arXiv subjects

Shu Yang

Publications and source records attributed to Shu Yang.

At least 163 records · Page 9Linked to original sources

arXiv2024

Broadband measurement of Feibelman's quantum surface response functions

The Feibelman $d$-parameter, a mesoscopic complement to the local bulk permittivity, describes quantum optical surface responses for interfaces, including nonlocality, spill-in and-out, and surface-enabled Landau damping. It has been incorporated into the macroscopic Maxwellian framework for convenient modeling and understanding of nanoscale electromagnetic phenomena, calling for the compilation of a $d$-parameter database for interfaces of interest in nano-optics. However, accurate first-principles calculations of $d$-parameters face computational challenges, whereas existing measurements of $d$-parameters are scarce and restricted to narrow spectral windows. We demonstrate a general broadband ellipsometric approach to measure $d$-parameters at a gold--air interface across the visible--ultraviolet regimes. Gold is found to spill in and spill out at different frequencies. We also observe gold's Bennett mode, a surface-dipole resonance associated with a pole of the $d$-parameter, around 2.5 eV. Our measurements give rise to and are further validated by the passivity and Kramers--Kronig causality analysis of $d$-parameters. Our work advances the understanding of quantum surface response and may enable applications like enhanced electron field emission.

physics.optics↗

arXiv2024

Synthetic gain for electron-beam spectroscopy

Electron-beam microscopy and spectroscopy featuring atomic-scale spatial resolution have become essential tools used daily in almost all branches of nanoscale science and technology. As a natural supercontinuum source of light, free electrons couple with phonons, plasmons, electron-hole pairs, inter- and intra-band transitions, and inner-shell ionization. The multiple excitations, intertwined with the intricate nature of nanostructured samples, present significant challenges in isolating specific spectral characteristics amidst complex experimental backgrounds. Here we introduce the approach of synthetic complex frequency waves to mitigate these challenges in free-electron--light interaction. The complex frequency waves, created through causality-informed coherent superposition of real-frequency waves induced by free electrons, offer virtual gain to offset material losses. This amplifies and enhances spectral features, as confirmed by our electron energy loss and cathodoluminescence measurements on multi-layer membranes, suspended nanoparticles, and film-coupled nanostructures. Strikingly, we reveal that our approach can retrieve resonance excitation completely buried underneath the zero-loss peak, substantially enhance the quality of hyperspectral imaging, and resolve entangled multiple-photon-electron events in their quantum interaction. Our findings indicate the versatile utility of complex frequency waves in various electron-beam spectroscopy and their promising diagnostic capabilities in free-electron quantum optics.

physics.optics↗

arXiv2024

Data fusion methods for the heterogeneity of treatment effect and confounding function

The heterogeneity of treatment effect (HTE) lies at the heart of precision medicine. Randomized controlled trials are gold-standard for treatment effect estimation but are typically underpowered for heterogeneous effects. In contrast, large observational studies have high predictive power but are often confounded due to the lack of randomization of treatment. We show that an observational study, even subject to hidden confounding, may be used to empower trials in estimating the HTE using the notion of confounding function. The confounding function summarizes the impact of unmeasured confounders on the difference between the observed treatment effect and the causal treatment effect, given the observed covariates, which is unidentifiable based only on the observational study. Coupling the trial and observational study, we show that the HTE and confounding function are identifiable. We then derive the semiparametric efficient scores and the integrative estimators of the HTE and confounding function. We clarify the conditions under which the integrative estimator of the HTE is strictly more efficient than the trial estimator. Finally, we illustrate the integrative estimators via simulation and an application.

stat.ME↗

arXiv2024

Improving randomized controlled trial analysis via data-adaptive borrowing

In recent years, real-world external controls have grown in popularity as a tool to empower randomized placebo-controlled trials, particularly in rare diseases or cases where balanced randomization is unethical or impractical. However, as external controls are not always comparable to the trials, direct borrowing without scrutiny may heavily bias the treatment effect estimator. Our paper proposes a data-adaptive integrative framework capable of preventing unknown biases of the external controls. The adaptive nature is achieved by dynamically sorting out a comparable subset of the external controls via bias penalization. Our proposed method can simultaneously achieve (a) the semiparametric efficiency bound when the external controls are comparable and (b) selective borrowing that mitigates the impact of the existence of incomparable external controls. Furthermore, we establish statistical guarantees, including consistency, asymptotic distribution, and inference, providing type-I error control and good power. Extensive simulations and two real-data applications show that the proposed method leads to improved performance over the trial-only estimator across various bias-generating scenarios.

stat.ME↗

arXiv2024

Visual Mamba: A Survey and New Outlooks

Mamba, a recent selective structured state space model, excels in long sequence modeling, which is vital in the large model era. Long sequence modeling poses significant challenges, including capturing long-range dependencies within the data and handling the computational demands caused by their extensive length. Mamba addresses these challenges by overcoming the local perception limitations of convolutional neural networks and the quadratic computational complexity of Transformers. Given its advantages over these mainstream foundation architectures, Mamba exhibits great potential to be a visual foundation architecture. Since January 2024, Mamba has been actively applied to diverse computer vision tasks, yielding numerous contributions. To help keep pace with the rapid advancements, this paper reviews visual Mamba approaches, analyzing over 200 papers. This paper begins by delineating the formulation of the original Mamba model. Subsequently, it delves into representative backbone networks, and applications categorized using different modalities, including image, video, point cloud, and multi-modal data. Particularly, we identify scanning techniques as critical for adapting Mamba to vision tasks, and decouple these scanning techniques to clarify their functionality and enhance their flexibility across various applications. Finally, we discuss the challenges and future directions, providing insights into new outlooks in this fast evolving area. A comprehensive list of visual Mamba models reviewed in this work is available at https://github.com/Ruixxxx/Awesome-Vision-Mamba-Models.

cs.CV↗

arXiv2024

Generalizing Hyperedge Expansion for Hyper-relational Knowledge Graph Modeling

By representing knowledge in a primary triple associated with additional attribute-value qualifiers, hyper-relational knowledge graph (HKG) that generalizes triple-based knowledge graph (KG) has been attracting research attention recently. Compared with KG, HKG is enriched with the semantic qualifiers as well as the hyper-relational graph structure. However, to model HKG, existing studies mainly focus on either semantic information or structural information therein, which however fail to capture both simultaneously. To tackle this issue, in this paper, we generalize the hyperedge expansion in hypergraph learning and propose an equivalent transformation for HKG modeling, referred to as TransEQ. Specifically, the equivalent transformation transforms a HKG to a KG, which considers both semantic and structural characteristics. Then an encoder-decoder framework is developed to bridge the modeling research between KG and HKG. In the encoder part, KG-based graph neural networks are leveraged for structural modeling; while in the decoder part, various HKG-based scoring functions are exploited for semantic modeling. Especially, we design the sharing embedding mechanism in the encoder-decoder framework with semantic relatedness captured. We further theoretically prove that TransEQ preserves complete information in the equivalent transformation, and also achieves full expressivity. Finally, extensive experiments on three benchmarks demonstrate the superior performance of TransEQ in terms of both effectiveness and efficiency. On the largest benchmark WikiPeople, TransEQ significantly improves the state-of-the-art models by 15\% on MRR.

cs.AI↗

arXiv2024

GSCo: Towards Generalizable AI in Medicine via Generalist-Specialist Collaboration

Generalist foundation models (GFMs) are renowned for their exceptional capability and flexibility in effectively generalizing across diverse tasks and modalities. In the field of medicine, while GFMs exhibit superior generalizability based on their extensive intrinsic knowledge as well as proficiency in instruction following and in-context learning, specialist models excel in precision due to their domain knowledge. In this work, for the first time, we explore the synergy between the GFM and specialist models, to enable precise medical image analysis on a broader scope. Specifically, we propose a cooperative framework, Generalist-Specialist Collaboration (GSCo), which consists of two stages, namely the construction of GFM and specialists, and collaborative inference on downstream tasks. In the construction stage, we develop MedDr, the largest open-source GFM tailored for medicine, showcasing exceptional instruction-following and in-context learning capabilities. Meanwhile, a series of lightweight specialists are crafted for downstream tasks with low computational cost. In the collaborative inference stage, we introduce two cooperative mechanisms, Mixture-of-Expert Diagnosis and Retrieval-Augmented Diagnosis, to harvest the generalist's in-context learning abilities alongside the specialists' domain expertise. For a comprehensive evaluation, we curate a large-scale benchmark featuring 28 datasets and about 250,000 images. Extensive results demonstrate that MedDr consistently outperforms state-of-the-art GFMs on downstream datasets. Furthermore, GSCo exceeds both GFMs and specialists across all out-of-domain disease diagnosis datasets. These findings indicate a significant paradigm shift in the application of GFMs, transitioning from separate models for specific tasks to a collaborative approach between GFMs and specialists, thereby advancing the frontiers of generalizable AI in medicine.

cs.CV↗

arXiv2024

Semi-Parametric Sensitivity Analysis for Trials with Irregular and Informative Assessment Times

Many trials are designed to collect outcomes at or around pre-specified times after randomization. If there is variability in the times when participants are actually assessed, this can pose a challenge to learning the effect of treatment, since not all participants have outcome assessments at the times of interest. Furthermore, observed outcome values may not be representative of all participants' outcomes at a given time. Methods have been developed that account for some types of such irregular and informative assessment times; however, since these methods rely on untestable assumptions, sensitivity analyses are needed. We develop a methodology that is benchmarked at the explainable assessmen (EA) assumption, under which assessment and outcomes at each time are related only through data collected prior to that time. Our method uses an exponential tilting assumption, governed by a sensitivity analysis parameter, that posits deviations from the EA assumption. Our inferential strategy is based on a new influence function-based, augmented inverse intensity-weighted estimator. Our approach allows for flexible semiparametric modeling of the observed data, which is separated from specification of the sensitivity parameter. We apply our method to a randomized trial of low-income individuals with uncontrolled asthma, and we illustrate implementation of our estimation procedure in detail.

stat.ME↗

arXiv2024

Prompt-SAW: Leveraging Relation-Aware Graphs for Textual Prompt Compression

Large Language Models (LLMs) have shown exceptional abilities for multiple different natural language processing tasks. While prompting is a crucial tool for LLM inference, we observe that there is a significant cost associated with exceedingly lengthy prompts. Existing attempts to compress lengthy prompts lead to substandard results in terms of readability/interpretability of the compressed prompt, with a detrimental impact on prompt utility. To address this, we propose PromptSAW: Prompt compresSion via Relation AWare graphs, an effective strategy for prompt compression over task-agnostic and task-aware prompts. Prompt-SAW uses the prompt's textual information to build a graph and later extracts key information elements in the graph to come up with the compressed prompt. We also propose GSM8K-aug, i.e., an extended version of the existing GSM8K benchmark for task-agnostic prompts in order to provide a comprehensive evaluation platform. Experimental evaluation using benchmark datasets shows that prompts compressed by Prompt-SAW are not only better in terms of readability, but they also outperform the best-performing baseline models by up to 10.1 and 77.1, respectively, for task-agnostic and task-aware settings while compressing the original prompt text by 34.9 and 56.7.

cs.CL↗

arXiv2024

DALK: Dynamic Co-Augmentation of LLMs and KG to answer Alzheimer's Disease Questions with Scientific Literature

Recent advancements in large language models (LLMs) have achieved promising performances across various applications. Nonetheless, the ongoing challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. In this work, we introduce DALK, a.k.a. Dynamic Co-Augmentation of LLMs and KG, to address this limitation and demonstrate its ability on studying Alzheimer's Disease (AD), a specialized sub-field in biomedicine and a global health priority. With a synergized framework of LLM and KG mutually enhancing each other, we first leverage LLM to construct an evolving AD-specific knowledge graph (KG) sourced from AD-related scientific literature, and then we utilize a coarse-to-fine sampling method with a novel self-aware knowledge retrieval approach to select appropriate knowledge from the KG to augment LLM inference capabilities. The experimental results, conducted on our constructed AD question answering (ADQA) benchmark, underscore the efficacy of DALK. Additionally, we perform a series of detailed analyses that can offer valuable insights and guidelines for the emerging topic of mutually enhancing KG and LLM. We will release the code and data at https://github.com/David-Li0406/DALK.

cs.CL↗

arXiv2024

Functional principal component analysis with informative observation times

Functional principal component analysis has been shown to be invaluable for revealing variation modes of longitudinal outcomes, which serves as important building blocks for forecasting and model building. Decades of research have advanced methods for functional principal component analysis often assuming independence between the observation times and longitudinal outcomes. Yet such assumptions are fragile in real-world settings where observation times may be driven by outcome-related reasons. Rather than ignoring the informative observation time process, we explicitly model the observational times by a counting process dependent on time-varying prognostic factors. Identification of the mean, covariance function, and functional principal components ensues via inverse intensity weighting. We propose using weighted penalized splines for estimation and establish consistency and convergence rates for the weighted estimators. Simulation studies demonstrate that the proposed estimators are substantially more accurate than the existing ones in the presence of a correlation between the observation time process and the longitudinal outcome process. We further examine the finite-sample performance of the proposed method using the Acute Infection and Early Disease Research Program study.

stat.ME↗

arXiv2024

Understanding Reasoning in Chain-of-Thought from the Hopfieldian View

Large Language Models have demonstrated remarkable abilities across various tasks, with Chain-of-Thought (CoT) prompting emerging as a key technique to enhance reasoning capabilities. However, existing research primarily focuses on improving performance, lacking a comprehensive framework to explain and understand the fundamental factors behind CoT's success. To bridge this gap, we introduce a novel perspective grounded in the Hopfieldian view of cognition in cognitive neuroscience. We establish a connection between CoT reasoning and key cognitive elements such as stimuli, actions, neural populations, and representation spaces. From our view, we can understand the reasoning process as the movement between these representation spaces. Building on this insight, we develop a method for localizing reasoning errors in the response of CoTs. Moreover, we propose the Representation-of-Thought (RoT) framework, which leverages the robustness of low-dimensional representation spaces to enhance the robustness of the reasoning process in CoTs. Experimental results demonstrate that RoT improves the robustness and interpretability of CoT reasoning while offering fine-grained control over the reasoning process.

cs.AI↗

arXiv2024

Clustering Alzheimer's Disease Subtypes via Similarity Learning and Graph Diffusion

Alzheimer's disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Due to the heterogeneous nature of AD, its diagnosis and treatment pose critical challenges. Consequently, there is a growing research interest in identifying homogeneous AD subtypes that can assist in addressing these challenges in recent years. In this study, we aim to identify subtypes of AD that represent distinctive clinical features and underlying pathology by utilizing unsupervised clustering with graph diffusion and similarity learning. We adopted SIMLR, a multi-kernel similarity learning framework, and graph diffusion to perform clustering on a group of 829 patients with AD and mild cognitive impairment (MCI, a prodromal stage of AD) based on their cortical thickness measurements extracted from magnetic resonance imaging (MRI) scans. Although the clustering approach we utilized has not been explored for the task of AD subtyping before, it demonstrated significantly better performance than several commonly used clustering methods. Specifically, we showed the power of graph diffusion in reducing the effects of noise in the subtype detection. Our results revealed five subtypes that differed remarkably in their biomarkers, cognitive status, and some other clinical features. To evaluate the resultant subtypes further, a genetic association study was carried out and successfully identified potential genetic underpinnings of different AD subtypes. Our source code is available at: https://github.com/PennShenLab/AD-SIMLR.

cs.LG↗

arXiv2024

SurgPETL: Parameter-Efficient Image-to-Surgical-Video Transfer Learning for Surgical Phase Recognition

Capitalizing on image-level pre-trained models for various downstream tasks has recently emerged with promising performance. However, the paradigm of "image pre-training followed by video fine-tuning" for high-dimensional video data inevitably poses significant performance bottlenecks. Furthermore, in the medical domain, many surgical video tasks encounter additional challenges posed by the limited availability of video data and the necessity for comprehensive spatial-temporal modeling. Recently, Parameter-Efficient Image-to-Video Transfer Learning has emerged as an efficient and effective paradigm for video action recognition tasks, which employs image-level pre-trained models with promising feature transferability and involves cross-modality temporal modeling with minimal fine-tuning. Nevertheless, the effectiveness and generalizability of this paradigm within intricate surgical domain remain unexplored. In this paper, we delve into a novel problem of efficiently adapting image-level pre-trained models to specialize in fine-grained surgical phase recognition, termed as Parameter-Efficient Image-to-Surgical-Video Transfer Learning. Firstly, we develop a parameter-efficient transfer learning benchmark SurgPETL for surgical phase recognition, and conduct extensive experiments with three advanced methods based on ViTs of two distinct scales pre-trained on five large-scale natural and medical datasets. Then, we introduce the Spatial-Temporal Adaptation module, integrating a standard spatial adapter with a novel temporal adapter to capture detailed spatial features and establish connections across temporal sequences for robust spatial-temporal modeling. Extensive experiments on three challenging datasets spanning various surgical procedures demonstrate the effectiveness of SurgPETL with STA.

cs.CV↗

arXiv2024

Off-Policy Evaluation with Irregularly-Spaced, Outcome-Dependent Observation Times

While the classic off-policy evaluation (OPE) literature commonly assumes decision time points to be evenly spaced for simplicity, in many real-world scenarios, such as those involving user-initiated visits, decisions are made at irregularly-spaced and potentially outcome-dependent time points. For a more principled evaluation of the dynamic policies, this paper constructs a novel OPE framework, which concerns not only the state-action process but also an observation process dictating the time points at which decisions are made. The framework is closely connected to the Markov decision process in computer science and with the renewal process in the statistical literature. Within the framework, two distinct value functions, derived from cumulative reward and integrated reward respectively, are considered, and statistical inference for each value function is developed under revised Markov and time-homogeneous assumptions. The validity of the proposed method is further supported by theoretical results, simulation studies, and a real-world application from electronic health records (EHR) evaluating periodontal disease treatments.

stat.ME↗

arXiv2024

Surgformer: Surgical Transformer with Hierarchical Temporal Attention for Surgical Phase Recognition

Existing state-of-the-art methods for surgical phase recognition either rely on the extraction of spatial-temporal features at a short-range temporal resolution or adopt the sequential extraction of the spatial and temporal features across the entire temporal resolution. However, these methods have limitations in modeling spatial-temporal dependency and addressing spatial-temporal redundancy: 1) These methods fail to effectively model spatial-temporal dependency, due to the lack of long-range information or joint spatial-temporal modeling. 2) These methods utilize dense spatial features across the entire temporal resolution, resulting in significant spatial-temporal redundancy. In this paper, we propose the Surgical Transformer (Surgformer) to address the issues of spatial-temporal modeling and redundancy in an end-to-end manner, which employs divided spatial-temporal attention and takes a limited set of sparse frames as input. Moreover, we propose a novel Hierarchical Temporal Attention (HTA) to capture both global and local information within varied temporal resolutions from a target frame-centric perspective. Distinct from conventional temporal attention that primarily emphasizes dense long-range similarity, HTA not only captures long-term information but also considers local latent consistency among informative frames. HTA then employs pyramid feature aggregation to effectively utilize temporal information across diverse temporal resolutions, thereby enhancing the overall temporal representation. Extensive experiments on two challenging benchmark datasets verify that our proposed Surgformer performs favorably against the state-of-the-art methods. The code is released at https://github.com/isyangshu/Surgformer.

cs.CV↗

arXiv2024

Enhancing convolutional neural network generalizability via low-rank weight approximation

Noise is ubiquitous during image acquisition. Sufficient denoising is often an important first step for image processing. In recent decades, deep neural networks (DNNs) have been widely used for image denoising. Most DNN-based image denoising methods require a large-scale dataset or focus on supervised settings, in which single/pairs of clean images or a set of noisy images are required. This poses a significant burden on the image acquisition process. Moreover, denoisers trained on datasets of limited scale may incur over-fitting. To mitigate these issues, we introduce a new self-supervised framework for image denoising based on the Tucker low-rank tensor approximation. With the proposed design, we are able to characterize our denoiser with fewer parameters and train it based on a single image, which considerably improves the model's generalizability and reduces the cost of data acquisition. Extensive experiments on both synthetic and real-world noisy images have been conducted. Empirical results show that our proposed method outperforms existing non-learning-based methods (e.g., low-pass filter, non-local mean), single-image unsupervised denoisers (e.g., DIP, NN+BM3D) evaluated on both in-sample and out-sample datasets. The proposed method even achieves comparable performances with some supervised methods (e.g., DnCNN).

cs.CV↗

arXiv2024

Estimating spatially varying health effects of wildland fire smoke using mobile health data

Wildland fire smoke exposures are an increasing threat to public health, and thus there is a growing need for studying the effects of protective behaviors on reducing health outcomes. Emerging smartphone applications provide unprecedented opportunities to deliver health risk communication messages to a large number of individuals when and where they experience the exposure and subsequently study the effectiveness, but also pose novel methodological challenges. Smoke Sense, a citizen science project, provides an interactive smartphone app platform for participants to engage with information about air quality and ways to protect their health and record their own health symptoms and actions taken to reduce smoke exposure. We propose a new, doubly robust estimator of the structural nested mean model parameter that accounts for spatially- and time-varying effects via a local estimating equation approach with geographical kernel weighting. Moreover, our analytical framework is flexible enough to handle informative missingness by inverse probability weighting of estimating functions. We evaluate the new method using extensive simulation studies and apply it to Smoke Sense data reported by the citizen scientists to increase the knowledge base about the relationship between health preventive measures and improved health outcomes. Our results estimate how the protective behaviors effects vary over space and time and find that protective behaviors have more significant effects on reducing health symptoms in the Southwest than the Northwest region of the USA.

stat.ME↗