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Chao Yan

Chao Yan contributes to research discovery and scholarly infrastructure.

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Published work

15 published item(s)

preprint2026arXiv

CLEAR: Revealing How Noise and Ambiguity Degrade Reliability in LLMs for Medicine

Medical large language model (LLM) evaluations rely on simplified, exam-style benchmarks that rarely reflect the ambiguity of real-world medical inquiries. We introduce the CLinical Evaluation of Ambiguity and Reliability (CLEAR) framework, which assesses how decision-space presentation, ambiguity, and uncertainty affect LLMs' reasoning on medical benchmarks. CLEAR systematically perturbs (1) the number of plausible answer options, (2) the presence of a ground truth or abstention option, and (3) the semantic framing of answer options. Applying CLEAR on three benchmarks evaluated across 17 LLMs reveals three notable limitations of existing evaluation methods. First, increasing the number of plausible answers degrades a model's ability to identify the correct answer and abstain against incorrect ones. Second, this lack of caution intensifies as the framing of abstention shifts from assertive rejection like "None of the Above" to uncertainty admission like "I don't know" (IDK). Notably, just including IDK in the answer space increases incorrect answer selections. Lastly, we formalize the performance gap between identifying the correct answer and abstaining from incorrect ones as the humility deficit, which worsens with model scale. Our findings reveal limitations in standard medical benchmarks and underscore that scaling alone does not resolve LLM reliability issues.

preprint2022arXiv

A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models

Synthetic health data have the potential to mitigate privacy concerns when sharing data to support biomedical research and the development of innovative healthcare applications. Modern approaches for data generation based on machine learning, generative adversarial networks (GAN) methods in particular, continue to evolve and demonstrate remarkable potential. Yet there is a lack of a systematic assessment framework to benchmark methods as they emerge and determine which methods are most appropriate for which use cases. In this work, we introduce a generalizable benchmarking framework to appraise key characteristics of synthetic health data with respect to utility and privacy metrics. We apply the framework to evaluate synthetic data generation methods for electronic health records (EHRs) data from two large academic medical centers with respect to several use cases. The results illustrate that there is a utility-privacy tradeoff for sharing synthetic EHR data. The results further indicate that no method is unequivocally the best on all criteria in each use case, which makes it evident why synthetic data generation methods need to be assessed in context.

preprint2022arXiv

Adaptive Model Refinement Approach for Bayesian Uncertainty Quantification in Turbulence Model

The Bayesian uncertainty quantification technique has become well established in turbulence modeling over the past few years. However, it is computationally expensive to construct a globally accurate surrogate model for Bayesian inference in a high-dimensional design space, which limits uncertainty quantification for complex flow configurations. Borrowing ideas from stratified sampling and inherited sampling, an adaptive model refinement approach is proposed in this work, which concentrates on asymptotically improving the local accuracy of the surrogate model in the high-posterior-density region by adaptively appending model evaluation points. To achieve this goal, a modification of inherited Latin hypercube sampling is proposed and then integrated into the Bayesian framework. The effectiveness and efficiency of the proposed approach are demonstrated through a two-dimensional heat source inversion problem and its extension to a high-dimensional design space. Compared with the prior-based method, the adaptive model refinement approach has the ability to obtain more reliable inference results using fewer evaluation points. Finally, the approach is applied to parametric uncertainty quantification of the Menter shear-stress transport turbulence model for an axisymmetric transonic bump flow and provides convincing numerical results.

preprint2022arXiv

Dissolved gas monitoring probe without liquid-gas separation under strong electromagnetic interference

Rapid and direct monitoring of dissolved gases in liquids under strong electromagnetic interference is very important. Electronic gas sensors that can be placed into liquids are difficult to work reliably under strong electromagnetic fields. The existing optical monitoring techniques for dissolved gases all require gas-liquid separation, and are conducted in gas phase, which have poor timeliness. In this paper, a dissolved gas monitoring probe without liquid-gas separation under strong electromagnetic interference is proposed. We take transformer oil-dissolved acetylene monitoring as an example, an oil-core photonic crystal fiber photothermal interferometry probe is proposed and demonstrates the feasibility of trace oil-dissolved acetylene directly monitoring without oil-gas separation. The minimum detection limit reaches 1.4 ppm, and the response time is about 70 minutes. Due to the good insulation performance and the compact size, the all-fiber probe provides applicability to be placed into transformer oil and perform on-line monitoring under strong electromagnetic interference.

preprint2022arXiv

Distillation to Enhance the Portability of Risk Models Across Institutions with Large Patient Claims Database

Artificial intelligence, and particularly machine learning (ML), is increasingly developed and deployed to support healthcare in a variety of settings. However, clinical decision support (CDS) technologies based on ML need to be portable if they are to be adopted on a broad scale. In this respect, models developed at one institution should be reusable at another. Yet there are numerous examples of portability failure, particularly due to naive application of ML models. Portability failure can lead to suboptimal care and medical errors, which ultimately could prevent the adoption of ML-based CDS in practice. One specific healthcare challenge that could benefit from enhanced portability is the prediction of 30-day readmission risk. Research to date has shown that deep learning models can be effective at modeling such risk. In this work, we investigate the practicality of model portability through a cross-site evaluation of readmission prediction models. To do so, we apply a recurrent neural network, augmented with self-attention and blended with expert features, to build readmission prediction models for two independent large scale claims datasets. We further present a novel transfer learning technique that adapts the well-known method of born-again network (BAN) training. Our experiments show that direct application of ML models trained at one institution and tested at another institution perform worse than models trained and tested at the same institution. We further show that the transfer learning approach based on the BAN produces models that are better than those trained on just a single institution's data. Notably, this improvement is consistent across both sites and occurs after a single retraining, which illustrates the potential for a cheap and general model transfer mechanism of readmission risk prediction.

preprint2022arXiv

Dynamically Adjusting Case Reporting Policy to Maximize Privacy and Utility in the Face of a Pandemic

Supporting public health research and the public's situational awareness during a pandemic requires continuous dissemination of infectious disease surveillance data. Legislation, such as the Health Insurance Portability and Accountability Act of 1996 (HIPAA) and recent state-level regulations, permits sharing de-identified person-level data; however, current de-identification approaches are limited. namely, they are inefficient, relying on retrospective disclosure risk assessments, and do not flex with changes in infection rates or population demographics over time. In this paper, we introduce a framework to dynamically adapt de-identification for near-real time sharing of person-level surveillance data. The framework leverages a simulation mechanism, capable of application at any geographic level, to forecast the re-identification risk of sharing the data under a wide range of generalization policies. The estimates inform weekly, prospective policy selection to maintain the proportion of records corresponding to a group size less than 11 (PK11) at or below 0.1. Fixing the policy at the start of each week facilitates timely dataset updates and supports sharing granular date information. We use August 2020 through October 2021 case data from Johns Hopkins University and the Centers for Disease Control and Prevention to demonstrate the framework's effectiveness in maintaining the PK!1 threshold of 0.01. When sharing COVID-19 county-level case data across all US counties, the framework's approach meets the threshold for 96.2% of daily data releases, while a policy based on current de-identification techniques meets the threshold for 32.3%. Periodically adapting the data publication policies preserves privacy while enhancing public health utility through timely updates and sharing epidemiologically critical features.

preprint2022arXiv

Necessary Conditions in Multi-Server Differential Privacy

We consider protocols where users communicate with multiple servers to perform a computation on the users' data. An adversary exerts semi-honest control over many of the parties but its view is differentially private with respect to honest users. Prior work described protocols that required multiple rounds of interaction or offered privacy against a computationally bounded adversary. Our work presents limitations of non-interactive protocols that offer privacy against unbounded adversaries. We show these protocols demand exponentially more samples for some learning and estimation tasks than centrally private counterparts. This means performing as well as the central model requires interactivity or computational differential privacy, or both.

preprint2022arXiv

Seeking Patterns, Not just Memorizing Procedures: Contrastive Learning for Solving Math Word Problems

Math Word Problem (MWP) solving needs to discover the quantitative relationships over natural language narratives. Recent work shows that existing models memorize procedures from context and rely on shallow heuristics to solve MWPs. In this paper, we look at this issue and argue that the cause is a lack of overall understanding of MWP patterns. We first investigate how a neural network understands patterns only from semantics, and observe that, if the prototype equations are the same, most problems get closer representations and those representations apart from them or close to other prototypes tend to produce wrong solutions. Inspired by it, we propose a contrastive learning approach, where the neural network perceives the divergence of patterns. We collect contrastive examples by converting the prototype equation into a tree and seeking similar tree structures. The solving model is trained with an auxiliary objective on the collected examples, resulting in the representations of problems with similar prototypes being pulled closer. We conduct experiments on the Chinese dataset Math23k and the English dataset MathQA. Our method greatly improves the performance in monolingual and multilingual settings.

preprint2021arXiv

Local Measurements of Shubnikov-de Haas Oscillations in Graphene Systems

Shubnikov-de Haas (SdH) oscillations, the most well-known magneto-oscillations caused by the quantization of electron energy levels in the presence of magnetic fields in two-dimensional (2D) electron systems, can be used to determine Fermi-surface properties and directly measure the Berry phase of the 2D systems. It is usually thought that transport measurements are required to measure the SdH oscillations. Contradicting this belief, we demonstrate that the SdH oscillations can be measured in graphene systems by carrying out scanning tunneling spectroscopy (STS) measurements. The energy-momentum dispersions and Berry phases of monolayer, Bernal-stacked bilayer, and ABC-stacked trilayer graphene are obtained according to the measured SdH oscillations in the STS spectra. It is possible to obtain the SdH oscillations when the size of the 2D systems is larger than the magnetic length and, importantly, no gate electrode is required in the STS measurement, therefore, the reported method in this work is applicable to a wide range of materials.

preprint2021arXiv

Overlapping boundary layers in coastal oceans

Boundary layer turbulence in coastal regions differs from that in deep ocean because of bottom interactions. In this paper, we focus on the merging of surface and bottom boundary layers in a finite-depth coastal ocean by numerically solving the wave-averaged equations using a large eddy simulation method. The ocean fluid is driven by combined effects of wind stress, surface wave, and a steady current in the presence of stable vertical stratification. The resulting flow consists of two overlapping boundary layers, i.e. surface and bottom boundary layers, separated by an interior stratification. The overlapping boundary layers evolve through three phases, i.e. a rapid deepening, an oscillatory equilibrium and a prompt merger, separated by two transitions. Before the merger, internal waves are observed in the stratified layer, and they are excited mainly by Langmuir turbulence in the surface boundary layer. These waves induce a clear modulation on the bottom-generated turbulence, facilitating the interaction between the surface and bottom boundary layers. After the merger, the Langmuir circulations originally confined to the surface layer are found to grow in size and extend down to the sea bottom (even though the surface waves do not feel the bottom), reminiscent of the well-organized Langmuir supercells. These full-depth Langmuir circulations promote the vertical mixing and enhance the bottom shear, leading to a significant enhancement of turbulence levels in the vertical column.

preprint2021arXiv

Realizing One-dimensional Metallic States in Graphene via Periodically Coupled Zeroth Pseudo-Landau Levels

Strain-induced pseudo-magnetic fields can mimic real magnetic fields to generate a zero-magnetic-field analogue of the Landau levels (LLs), i.e., the pseudo-LLs, in graphene. The distinct nature of the pseudo-LLs enables one to realize novel electronic states beyond that can be feasible with real LLs. Here, we report the realization of one-dimensional (1D) metallic states, which can be described well by the Su-Schrieffer-Heeger model, in graphene via periodically coupled zeroth pseudo-LLs. In our experiment, nanoscale strained structures embedded with pseudo-LLs are generated periodically along 1D channel of suspended graphene monolayer. Our experiments demonstrate that the zeroth pseudo-LLs of these strained structures are coupled to form metallic states, exhibiting a serpentine pattern that snakes back and forth along the 1D suspended graphene monolayer. These results are verified theoretically by large-scale tight-binding calculations of the strained samples. Our result provides a new pathway to realize novel quantum states and engineer the electronic properties of graphene by using the localized pseudo-LLs as building blocks.

preprint2020arXiv

A new paradigm of dissipation-controllable, multi-scale resolving schemes for compressible flows

The scale-resolving simulation of high speed compressible flow through direct numerical simulation (DNS) or large eddy simulation (LES) requires shock-capturing schemes to be more accurate for resolving broadband turbulence and robust for capturing strong shock waves. In this work, we develop a new paradigm of dissipation-controllable, shock capturing scheme to resolve multi-scale flow structures in high speed compressible flow. This novel paradigm of shock-capturing scheme is named as PnTm-BVD-CD. The proposed PnTm-BVD-CD scheme has following desirable properties. First, it can capture large-scale discontinuous structures such as strong shock waves without obvious non-physical oscillations while resolving sharp contact, material interface and shear layer. Secondly, the numerical dissipation property of PnTm-BVD-CD can be effectively controlled between n+1 order upwind-biased scheme and non-dissipative n+2 order central scheme through a simple tunable parameter $λ$. Thirdly, with $λ=0.5$ the scheme can recover to n+2 order non-dissipative central interpolation for smooth solution over all wavenumber, which is preferable for solving small-scale structures in DNS as well as resolvable-scale in explicit LES. Finally, the under-resolved small-scale can be solved with dissipation controllable algorithm through so-called implicit LES (ILES) approach.

preprint2020arXiv

Generating Electronic Health Records with Multiple Data Types and Constraints

Sharing electronic health records (EHRs) on a large scale may lead to privacy intrusions. Recent research has shown that risks may be mitigated by simulating EHRs through generative adversarial network (GAN) frameworks. Yet the methods developed to date are limited because they 1) focus on generating data of a single type (e.g., diagnosis codes), neglecting other data types (e.g., demographics, procedures or vital signs) and 2) do not represent constraints between features. In this paper, we introduce a method to simulate EHRs composed of multiple data types by 1) refining the GAN model, 2) accounting for feature constraints, and 3) incorporating key utility measures for such generation tasks. Our analysis with over $770,000$ EHRs from Vanderbilt University Medical Center demonstrates that the new model achieves higher performance in terms of retaining basic statistics, cross-feature correlations, latent structural properties, feature constraints and associated patterns from real data, without sacrificing privacy.

preprint2020arXiv

Spectroscopic evidence for a spin and valley polarized metallic state in a non-magic-angle twisted bilayer graphene

In the magic-angle twisted bilayer graphene (MA-TBG), strong electron-electron (e-e) correlations caused by the band-flattening lead to many exotic quantum phases such as superconductivity, correlated insulator, ferromagnetism, and quantum anomalous Hall effects, when its low-energy van Hove singularities (VHSs) are partially filled. Here our high-resolution scanning tunneling microscope and spectroscopy measurements demonstrate that the e-e correlation in a non-magic-angle TBG with a twist angle θ = 1.49 still plays an important role in determining its electronic properties. Our most interesting observation on that sample is that when one of its VHS is partially filled, the one associated peak in the spectrum splits into four peaks. Our analysis based on the continuum model suggests that such a one-to-four split of the VHS originates from the formation of an interaction-driven spin-valley-polarized metallic state near the VHS, lifting both the spin and valley degeneracies. Our results for this non-magic-angle TBG reveal a new symmetry-breaking phase, which has not been identified in the MA-TBG or in other systems.

preprint2020arXiv

Tunable lattice reconstruction and bandwidth of flat bands in magic-angle twisted bilayer graphene

The interplay between interlayer van der Waals interaction and intralayer lattice distortion can lead to structural reconstruction in slightly twisted bilayer graphene (TBG) with the twist angle being smaller than a characteristic angle θc. Experimentally, the θc is demonstrated to be very close to the magic angle (θ ~ 1.05°). In this work, we address the transition between reconstructed and unreconstructed structures of the TBG across the magic angle by using scanning tunnelling microscopy (STM). Our experiment demonstrates that both the two structures are stable in the TBG around the magic angle. By applying a STM tip pulse, we show that the two structures can be switched to each other and the bandwidth of the flat bands, which plays a vital role in the emergent strongly correlated states in the magic-angle TBG, can be tuned. The observed tunable lattice reconstruction and bandwidth of the flat bands provide an extra control knob to manipulate the exotic electronic states of the TBG near the magic angle.