arXiv subjects

Yikun Zhang

Publications and source records attributed to Yikun Zhang.

At least 19 recordsLinked to original sources

arXiv2026

Magnetically Self-Sealed MR Haptic Actuator With PWM-Based Excitation and High-Fidelity Torque Control

Accurate and stable torque rendering is essential for safe and perceptive human--machine interaction. Magnetorheological fluid (MRF)-based actuators offer a compact and rapidly controllable solution for haptic feedback, but their practical implementation requires reliable fluid sealing, low-hysteresis excitation, accurate torque control, and stable long-duration operation. This article presents an integrated MRF haptic system featuring a compact magnetically self-sealed rotary actuator, low-hysteresis PWM operation, high-fidelity model-based torque rendering, and stable performance during long-time operation. Magnetostatic simulation guides the arrangement of magnetic and nonmagnetic materials to focus flux in the multidisk torque and permanent-magnet sealing regions, enabling a maximum 600 N$\cdot$mm/A output. Experiments show that higher PWM frequencies reduce hysteresis and improve repeatability. At 10 kHz, the response is represented by a nonlinear model that varies with the direction and speed of torque change. The real-time controller combines feedforward, hysteresis compensation, PI feedback, and sliding-mode correction. Compared with PID, it reduces square-wave overshoot, undershoot, and steady-state RMSE by 77.4\%, 61.9\%, and 68.3\%, respectively. It tracks sinusoidal and biomechanics-model-based references, and a 1.5-h test shows only a 2.5 $^\circ$C rise near the coil with no clear tracking loss. This high-fidelity torque rendering will fundamentally transform human--robot collaboration by making interactions safer, more efficient, and more intuitive.

cs.RO↗

arXiv2026

Emputation: Identification-Guided Neural Imputation Framework

We propose Emputation, a deep generative framework for learning imputation models. Emputation targets the extrapolation distribution of missing variables given observed variables, and training is guided by specific missingness assumptions that guarantee identification of the target distribution. The training objective, called the emputation risk, is an energy-score-based risk in which the identification assumption determines how observed entries are masked and which observations contribute to training. The resulting framework enables direct conditional sampling for multiple imputation. We show that the population minimizer of the emputation risk recovers the target extrapolation distribution under a broad class of identification assumptions, including several missing-not-at-random assumptions. Simulations show strong performance under both pointwise and distributional evaluation metrics, and an application to an Alzheimer's disease dataset demonstrates its practical value.

stat.ME↗

arXiv2026

DrugSAGE:Self-evolving Agent Experience for Efficient State-of-the-Art Drug Discovery

Building state-of-the-art (SOTA) predictive models for drug discovery requires expensive search over tools, architectures, and training strategies. Current LLM-based agents can find SOTA solutions through extensive trial and error, but they do not retain the experience accumulated along the way and therefore pay the full search cost on every new task. We propose \method (Self-evolving Agent Experience), a framework that accumulates and reuses experience across tasks to build SOTA drug discovery models efficiently. \method maintains a cross-task memory of verified skills, statistical evidence about effective strategies, and a record of recurring errors and their fixes. In some cases, \method transfers a working solution directly without test-time search. In 33 molecular property prediction tasks, \method ranks first among nine SOTA agents in a single-task setting. With memory accumulated from 16 smaller tasks, \method achieves an averaged normalized score of 0.935 on 17 held-out tasks in a cross-task evaluation setting and outperforms all baseline agents by 10-30\% in a zero-test-time search regime. In summary, our work shows the advantage of cross-task memory for efficient SOTA model development in drug discovery.

cs.LG↗

arXiv2026

Residual Gaussian Splatting for Ultra Sparse-View CBCT Reconstruction

While 3D Gaussian splatting (3DGS) offers explicit and efficient scene representations for cone-beam computed tomography reconstruction, conventional photometric optimization inherently suffers from spectral bias under ultra sparse-view conditions, leading to over-smoothing and a loss of high-frequency anatomical details. Since wavelet transforms provide rich high-frequency information and have been widely utilized to enhance sparse reconstruction, this work integrates wavelet multi-resolution analysis with 3DGS. To circumvent the mathematical mismatch between the strict non-negativity of physical X-ray attenuation and the bipolar nature of high-frequency wavelet coefficients, we propose Residual Gaussian Splatting (RGS). Methodologically, we introduce a spectrally-decoupled Gaussian representation that stratifies the volumetric field into a geometric base component and a residual detail component. This decomposition systematically transforms explicit high-frequency fitting into a physically consistent, implicit residual compensation task. Furthermore, we devise a spectral-spatial collaborative optimization strategy to coordinate the interplay between geometric anchoring and texture refinement, effectively preventing spectral crosstalk. Extensive experiments on clinical datasets demonstrate that RGS enables the reconstructed images to capture highly refined geometric textures. It successfully resolves the trade-off between artifact suppression and detail preservation, yielding superior visual fidelity in complex trabecular and vascular structures compared to existing neural rendering baselines.

cs.CV↗

arXiv2026

VCC-DSA: A Novel Vascular Consistency Constrained DSA Imaging Model for Motion Artifact Suppression

Digital Subtraction Angiography (DSA) is a clinically significant imaging technique for diagnosing cerebrovascular disease, as gold-standard. However, the artifacts caused by motion of high-attenuation tissues such as bones, teeth, and catheters, seriously reduce the visibility of blood vessels. This paper presents a novel Vascular Consistency Constrained DSA Imaging Model (VCC-DSA) for robust motion suppression and precise vascular imaging with the following designs: 1) We specially design a Learning-based Subtraction Mapping Paradigm, so that the ill-posed problem of existing learning-based methods can be solved to enhance the stability of the algorithm. 2) Our model effectively develops Residual Dense Blocks and details-shortcut to improve the performance under complex structures, such as moving bones overlapping with blood vessels, and small features, like peripheral vessels. 3) An innovative Vascular Consistency Strategy is proposed to extract intrinsically consistency from the various relative motions in mask-live images, so that spontaneously distils the vascular structure with contrast-agent development and robustly suppress motion artifacts, and also naturally alleviates the high matching requirements of data. 4) We creatively design a Mixup-based Data Self-evolution Strategy for data-intra self-enhancement in training loop, so that the training data gains dynamically optimized to promote model better learning the vascular features, and excluding the irrelevant structures in live/mask image and even the inevitable-artifacts/fake-structure in label. Prospectively, to further evaluate practical value, an actual general anesthesia animal experiment is specially conducted, besides the assessment on human clinical data. Compared with other method, our model improves the PSNR and SSIM by 73.4% and 8.56%, respectively.

eess.IV↗

arXiv2026

Accelerating Scientific Discovery with Autonomous Goal-evolving Agents

There has been unprecedented interest in developing agents that expand the boundary of scientific discovery, primarily by optimizing quantitative objective functions specified by scientists. However, for grand challenges in science, these objectives may only be imperfect proxies. We argue that automating objective function design is a central, yet unmet need for scientific discovery agents. In this work, we introduce the Scientific Autonomous Goal-evolving Agent (SAGA) to address this challenge. SAGA employs a bi-level architecture in which an outer loop of LLM agents analyzes optimization outcomes, proposes new objectives, and converts them into computable scoring functions, while an inner loop performs solution optimization under the current objectives. This bi-level design enables systematic exploration of the space of objectives and their trade-offs, rather than treating them as fixed inputs. We demonstrate the framework through a wide range of design applications, including antibiotics, nanobodies, functional DNA sequences, inorganic materials, and chemical processes. Notably, our experimental validation identifies a structurally novel hit with promising potency and safety profiles for E. coli in the antibiotic design task, and three de novo PD-L1 binders in the nanobody design task. These results suggest that automating objective formulation can substantially improve the effectiveness of scientific discovery agents.

cs.AI↗

arXiv2026

Physically Valid Biomolecular Interaction Modeling with Gauss-Seidel Projection

Biomolecular interaction modeling has been substantially advanced by foundation models, yet they often produce all-atom structures that violate basic steric feasibility. We address this limitation by enforcing physical validity as a strict constraint during both training and inference with a uniffed module. At its core is a differentiable projection that maps the provisional atom coordinates from the diffusion model to the nearest physically valid conffguration. This projection is achieved using a Gauss-Seidel scheme, which exploits the locality and sparsity of the constraints to ensure stable and fast convergence at scale. By implicit differentiation to obtain gradients, our module integrates seamlessly into existing frameworks for end-to-end ffnetuning. With our Gauss-Seidel projection module in place, two denoising steps are sufffcient to produce biomolecular complexes that are both physically valid and structurally accurate. Across six benchmarks, our 2-step model achieves the same structural accuracy as state-of-the-art 200-step diffusion baselines, delivering approximately 10 times faster wall-clock speed while guaranteeing physical validity. The code is available at https://github.com/chensiyuan030105/ProteinGS.git.

q-bio.BM↗

arXiv2026

PLOT-CT: Pre-log Voronoi Decomposition Assisted Generation for Low-dose CT Reconstruction

Low-dose computed tomography (LDCT) reconstruction is fundamentally challenged by severe noise and compromised data fidelity under reduced radiation exposure. Most existing methods operate either in the image or post-log projection domain, which fails to fully exploit the rich structural information in pre-log measurements while being highly susceptible to noise. The requisite logarithmic transformation critically amplifies noise within these data, imposing exceptional demands on reconstruction precision. To overcome these challenges, we propose PLOT-CT, a novel framework for Pre-Log vOronoi decomposiTion-assisted CT generation. Our method begins by applying Voronoi decomposition to pre-log sinograms, disentangling the data into distinct underlying components, which are embedded in separate latent spaces. This explicit decomposition significantly enhances the model's capacity to learn discriminative features, directly improving reconstruction accuracy by mitigating noise and preserving information inherent in the pre-log domain. Extensive experiments demonstrate that PLOT-CT achieves state-of-the-art performance, attaining a 2.36dB PSNR improvement over traditional methods at the 1e4 incident photon level in the pre-log domain.

cs.CV↗

arXiv2026

Transfer Learning Through Conditional Quantile Matching

We introduce a transfer learning framework for regression that leverages heterogeneous source domains to improve predictive performance in a data-scarce target domain. Our approach learns a conditional generative model separately for each source domain and calibrates the generated responses to the target domain via conditional quantile matching. This distributional alignment step corrects general discrepancies between source and target domains without imposing restrictive assumptions such as covariate or label shift. The resulting framework provides a principled and flexible approach to high-quality data augmentation for downstream learning tasks in the target domain. From a theoretical perspective, we show that an empirical risk minimizer (ERM) trained on the augmented dataset achieves a tighter excess risk bound than the target-only ERM under mild conditions. In particular, we establish new convergence rates for the quantile matching estimator that governs the transfer bias-variance tradeoff. From a practical perspective, extensive simulations and real data applications demonstrate that the proposed method consistently improves prediction accuracy over target-only learning and competing transfer learning methods.

stat.ML↗

arXiv2025

Iterative Diffusion-Refined Neural Attenuation Fields for Multi-Source Stationary CT Reconstruction: NAF Meets Diffusion Model

Multi-source stationary computed tomography (CT) has recently attracted attention for its ability to achieve rapid image reconstruction, making it suitable for time-sensitive clinical and industrial applications. However, practical systems are often constrained by ultra-sparse-view sampling, which significantly degrades reconstruction quality. Traditional methods struggle under ultra-sparse-view settings, where interpolation becomes inaccurate and the resulting reconstructions are unsatisfactory. To address this challenge, this study proposes Diffusion-Refined Neural Attenuation Fields (Diff-NAF), an iterative framework tailored for multi-source stationary CT under ultra-sparse-view conditions. Diff-NAF combines a Neural Attenuation Field representation with a dual-branch conditional diffusion model. The process begins by training an initial NAF using ultra-sparse-view projections. New projections are then generated through an Angle-Prior Guided Projection Synthesis strategy that exploits inter view priors, and are subsequently refined by a Diffusion-driven Reuse Projection Refinement Module. The refined projections are incorporated as pseudo-labels into the training set for the next iteration. Through iterative refinement, Diff-NAF progressively enhances projection completeness and reconstruction fidelity under ultra-sparse-view conditions, ultimately yielding high-quality CT reconstructions. Experimental results on multiple simulated 3D CT volumes and real projection data demonstrate that Diff-NAF achieves the best performance under ultra-sparse-view conditions.

cs.CV↗

arXiv2025

BLADE: Benchmarking Language Model Agents for Data-Driven Science

Data-driven scientific discovery requires the iterative integration of scientific domain knowledge, statistical expertise, and an understanding of data semantics to make nuanced analytical decisions, e.g., about which variables, transformations, and statistical models to consider. LM-based agents equipped with planning, memory, and code execution capabilities have the potential to support data-driven science. However, evaluating agents on such open-ended tasks is challenging due to multiple valid approaches, partially correct steps, and different ways to express the same decisions. To address these challenges, we present BLADE, a benchmark to automatically evaluate agents' multifaceted approaches to open-ended research questions. BLADE consists of 12 datasets and research questions drawn from existing scientific literature, with ground truth collected from independent analyses by expert data scientists and researchers. To automatically evaluate agent responses, we developed corresponding computational methods to match different representations of analyses to this ground truth. Though language models possess considerable world knowledge, our evaluation shows that they are often limited to basic analyses. However, agents capable of interacting with the underlying data demonstrate improved, but still non-optimal, diversity in their analytical decision making. Our work enables the evaluation of agents for data-driven science and provides researchers deeper insights into agents' analysis approaches.

cs.CL↗

arXiv2025

A Practical Introduction to Regression-based Causal Inference in Meteorology (II): Unmeasured confounders

One obstacle to ``elevating'' correlation to causation is the phenomenon of confounding, i.e., when a correlation between two variables exists because both variables are in fact caused by a third variable, called a confounder. The situation where the confounders are measured is examined in an earlier, accompanying article. Here, it is shown that even when the confounding variables are not measured, under certain conditions it is still possible to estimate the causal effect via a regression-based method that uses the notion of instrumental variables. Using a meteorological data set, similar to that in the sister article, a number of different estimates of the causal effect are compared and contrasted. It is shown that the instrumental-variable estimates of causal effect depend on the choice of the instrumental variable, and that meteorological considerations are important in resolving the ambiguity. R code is provided for generating all of the results, and numerous directions for future work are outlined.

stat.AP↗

arXiv2025

A Practical Introduction to Regression-based Causal Inference in Meteorology (I): All confounders measured

Whether a variable is the cause of another, or simply associated with it, is often an important scientific question. Causal Inference is the name associated with the body of techniques for addressing that question in a statistical setting. Although assessing causality is relatively straightforward in the presence of temporal information, outside of that setting - the situation considered here - it is more difficult to assess causal effects. The development of the field of causal inference has involved concepts from a wide range of topics, thereby limiting its adoption across some fields, including meteorology. However, at its core, the requisite knowledge for causal inference involves little more than basic probability theory and regression, topics familiar to most meteorologists. By focusing on these core areas, this and a companion article provide a steppingstone for the meteorology community into the field of (non-temporal) causal inference. Although some theoretical foundations are presented, the main goal is the application of a specific method, called matching, to a problem in meteorology. The data for the application are in public domain, and R code is provided as well, forming an easy path for meteorology students and researchers to enter the field.

stat.AP↗

arXiv2025

A Comparative Review of RNA Language Models

Given usefulness of protein language models (LMs) in structure and functional inference, RNA LMs have received increased attentions in the last few years. However, these RNA models are often not compared against the same standard. Here, we divided RNA LMs into three classes (pretrained on multiple RNA types (especially noncoding RNAs), specific-purpose RNAs, and LMs that unify RNA with DNA or proteins or both) and compared 13 RNA LMs along with 3 DNA and 1 protein LMs as controls in zero-shot prediction of RNA secondary structure and functional classification. Results shows that the models doing well on secondary structure prediction often perform worse in function classification or vice versa, suggesting that more balanced unsupervised training is needed.

q-bio.BM↗

arXiv2025

Mode and Ridge Estimation in Euclidean and Directional Product Spaces: A Mean Shift Approach

The set of local modes and density ridge lines are important summary characteristics of the data-generating distribution. In this work, we focus on estimating local modes and density ridges from point cloud data in a product space combining two or more Euclidean and/or directional metric spaces. Specifically, our approach extends the (subspace constrained) mean shift algorithm to such product spaces, addressing potential challenges in the generalization process. We establish the algorithmic convergence of the proposed methods, along with practical implementation guidelines. Experiments on simulated and real-world datasets demonstrate the effectiveness of our proposed methods.

stat.ML↗

arXiv2025

Doubly Robust Inference on Causal Derivative Effects for Continuous Treatments

Statistical methods for causal inference with continuous treatments mainly focus on estimating the mean potential outcome function, commonly known as the dose-response curve. However, it is often not the dose-response curve but its derivative function that signals the treatment effect. In this paper, we investigate nonparametric inference on the derivative of the dose-response curve with and without the positivity condition. Under the positivity and other regularity conditions, we propose a doubly robust (DR) inference method for estimating the derivative of the dose-response curve using kernel smoothing. When the positivity condition is violated, we demonstrate the inconsistency of conventional inverse probability weighting (IPW) and DR estimators, and introduce novel bias-corrected IPW and DR estimators. In all settings, our DR estimator achieves asymptotic normality at the standard nonparametric rate of convergence with nonparametric efficiency guarantees. Additionally, our approach reveals an interesting connection to nonparametric support and level set estimation problems. Finally, we demonstrate the applicability of our proposed estimators through simulations and a case study of evaluating a job training program.

stat.ME↗

arXiv2025

Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset. In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas's robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on https://github.com/yikunpku/Atomas.

q-bio.QM↗

arXiv2025

Nonparametric Inference on Dose-Response Curves Without the Positivity Condition

Existing statistical methods in causal inference often assume the positivity condition, where every individual has some chance of receiving any treatment level regardless of covariates. This assumption could be violated in observational studies with continuous treatments. In this paper, we develop identification and estimation theories for causal effects with continuous treatments (i.e., dose-response curves) without relying on the positivity condition. Our approach identifies and estimates the derivative of the treatment effect for each observed sample, integrating it to the treatment level of interest to mitigate bias from the lack of positivity. The method is grounded in a weaker assumption, satisfied by additive confounding models. We propose a fast and reliable numerical recipe for computing our integral estimator in practice and derive its asymptotic properties. To enable valid inference on the dose-response curve and its derivative, we use the nonparametric bootstrap and establish its consistency. The performances of our proposed estimators are validated through simulation studies and an analysis of the effect of air pollution exposure (PM$_{2.5}$) on cardiovascular mortality rates.

stat.ME↗