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Yixin Wang

Publications and source records attributed to Yixin Wang.

At least 109 records · Page 6Linked to original sources

Statistical and Computational Trade-offs in Variational Inference: A Case Study in Inferential Model Selection

Variational inference has recently emerged as a popular alternative to the classical Markov chain Monte Carlo (MCMC) in large-scale Bayesian inference. The core idea is to trade statistical accuracy for computational efficiency. In this work, we study these statistical and computational trade-offs in variational inference via a case study in inferential model selection. Focusing on Gaussian inferential models (or variational approximating families) with diagonal plus low-rank precision matrices, we initiate a theoretical study of the trade-offs in two aspects, Bayesian posterior inference error and frequentist uncertainty quantification error. From the Bayesian posterior inference perspective, we characterize the error of the variational posterior relative to the exact posterior. We prove that, given a fixed computation budget, a lower-rank inferential model produces variational posteriors with a higher statistical approximation error, but a lower computational error; it reduces variance in stochastic optimization and, in turn, accelerates convergence. From the frequentist uncertainty quantification perspective, we consider the precision matrix of the variational posterior as an uncertainty estimate, which involves an additional statistical error originating from the sampling uncertainty of the data. As a consequence, for small datasets, the inferential model need not be full-rank to achieve optimal estimation error (even with unlimited computation budget).

stat.ML↗

Rethinking Medical Report Generation: Disease Revealing Enhancement with Knowledge Graph

Knowledge Graph (KG) plays a crucial role in Medical Report Generation (MRG) because it reveals the relations among diseases and thus can be utilized to guide the generation process. However, constructing a comprehensive KG is labor-intensive and its applications on the MRG process are under-explored. In this study, we establish a complete KG on chest X-ray imaging that includes 137 types of diseases and abnormalities. Based on this KG, we find that the current MRG data sets exhibit a long-tailed problem in disease distribution. To mitigate this problem, we introduce a novel augmentation strategy that enhances the representation of disease types in the tail-end of the distribution. We further design a two-stage MRG approach, where a classifier is first trained to detect whether the input images exhibit any abnormalities. The classified images are then independently fed into two transformer-based generators, namely, ``disease-specific generator" and ``disease-free generator" to generate the corresponding reports. To enhance the clinical evaluation of whether the generated reports correctly describe the diseases appearing in the input image, we propose diverse sensitivity (DS), a new metric that checks whether generated diseases match ground truth and measures the diversity of all generated diseases. Results show that the proposed two-stage generation framework and augmentation strategies improve DS by a considerable margin, indicating a notable reduction in the long-tailed problem associated with under-represented diseases.

cs.CV↗

A neural network-based scale-adaptive cloud-fraction scheme for GCMs

Cloud fraction significantly affects the short- and long-wave radiation. Its realistic representation in general circulation models (GCMs) still poses great challenges in modeling the atmosphere. Here, we present a neural network-based diagnostic scheme that uses the grid-mean temperature, pressure, liquid and ice water mixing ratios, and relative humidity to simulate the sub-grid cloud fraction. The scheme, trained using CloudSat data with explicit consideration of grid sizes, realistically simulates the observed cloud fraction with a correlation coefficient (r) > 0.9 for liquid-, mixed-, and ice-phase clouds. The scheme also captures the observed non-monotonic relationship between cloud fraction and relative humidity and is computationally efficient, and robust for GCMs with a variety of horizontal and vertical resolutions. For illustrative purposes, we conducted comparative analyses of the 2006-2019 climatological-mean cloud fractions among CloudSat, and simulations from the new scheme and the Xu-Randall scheme (optimized the same way as the new scheme). The network-based scheme improves not only the spatial distribution of the total cloud fraction but also the cloud vertical structure (r > 0.99). For example, the biases of too-many high-level clouds over the tropics and too-many low-level clouds over regions around 60°S and 60°N in the Xu-Randall scheme are significantly reduced. These improvements are also found to be insensitive to the spatio-temporal variability of large-scale meteorology conditions, implying that the scheme can be used in different climate regimes.

physics.ao-ph↗

The Sample Complexity of Online Contract Design

We study the hidden-action principal-agent problem in an online setting. In each round, the principal posts a contract that specifies the payment to the agent based on each outcome. The agent then makes a strategic choice of action that maximizes her own utility, but the action is not directly observable by the principal. The principal observes the outcome and receives utility from the agent's choice of action. Based on past observations, the principal dynamically adjusts the contracts with the goal of maximizing her utility. We introduce an online learning algorithm and provide an upper bound on its Stackelberg regret. We show that when the contract space is $[0,1]^m$, the Stackelberg regret is upper bounded by $\widetilde O(\sqrt{m} \cdot T^{1-1/(2m+1)})$, and lower bounded by $Ω(T^{1-1/(m+2)})$, where $\widetilde O$ omits logarithmic factors. This result shows that exponential-in-$m$ samples are sufficient and necessary to learn a near-optimal contract, resolving an open problem on the hardness of online contract design. Moreover, when contracts are restricted to some subset $\mathcal{F} \subset [0,1]^m$, we define an intrinsic dimension of $\mathcal{F}$ that depends on the covering number of the spherical code in the space and bound the regret in terms of this intrinsic dimension. When $\mathcal{F}$ is the family of linear contracts, we show that the Stackelberg regret grows exactly as $Θ(T^{2/3})$. The contract design problem is challenging because the utility function is discontinuous. Bounding the discretization error in this setting has been an open problem. In this paper, we identify a limited set of directions in which the utility function is continuous, allowing us to design a new discretization method and bound its error. This approach enables the first upper bound with no restrictions on the contract and action space.

cs.GT↗

Delayed and Indirect Impacts of Link Recommendations

The impacts of link recommendations on social networks are challenging to evaluate, and so far they have been studied in limited settings. Observational studies are restricted in the kinds of causal questions they can answer and naive A/B tests often lead to biased evaluations due to unaccounted network interference. Furthermore, evaluations in simulation settings are often limited to static network models that do not take into account the potential feedback loops between link recommendation and organic network evolution. To this end, we study the impacts of recommendations on social networks in dynamic settings. Adopting a simulation-based approach, we consider an explicit dynamic formation model -- an extension of the celebrated Jackson-Rogers model -- and investigate how link recommendations affect network evolution over time. Empirically, we find that link recommendations have surprising delayed and indirect effects on the structural properties of networks. Specifically, we find that link recommendations can exhibit considerably different impacts in the immediate term and in the long term. For instance, we observe that friend-of-friend recommendations can have an immediate effect in decreasing degree inequality, but in the long term, they can make the degree distribution substantially more unequal. Moreover, we show that the effects of recommendations can persist in networks, in part due to their indirect impacts on natural dynamics even after recommendations are turned off. We show that, in counterfactual simulations, removing the indirect effects of link recommendations can make the network trend faster toward what it would have been under natural growth dynamics.

cs.SI↗

SAP-DETR: Bridging the Gap Between Salient Points and Queries-Based Transformer Detector for Fast Model Convergency

Recently, the dominant DETR-based approaches apply central-concept spatial prior to accelerate Transformer detector convergency. These methods gradually refine the reference points to the center of target objects and imbue object queries with the updated central reference information for spatially conditional attention. However, centralizing reference points may severely deteriorate queries' saliency and confuse detectors due to the indiscriminative spatial prior. To bridge the gap between the reference points of salient queries and Transformer detectors, we propose SAlient Point-based DETR (SAP-DETR) by treating object detection as a transformation from salient points to instance objects. In SAP-DETR, we explicitly initialize a query-specific reference point for each object query, gradually aggregate them into an instance object, and then predict the distance from each side of the bounding box to these points. By rapidly attending to query-specific reference region and other conditional extreme regions from the image features, SAP-DETR can effectively bridge the gap between the salient point and the query-based Transformer detector with a significant convergency speed. Our extensive experiments have demonstrated that SAP-DETR achieves 1.4 times convergency speed with competitive performance. Under the standard training scheme, SAP-DETR stably promotes the SOTA approaches by 1.0 AP. Based on ResNet-DC-101, SAP-DETR achieves 46.9 AP.

cs.CV↗

Clarifying Trust of Materials Property Predictions using Neural Networks with Distribution-Specific Uncertainty Quantification

It is critical that machine learning (ML) model predictions be trustworthy for high-throughput catalyst discovery approaches. Uncertainty quantification (UQ) methods allow estimation of the trustworthiness of an ML model, but these methods have not been well explored in the field of heterogeneous catalysis. Herein, we investigate different UQ methods applied to a crystal graph convolutional neural network (CGCNN) to predict adsorption energies of molecules on alloys from the Open Catalyst 2020 (OC20) dataset, the largest existing heterogeneous catalyst dataset. We apply three UQ methods to the adsorption energy predictions, namely k-fold ensembling, Monte Carlo dropout, and evidential regression. The effectiveness of each UQ method is assessed based on accuracy, sharpness, dispersion, calibration, and tightness. Evidential regression is demonstrated to be a powerful approach for rapidly obtaining tunable, competitively trustworthy UQ estimates for heterogeneous catalysis applications when using neural networks. Recalibration of model uncertainties is shown to be essential in practical screening applications of catalysts using uncertainties.

cs.LG↗

Learning Equilibria in Matching Markets from Bandit Feedback

Large-scale, two-sided matching platforms must find market outcomes that align with user preferences while simultaneously learning these preferences from data. Classical notions of stability (Gale and Shapley, 1962; Shapley and Shubik, 1971) are unfortunately of limited value in the learning setting, given that preferences are inherently uncertain and destabilizing while they are being learned. To bridge this gap, we develop a framework and algorithms for learning stable market outcomes under uncertainty. Our primary setting is matching with transferable utilities, where the platform both matches agents and sets monetary transfers between them. We design an incentive-aware learning objective that captures the distance of a market outcome from equilibrium. Using this objective, we analyze the complexity of learning as a function of preference structure, casting learning as a stochastic multi-armed bandit problem. Algorithmically, we show that "optimism in the face of uncertainty," the principle underlying many bandit algorithms, applies to a primal-dual formulation of matching with transfers and leads to near-optimal regret bounds. Our work takes a first step toward elucidating when and how stable matchings arise in large, data-driven marketplaces.

cs.LG↗

Team Resilience under Shock: An Empirical Analysis of GitHub Repositories during Early COVID-19 Pandemic

While many organizations have shifted to working remotely during the COVID-19 pandemic, how the remote workforce and the remote teams are influenced by and would respond to this and future shocks remain largely unknown. Software developers have relied on remote collaborations long before the pandemic, working in virtual teams (GitHub repositories). The dynamics of these repositories through the pandemic provide a unique opportunity to understand how remote teams react under shock. This work presents a systematic analysis. We measure the overall effect of the early pandemic on public GitHub repositories by comparing their sizes and productivity with the counterfactual outcomes forecasted as if there were no pandemic. We find that the productivity level and the number of active members of these teams vary significantly during different periods of the pandemic. We then conduct a finer-grained investigation and study the heterogeneous effects of the shock on individual teams. We find that the resilience of a team is highly correlated to certain properties of the team before the pandemic. Through a bootstrapped regression analysis, we reveal which types of teams are robust or fragile to the shock.

cs.LG↗

Posterior Collapse and Latent Variable Non-identifiability

Variational autoencoders model high-dimensional data by positing low-dimensional latent variables that are mapped through a flexible distribution parametrized by a neural network. Unfortunately, variational autoencoders often suffer from posterior collapse: the posterior of the latent variables is equal to its prior, rendering the variational autoencoder useless as a means to produce meaningful representations. Existing approaches to posterior collapse often attribute it to the use of neural networks or optimization issues due to variational approximation. In this paper, we consider posterior collapse as a problem of latent variable non-identifiability. We prove that the posterior collapses if and only if the latent variables are non-identifiable in the generative model. This fact implies that posterior collapse is not a phenomenon specific to the use of flexible distributions or approximate inference. Rather, it can occur in classical probabilistic models even with exact inference, which we also demonstrate. Based on these results, we propose a class of latent-identifiable variational autoencoders, deep generative models which enforce identifiability without sacrificing flexibility. This model class resolves the problem of latent variable non-identifiability by leveraging bijective Brenier maps and parameterizing them with input convex neural networks, without special variational inference objectives or optimization tricks. Across synthetic and real datasets, latent-identifiable variational autoencoders outperform existing methods in mitigating posterior collapse and providing meaningful representations of the data.

stat.ML↗

A Survey of Visual Transformers

Transformer, an attention-based encoder-decoder model, has already revolutionized the field of natural language processing (NLP). Inspired by such significant achievements, some pioneering works have recently been done on employing Transformer-liked architectures in the computer vision (CV) field, which have demonstrated their effectiveness on three fundamental CV tasks (classification, detection, and segmentation) as well as multiple sensory data stream (images, point clouds, and vision-language data). Because of their competitive modeling capabilities, the visual Transformers have achieved impressive performance improvements over multiple benchmarks as compared with modern Convolution Neural Networks (CNNs). In this survey, we have reviewed over one hundred of different visual Transformers comprehensively according to three fundamental CV tasks and different data stream types, where a taxonomy is proposed to organize the representative methods according to their motivations, structures, and application scenarios. Because of their differences on training settings and dedicated vision tasks, we have also evaluated and compared all these existing visual Transformers under different configurations. Furthermore, we have revealed a series of essential but unexploited aspects that may empower such visual Transformers to stand out from numerous architectures, e.g., slack high-level semantic embeddings to bridge the gap between the visual Transformers and the sequential ones. Finally, three promising research directions are suggested for future investment. We will continue to update the latest articles and their released source codes at https://github.com/liuyang-ict/awesome-visual-transformers.

cs.CV↗

Deep Learning in Single-Cell Analysis

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

q-bio.QM↗

Dynamic Survival Transformers for Causal Inference with Electronic Health Records

In medicine, researchers often seek to infer the effects of a given treatment on patients' outcomes. However, the standard methods for causal survival analysis make simplistic assumptions about the data-generating process and cannot capture complex interactions among patient covariates. We introduce the Dynamic Survival Transformer (DynST), a deep survival model that trains on electronic health records (EHRs). Unlike previous transformers used in survival analysis, DynST can make use of time-varying information to predict evolving survival probabilities. We derive a semi-synthetic EHR dataset from MIMIC-III to show that DynST can accurately estimate the causal effect of a treatment intervention on restricted mean survival time (RMST). We demonstrate that DynST achieves better predictive and causal estimation than two alternative models.

cs.LG↗

Anticipating Performativity by Predicting from Predictions

Predictions about people, such as their expected educational achievement or their credit risk, can be performative and shape the outcome that they aim to predict. Understanding the causal effect of these predictions on the eventual outcomes is crucial for foreseeing the implications of future predictive models and selecting which models to deploy. However, this causal estimation task poses unique challenges: model predictions are usually deterministic functions of input features and highly correlated with outcomes. This can make the causal effects of predictions on outcomes impossible to disentangle from the direct effect of the covariates. We study this problem through the lens of causal identifiability, and despite the hardness of this problem in full generality, we highlight three natural scenarios where the causal relationship between covariates, predictions and outcomes can be identified from observational data: randomization in predictions, overparameterization of the predictive model deployed during data collection, and discrete prediction outputs. Empirically we show that given our identifiability conditions hold, standard variants of supervised learning that predict from predictions by treating the prediction as an input feature can indeed find transferable functional relationships that allow for conclusions about newly deployed predictive models. These positive results fundamentally rely on model predictions being recorded during data collection, bringing forward the importance of rethinking standard data collection practices to enable progress towards a better understanding of social outcomes and performative feedback loops.

stat.ML↗

Augmenting Neural Networks with Priors on Function Values

The need for function estimation in label-limited settings is common in the natural sciences. At the same time, prior knowledge of function values is often available in these domains. For example, data-free biophysics-based models can be informative on protein properties, while quantum-based computations can be informative on small molecule properties. How can we coherently leverage such prior knowledge to help improve a neural network model that is quite accurate in some regions of input space -- typically near the training data -- but wildly wrong in other regions? Bayesian neural networks (BNN) enable the user to specify prior information only on the neural network weights, not directly on the function values. Moreover, there is in general no clear mapping between these. Herein, we tackle this problem by developing an approach to augment BNNs with prior information on the function values themselves. Our probabilistic approach yields predictions that rely more heavily on the prior information when the epistemic uncertainty is large, and more heavily on the neural network when the epistemic uncertainty is small.

cs.LG↗

Semi-supervised Cardiac Image Segmentation via Label Propagation and Style Transfer

Accurate segmentation of cardiac structures can assist doctors to diagnose diseases, and to improve treatment planning, which is highly demanded in the clinical practice. However, the shortage of annotation and the variance of the data among different vendors and medical centers restrict the performance of advanced deep learning methods. In this work, we present a fully automatic method to segment cardiac structures including the left (LV) and right ventricle (RV) blood pools, as well as for the left ventricular myocardium (MYO) in MRI volumes. Specifically, we design a semi-supervised learning method to leverage unlabelled MRI sequence timeframes by label propagation. Then we exploit style transfer to reduce the variance among different centers and vendors for more robust cardiac image segmentation. We evaluate our method in the M&Ms challenge 7 , ranking 2nd place among 14 competitive teams.

eess.IV↗

Breaking Feedback Loops in Recommender Systems with Causal Inference

Recommender systems play a key role in shaping modern web ecosystems. These systems alternate between (1) making recommendations (2) collecting user responses to these recommendations, and (3) retraining the recommendation algorithm based on this feedback. During this process the recommender system influences the user behavioral data that is subsequently used to update it, thus creating a feedback loop. Recent work has shown that feedback loops may compromise recommendation quality and homogenize user behavior, raising ethical and performance concerns when deploying recommender systems. To address these issues, we propose the Causal Adjustment for Feedback Loops (CAFL), an algorithm that provably breaks feedback loops using causal inference and can be applied to any recommendation algorithm that optimizes a training loss. Our main observation is that a recommender system does not suffer from feedback loops if it reasons about causal quantities, namely the intervention distributions of recommendations on user ratings. Moreover, we can calculate this intervention distribution from observational data by adjusting for the recommender system's predictions of user preferences. Using simulated environments, we demonstrate that CAFL improves recommendation quality when compared to prior correction methods.

cs.IR↗

Conformal Sensitivity Analysis for Individual Treatment Effects

Estimating an individual treatment effect (ITE) is essential to personalized decision making. However, existing methods for estimating the ITE often rely on unconfoundedness, an assumption that is fundamentally untestable with observed data. To assess the robustness of individual-level causal conclusion with unconfoundedness, this paper proposes a method for sensitivity analysis of the ITE, a way to estimate a range of the ITE under unobserved confounding. The method we develop quantifies unmeasured confounding through a marginal sensitivity model [Ros2002, Tan2006], and adapts the framework of conformal inference to estimate an ITE interval at a given confounding strength. In particular, we formulate this sensitivity analysis problem as a conformal inference problem under distribution shift, and we extend existing methods of covariate-shifted conformal inference to this more general setting. The result is a predictive interval that has guaranteed nominal coverage of the ITE, a method that provides coverage with distribution-free and nonasymptotic guarantees. We evaluate the method on synthetic data and illustrate its application in an observational study.

stat.ME↗