluated. To address this gap, we introduce RoboJudge-Bench, a benchmark for evaluating MLLMs as judges of embodied video generation. The benchmark measures two fundamental dimensions, Physical Adherence and Instruction Alignment, across 800 human-annotated videos from 8 source corpora and 10 video generators, spanning grippers, human hands, and dexterous hands. Experiments reveal uneven alignment between existing judges and human ratings: general-purpose MLLMs show lower agreement on physical adherence, while specialized video judges designed for general-domain physical reasoning do not consistently transfer to embodied scenarios. Motivated by these findings, we construct RoboJudge-Train, comprising 12K videos annotated with 25K human-verified scores and model-assisted rationales for Physical Adherence and Instruction Alignment. We fine-tune a 9B MLLM on this dataset with supervised learning followed by reinforcement learning, yielding RoboJudge-9B. Among the model judges evaluated on RoboJudge-Bench, RoboJudge-9B achieves the highest overall agreement, reaching a Pearson correlation of 0.719 with a statistically significant 0.089 gain over Gemini-3.7-Flash, the best-performing proprietary baseline in our evaluation. Training on RoboJudge-Train also yields gains on external benchmarks, including VideoPhy2 and Physion-Eval. We further use RoboJudge-9B as a downstream evaluator to benchmark video generation models according to Physical Adherence and Instruction Alignment.

cs.CV↗

arXiv2026

ReviewPilot: A Multi-Agent System for Screening and Data Extraction in Systematic Reviews

Systematic literature reviews follow the PRISMA process of screening scholarly works and extracting evidence from included studies. Deep research tools based on large language models (LLMs) can search and summarize the literature but do not record which studies are excluded or where extracted values come from. We develop a conversational multi-agent system called ReviewPilot that automates the PRISMA workflow from paper screening to information extraction. Researchers can tailor criteria and schemas through dialogue, and a project memory keeps their configurations and revisions. Each screening decision comes with its reason and each extracted value with its source. On epidemiological expert reviews, ReviewPilot outperforms a single-prompt LLM and AgentSLR across three LLMs, with screening macro F1 up to 0.776 and extraction F1 up to 0.788. Case studies in biomedicine and human-computer interaction show close agreement with human annotators, suggesting that ReviewPilot can transfer beyond epidemiology. Code is available at https://github.com/ZhaoqianXue/ReviewPilot.

cs.CL↗

arXiv2026

Probabilistic Multi-Source Data Selection via Learnable Categorical Priors: Variance Reduction and Guaranteed Derandomization

Bilevel data selection is a fundamental task with numerous applications in machine learning and statistics. A common strategy for tackling this problem is to relax the original bilevel combinatorial optimization into a continuous one. However, existing methods, including 0-1 relaxation and probabilistic relaxation, still suffer from several limitations, such as unstable gradient estimation and infeasible rounding. To address these issues, this paper proposes a new probabilistic relaxation for the multi-source bilevel data selection problem. Our key idea is to introduce multiple learnable categorical priors to parameterize a probability distribution supported only on feasible data subsets, thus naturally yielding a lossless rounding scheme. We further show that our proposed relaxation admits an effective two-point gradient estimator, which can simultaneously avoid the inverse-Hessian computation required by existing 0-1 relaxation and the unbounded score term appearing in prior probabilistic relaxation. Furthermore, we develop a reducible representation of this estimator, which substantially reduces the number of lower-level retrainings required for gradient computation. Built upon this reducible two-point estimator, we then design a novel stochastic gradient algorithm, termed ReSGD, for multi-source bilevel data selection problem, and establish a rigorous approximation guarantee for the subset returned by ReSGD under weak submodularity. Finally, extensive experiments are conducted to validate the effectiveness of our proposed ReSGD.

cs.LG↗

arXiv2026

Atomic Motion Coordinate for Language-Steerable and Force-Responsive Manipulation

Can changing only the language instruction redirect a VLA policy's end effector, or does the visually driven motion prior dominate? We present Atomic Motion Coordinate, a geometry-grounded coordinate for steerable and force-responsive manipulation. Each arm owns thirteen signed translation, rotation, and hold atoms grounded from text and forward kinematics with vision withheld, and the coordinate is injected into every action-expert block via weighted codebook alignment. Contact history modulates the same coordinate through a bounded spherical residual that is recomputed from a fixed nominal latent to regenerate only the unexecuted horizon suffix. Across 7,520 offline horizon interventions, opposite-atom separation reaches 92.5/83.1% (single/dual) versus 39.1/24.0% for LA4VLA-style. Across 50 real-robot trials per task, AMC raises OOD fruit progress from 60.5% to 87.8%; force adaptation raises Plug/Vase from 59.0/71.5% to 78.5/75.2%.

cs.RO↗

arXiv2026

VOMMI: Collecting and Leveraging Portable Demonstrations for Mobile Manipulation

Portable mobile-manipulation demonstrations can help alleviate data scarcity for embodied intelligence, but obtaining reliable, low-cost, and robot-free motion supervision from RGB observations remains challenging. Existing approaches often rely on teleoperation or specialized devices equipped with additional sensing hardware, while directly using estimated visual odometry (VO) trajectories can introduce inconsistencies due to accumulated drift and imperfect motion supervision. We present the Visual-Odometry-Conditioned Mobile Manipulation Interface (VOMMI), a portable demonstration collection and learning framework that connects portable RGB demonstrations to vision-language-action (VLA) post-training through offline trajectory reconstruction and online visual-motion conditioning. VOMMI synchronizes body and hand views to capture navigation context and local object interactions without requiring human-robot kinematic correspondence calibration. R2-VO refines offline demonstration trajectories using sparse geometric anchors and produces causal local-motion tokens over multiple prediction horizons for online policy conditioning. An action-group residual adapter incorporates these tokens only into the base branch. Experiments use a 500-trajectory portable for each task, with 75 trajectories held out for RGB-VO evaluation, and 200 robot demonstrations as references. Our policy, post-trained only on portable demonstrations, achieves 18.2% lower base-velocity error than a policy trained with robot-collected demonstrations, while maintaining comparable end-effector translation accuracy. Offline reconstruction reduces absolute trajectory errors for the body and hand streams by 24.6% on average relative to the best evaluated baseline for each stream. The complete system improves the mean success rate by 8.3 percentage points over OpenPI 0.5 across three real-robot tasks.

cs.RO↗

arXiv2026

Teaching agentic AI to generalize expert diagnostic reasoning in rare diseases

Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer. Large language models rank the correct disease first in only 35.4% of benchmark cases and often rely on learned phenotype-disease associations rather than reusable diagnostic reasoning strategies. We developed liteOdyssey through Policy Iteration with Human Feedback, a process in which model failures and expert corrections are iteratively consolidated into a clinician-gated, natural-language policy executed by a language model. Across 1,243 public benchmark cases spanning 722 rare diseases, liteOdyssey ranked the correct disease first in 59.3% of cases versus 26.5% without the policy, with comparable gains in cases involving diseases excluded from policy development. The same policy transferred across model families and sizes without retraining. Adaptation of the policy to the Undiagnosed Diseases Network (UDN) improved diagnostic accuracy among 515 UDN patients, with gains confirmed by blinded physician adjudication. These results show that expert reasoning can be externalized into an inspectable and revisable natural-language policy that generalizes across rare diseases, transfers across model backbones, and adapts to a real-world patient cohort.

cs.AI↗

arXiv2026

FWBC-VLA: Force-Aware Whole-Body Compensation for Contact-Rich Loco-Manipulation

Contact-rich loco-manipulation requires a bridge between semantic action generation and physical interaction control. Existing Vision-language-action (VLA) models generate task-level actions from visual and linguistic observations, but cannot interpret the physical interactions induced by those actions. While the whole-body control (WBC) policy can stabilize the robot, it cannot distinguish task-relevant interaction forces from forces induced by external disturbances during manipulation. Although force/torque sensors provide direct measurements of physical interactions, retrofitting them entails additional hardware costs and substantial integration effort, particularly for platforms not designed with sensor integration in mind. To address this problem, we propose FWBC-VLA, a force-aware framework that bridges task-level VLA action generation and low-level whole-body compensation control for wheeled-legged robots. First, we introduce HSR-Force, a sensorless residual-torque estimator for inferring contact strength and its temporal variation. These contact estimates are then encoded as tokens and injected into the VLA action expert during action decoding, enabling the policy to perceive contact onset, sustained loading, and release. For loco-manipulation tasks, all parameters of the pretrained VLA backbone are fine-tuned on our WL\&Arm Dataset, which comprises more than 5,000 episodes. Moreover, the robot's proprioceptive state, the Jacobian-derived body-frame force estimate, and the estimated contact state are jointly fed into a compensation generator to produce corrective actions. The manipulation-centric actions are subsequently combined with the corrective actions and passed to the WBC policy for execution. Real-world experiments on whiteboard wiping and door opening with a door closer demonstrate the effectiveness of our FWBC-VLA in contact-rich loco-manipulation.

cs.RO↗

arXiv2026

Learning Whole-Body Kinetic Coordination for Wheeled-Quadruped Long-Range Throwing

Long-range throwing on unstructured terrain is a key capability for mobile robots in delivery and retrieval tasks, but it requires high release velocity, coordinated whole-body motion, and robustness to terrain-induced disturbances. We present a whole-body kinetic-coordination framework for a wheeled-quadruped manipulator that combines kinetic-chain arm modeling with SQP-based trajectory optimization and a reference-guided reinforcement learning policy for coordinated base motion. The manipulator is first reduced to a kinetic-chain model and optimized under kinematic and dynamic constraints to produce a high-speed throwing reference. On a stationary base, the optimized arm trajectory reaches a release speed of 12.75 m/s and a throwing distance of 16.68 m. When whole-body coordination is enabled, the system further increases the release speed to 16.64 m/s and the throwing distance to 28.25 m. We then integrate the mobility of the wheeled-quadruped platform and validate the complete policy through hardware experiments on flat ground, grass, slopes, and rough roads. The results show that kinetic-chain optimization and whole-body coordination together enable robust long-range throwing across diverse unstructured terrains.

cs.RO↗

arXiv2026

RegimeFormer: A Large Protein Model of Global Perturbation Regimes

Protein language models organize sequence and structure at scale, but a global representation of how proteins respond to mutation remains lacking. We present RegimeFormer, a large protein perturbation model coupled to RegimeAtlas, constructed by harmonizing and indexing 202,556,313 non-redundant protein sequences across the tree of life. A diversity-preserving one-million-protein subset provides the high-resolution training and inference layer, with 995,995 proteins yielding residue-level summaries across 407,048,356 residues and substitution-specific predictions available on demand. Across experimental deep mutational scanning, molecular benchmarks, structural confidence and evolutionary constraint, RegimeFormer identifies reproducible protein-level perturbation regimes that organize residue fragility, adaptability and predictive uncertainty. Regime conditioning improves substitution-specific prediction, with the largest relative gains under unseen-protein, unseen-family and low-homology evaluation. RegimeFormer-derived molecular priors further improve downstream transcriptomic and drug-response modelling. Together, RegimeFormer and RegimeAtlas provide a scalable framework for mapping, predicting and querying protein perturbation landscapes across global sequence space.

q-bio.QM↗

arXiv2026

Analytical and Bootstrap Confidence Intervals for Double Machine Learning: Simulation Studies and an Application to Rural-Urban Differences in Obesity Prevalence

Double Machine Learning (DML) is a popular approach for treatment effect estimation in various settings, which allows a wide range of flexible machine learning methods to be used for nuisance parameter estimation while preserving valid inference. In practice, however, applied researchers must choose among many machine learning algorithms for nuisance models, and the impact of this choice on the variance estimation of DML is not well characterized. We conduct a comprehensive simulation study to compare the coverage probability of DML confidence intervals across different machine learning algorithms. In this study, we compare (1) analytical confidence intervals derived by DML theory versus (2) bootstrap confidence interval. We use a set of learners including ordinary least squares, LASSO, Random Forest, LightGBM, and Neural Networks under different data generation settings. We evaluate the performance across difference settings by bias, confidence interval width, and most importantly, coverage probability. Our results show substantial variability in coverage performance across analytical and bootstrap confidence intervals, highlighting that learner choice plays a critical role in reliable DML inference. Surprisingly, we find that in many settings, when sample size increases, the coverage probability of both DML analytical and bootstrap confidence interval decreases. We further investigate coverage probabilities using a real dataset on rural urban differences among U.S. counties. The real data analysis discovers that (1) the model performance still varies by the learner choices and (2) greater rurality has a statistically significant increasing effect on county level obesity prevalence.

stat.ML↗

arXiv2026

ForeTime-VLA: Causal Future-Token Distillation from a World Action Model for Conveyor-Belt Manipulation

Manipulating moving objects requires a policy to anticipate contact events, yet vision-language-action (VLA) policies are commonly fine-tuned from the current observation alone. World action models (WAMs) learn predictive dynamics, but running a video-scale teacher or explicitly imagining future frames at deployment is costly. We introduce ForeTime-VLA, a dense pi0.5 policy that distills a future-aware, action-equivalent representation from a frozen Fast-WAM-derived teacher while remaining causal at inference. Offline, current and future video latents are compressed into a whitened 64-D target. Online, an eight-frame history encoder predicts this target together with manipulation phase and normalized time-to-transition. Four future tokens and one phase token condition the VLM prefix, while the predicted future and transition horizon condition the action expert. Training retains the original flow-matching action target and adds cosine, relational geometry, phase, time-to-transition, and action-equivalence objectives. On a deduplicated conveyor-belt dataset, we compare 40k-step checkpoints on 768 matched windows per split. Test MAE decreases from 0.134119 to 0.130593 (2.63%; paired-bootstrap 95% CI: 0.82-4.48% improvement), and test L2 decreases by 3.02%, at a 2.46-2.93% latency cost. In quantitative real-robot evaluation, ForeTime-VLA achieves 81.1% stationary and 58.9% slow-moving grasp success, exceeding the next-best reference by 12.2 and 22.2 percentage points, respectively. Across three belt speeds, it completes 44/90 grasps versus 23/90 for pi0.5, including 11/30 versus 2/30 at fast speed. The agreement between offline orientation gains and reduced real-robot contact-pose failures supports causal future-token distillation as an effective way to improve dynamic manipulation without deploying the world-model teacher.

cs.AI↗

arXiv2026

Your Harness is Not Secure: Benchmarking Real-world Threat of Command Line Interface Agent

Command-line interface (CLI) agents powered by large language models (LLMs) can interpret natural-language requests, plan multi-step tasks, execute shell commands, and modify files and system state. As these agents are increasingly used for operating-system (OS) workflows, it is important to evaluate whether they can be misused to carry out security-relevant operations. Existing benchmarks often lack an attacker-knowledge model grounded in tactics, techniques, and procedures (TTPs), provide limited coverage of end-to-end kill chains, rely on simplified single-host environments, or use LLM-as-a-judge for success evaluation. We introduce AdvCLI, an MITRE ATT&CK-aligned benchmark for evaluating OS-level misuse risks of CLI agents in a controlled multi-host sandbox. AdvCLI contains 140 tasks: 40 direct malicious requests, 74 TTP-based tasks, and 26 end-to-end kill chains. Each task is paired with deterministic hard-coded verification protocols that check whether the requested OS-level effect is realized. We evaluate seven CLI agents and products built on nine foundation models, including ReAct, OpenClaw, OpenAI Agent SDK, Claude Code, Gemini CLI, Cursor CLI, and Cursor IDE. Results show that current CLI agents frequently proceed beyond refusal and can complete a non-negligible fraction of malicious OS-level tasks, especially when requests include TTP-style attacker knowledge. AdvCLI provides a reproducible testbed for evaluating these risks and for developing stronger safety mechanisms for tool-using CLI agents in the future.

cs.CR↗

arXiv2026

DECOWAM: Decoupled Whole-Body World-Action Model for Legged Mobile Manipulation

Mobile manipulation requires a robot to predict how locomotion and arm motion jointly alter future observations and control. Existing world-action models, developed largely for fixed-base platforms, do not explicitly distinguish camera ego-motion from base and arm actions. Here we introduce DECOWAM, a whole-body world-action model that separates these factors through dedicated conditional interfaces. DECOWAM freezes an adapted FastWAM backbone and trains residual adapters, an action-equivalent future bottleneck distilled from privileged observations, adversarially separated base and arm latents, and base-velocity conditioning for video prediction. We further introduce ARMDOG, a real-robot dataset that synchronizes video, whole-body state and action, and language. On a fixed replay protocol, DECOWAM improved both future-video and action prediction over FastWAM, reducing action MSE by 21.7% with 25.95M trainable adaptation parameters. Across 79 closed-loop trials per method, it achieved the highest observed whole-body coordination and base-displacement robustness among the compared systems, while task completion remained comparable to the strongest baseline. These results show that embodiment-aware factorization can support parameter-efficient joint visual prediction and whole-body control under moving viewpoints.

cs.AI↗

arXiv2026

A cross-modal generative model for incomplete and degraded prostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

eess.IV↗

arXiv2026

Dissecting Embodied Abilities in Multimodal Language Models through Skill-level Evaluation and Diagnosis

Understanding the capability bottlenecks of embodied multimodal large language models (MLLMs) is crucial for improving embodied agents. However, existing embodied benchmarks mainly focus on task-level evaluation and fail to provide actionable insights into the underlying causes of model failures. To address this limitation, we introduce BEAR, a benchmark that decomposes embodied tasks into 14 atomic skills for fine-grained skill-level evaluation. BEAR comprises 4,469 interleaved image-video-text samples spanning 14 skills across 6 categories, ranging from low-level perception to high-level planning. We evaluate 20 MLLMs on BEAR under a hierarchical skill-level diagnosis framework and uncover two key findings: (1) perceptual capabilities are major bottlenecks behind reasoning failures, and (2) current models suffer from unstable spatiotemporal modeling that remains largely unexposed in prior benchmarks. Motivated by these findings, we further propose BEAR-Agent, a multimodal conversational agent that augments MLLMs with visual and spatial reasoning tools. BEAR-Agent substantially improves performance across embodied skills, achieving a relative improvement of 17.5% on GPT-5 over the base model on BEAR, while also outperforming strong baselines in both simulation and real-world robotic experiments. Project page: https://bear-official66.github.io/

cs.CV↗

arXiv2026

FutureBridge: Token Selection Beyond Local Preference in Collaborative Decoding

Token-level collaboration allows a large language model (LLM) to assist a small language model (SLM) when their predictions diverge. Existing methods either use LLM-generated intervention tokens or rank candidates with the LLM's next-token probabilities. Both rely on the LLM's local preference, even though an LLM-selected token may be difficult for the SLM to build on. We present FutureBridge, which ranks joint LLM-SLM token candidates according to how well they support the SLM's subsequent reasoning. During training, an answer-verified LLM trajectory supplies a fixed shared future, and a frozen SLM evaluates every candidate under this common context. The resulting counterfactual scores supervise a lightweight token reranker that observes only the current state and candidate token. At inference, FutureBridge uses the LLM only to expand the candidate pool, selects one token, and returns generation to the SLM without generating or appending a future suffix. Across five mathematical reasoning benchmarks, FutureBridge improves the Qwen3-1.7B SLM's Math Avg. by 35.1% relative to greedy SLM decoding. These results indicate that token selection benefits from modeling whether the receiving SLM can use each candidate to continue reasoning, rather than relying on the LLM's local preference alone.

cs.CL↗