arXiv subjects

Anqi Liu

Publications and source records attributed to Anqi Liu.

At least 73 records · Page 4Linked to original sources

arXiv2024

Conformal Validity Guarantees Exist for Any Data Distribution (and How to Find Them)

As artificial intelligence (AI) / machine learning (ML) gain widespread adoption, practitioners are increasingly seeking means to quantify and control the risk these systems incur. This challenge is especially salient when such systems have autonomy to collect their own data, such as in black-box optimization and active learning, where their actions induce sequential feedback-loop shifts in the data distribution. Conformal prediction is a promising approach to uncertainty and risk quantification, but prior variants' validity guarantees have assumed some form of ``quasi-exchangeability'' on the data distribution, thereby excluding many types of sequential shifts. In this paper we prove that conformal prediction can theoretically be extended to \textit{any} joint data distribution, not just exchangeable or quasi-exchangeable ones. Although the most general case is exceedingly impractical to compute, for concrete practical applications we outline a procedure for deriving specific conformal algorithms for any data distribution, and we use this procedure to derive tractable algorithms for a series of AI/ML-agent-induced covariate shifts. We evaluate the proposed algorithms empirically on synthetic black-box optimization and active learning tasks.

cs.LG↗

arXiv2024

Density-Softmax: Efficient Test-time Model for Uncertainty Estimation and Robustness under Distribution Shifts

Sampling-based methods, e.g., Deep Ensembles and Bayesian Neural Nets have become promising approaches to improve the quality of uncertainty estimation and robust generalization. However, they suffer from a large model size and high latency at test-time, which limits the scalability needed for low-resource devices and real-time applications. To resolve these computational issues, we propose Density-Softmax, a sampling-free deterministic framework via combining a density function built on a Lipschitz-constrained feature extractor with the softmax layer. Theoretically, we show that our model is the solution of minimax uncertainty risk and is distance-aware on feature space, thus reducing the over-confidence of the standard softmax under distribution shifts. Empirically, our method enjoys competitive results with state-of-the-art techniques in terms of uncertainty and robustness, while having a lower number of model parameters and a lower latency at test-time.

cs.LG↗

arXiv2024

A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

q-bio.QM↗

arXiv2024

Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics

Background: Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. The integration of whole-genome sequencing (WGS) data with metabolomics data has emerged as a promising approach to enhance the accuracy of data imputation in metabolomics studies. Method: In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. Our approach utilizes a multi-view variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing metabolomics data imputation. By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information. Results: We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. Using 35 template metabolites derived burden scores, PGS and LD-pruned SNPs, the proposed methods achieved R^2-scores > 0.01 for 71.55% of metabolites. Conclusion: The integration of WGS data in metabolomics imputation not only improves data completeness but also enhances downstream analyses, paving the way for more comprehensive and accurate investigations of metabolic pathways and disease associations. Our findings offer valuable insights into the potential benefits of utilizing WGS data for metabolomics data imputation and underscore the importance of leveraging multi-modal data integration in precision medicine research.

q-bio.GN↗

arXiv2024

Density-Regression: Efficient and Distance-Aware Deep Regressor for Uncertainty Estimation under Distribution Shifts

Morden deep ensembles technique achieves strong uncertainty estimation performance by going through multiple forward passes with different models. This is at the price of a high storage space and a slow speed in the inference (test) time. To address this issue, we propose Density-Regression, a method that leverages the density function in uncertainty estimation and achieves fast inference by a single forward pass. We prove it is distance aware on the feature space, which is a necessary condition for a neural network to produce high-quality uncertainty estimation under distribution shifts. Empirically, we conduct experiments on regression tasks with the cubic toy dataset, benchmark UCI, weather forecast with time series, and depth estimation under real-world shifted applications. We show that Density-Regression has competitive uncertainty estimation performance under distribution shifts with modern deep regressors while using a lower model size and a faster inference speed.

cs.LG↗

arXiv2024

Learning Calibrated Uncertainties for Domain Shift: A Distributionally Robust Learning Approach

We propose a framework for learning calibrated uncertainties under domain shifts, where the source (training) distribution differs from the target (test) distribution. We detect such domain shifts via a differentiable density ratio estimator and train it together with the task network, composing an adjusted softmax predictive form concerning domain shift. In particular, the density ratio estimation reflects the closeness of a target (test) sample to the source (training) distribution. We employ it to adjust the uncertainty of prediction in the task network. This idea of using the density ratio is based on the distributionally robust learning (DRL) framework, which accounts for the domain shift by adversarial risk minimization. We show that our proposed method generates calibrated uncertainties that benefit downstream tasks, such as unsupervised domain adaptation (UDA) and semi-supervised learning (SSL). On these tasks, methods like self-training and FixMatch use uncertainties to select confident pseudo-labels for re-training. Our experiments show that the introduction of DRL leads to significant improvements in cross-domain performance. We also show that the estimated density ratios align with human selection frequencies, suggesting a positive correlation with a proxy of human perceived uncertainties.

cs.LG↗

arXiv2024

Designing for Appropriate Reliance: The Roles of AI Uncertainty Presentation, Initial User Decision, and User Demographics in AI-Assisted Decision-Making

Appropriate reliance is critical to achieving synergistic human-AI collaboration. For instance, when users over-rely on AI assistance, their human-AI team performance is bounded by the model's capability. This work studies how the presentation of model uncertainty may steer users' decision-making toward fostering appropriate reliance. Our results demonstrate that showing the calibrated model uncertainty alone is inadequate. Rather, calibrating model uncertainty and presenting it in a frequency format allow users to adjust their reliance accordingly and help reduce the effect of confirmation bias on their decisions. Furthermore, the critical nature of our skin cancer screening task skews participants' judgment, causing their reliance to vary depending on their initial decision. Additionally, step-wise multiple regression analyses revealed how user demographics such as age and familiarity with probability and statistics influence human-AI collaborative decision-making. We discuss the potential for model uncertainty presentation, initial user decision, and user demographics to be incorporated in designing personalized AI aids for appropriate reliance.

cs.HC↗

arXiv2023

ImageNomer: description of a functional connectivity and omics analysis tool and case study identifying a race confound

Most packages for the analysis of fMRI-based functional connectivity (FC) and genomic data are used with a programming language interface, lacking an easy-to-navigate GUI frontend. This exacerbates two problems found in these types of data: demographic confounds and quality control in the face of high dimensionality of features. The reason is that it is too slow and cumbersome to use a programming interface to create all the necessary visualizations required to identify all correlations, confounding effects, or quality control problems in a dataset. To remedy this situation, we have developed ImageNomer, a data visualization and analysis tool that allows inspection of both subject-level and cohort-level demographic, genomic, and imaging features. The software is Python-based, runs in a self-contained Docker image, and contains a browser-based GUI frontend. We demonstrate the usefulness of ImageNomer by identifying an unexpected race confound when predicting achievement scores in the Philadelphia Neurodevelopmental Cohort (PNC) dataset. In the past, many studies have attempted to use FC to identify achievement-related features in fMRI. Using ImageNomer, we find a clear potential for confounding effects of race. Using correlation analysis in the ImageNomer software, we show that FCs correlated with Wide Range Achievement Test (WRAT) score are in fact more highly correlated with race. Investigating further, we find that whereas both FC and SNP (genomic) features can account for 10-15\% of WRAT score variation, this predictive ability disappears when controlling for race. In this work, we demonstrate the advantage of our ImageNomer GUI tool in data exploration and confound detection. Additionally, this work identifies race as a strong confound in FC data and casts doubt on the possibility of finding unbiased achievement-related features in fMRI and SNP data of healthy adolescents.

q-bio.PE↗

arXiv2023

Identifiability in Functional Connectivity May Unintentionally Inflate Prediction Results

Functional magnetic resonance (fMRI) is an invaluable tool in studying cognitive processes in vivo. Many recent studies use functional connectivity (FC), partial correlation connectivity (PC), or fMRI-derived brain networks to predict phenotypes with results that sometimes cannot be replicated. At the same time, FC can be used to identify the same subject from different scans with great accuracy. In this paper, we show a method by which one can unknowingly inflate classification results from 61% accuracy to 86% accuracy by treating longitudinal or contemporaneous scans of the same subject as independent data points. Using the UK Biobank dataset, we find one can achieve the same level of variance explained with 50 training subjects by exploiting identifiability as with 10,000 training subjects without double-dipping. We replicate this effect in four different datasets: the UK Biobank (UKB), the Philadelphia Neurodevelopmental Cohort (PNC), the Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP), and an OpenNeuro Fibromyalgia dataset (Fibro). The unintentional improvement ranges between 7% and 25% in the four datasets. Additionally, we find that by using dynamic functional connectivity (dFC), one can apply this method even when one is limited to a single scan per subject. One major problem is that features such as ROIs or connectivities that are reported alongside inflated results may confuse future work. This article hopes to shed light on how even minor pipeline anomalies may lead to unexpectedly superb results.

q-bio.NC↗

arXiv2023

MegaWika: Millions of reports and their sources across 50 diverse languages

To foster the development of new models for collaborative AI-assisted report generation, we introduce MegaWika, consisting of 13 million Wikipedia articles in 50 diverse languages, along with their 71 million referenced source materials. We process this dataset for a myriad of applications, going beyond the initial Wikipedia citation extraction and web scraping of content, including translating non-English articles for cross-lingual applications and providing FrameNet parses for automated semantic analysis. MegaWika is the largest resource for sentence-level report generation and the only report generation dataset that is multilingual. We manually analyze the quality of this resource through a semantically stratified sample. Finally, we provide baseline results and trained models for crucial steps in automated report generation: cross-lingual question answering and citation retrieval.

cs.CL↗

arXiv2023

Double-Weighting for Covariate Shift Adaptation

Supervised learning is often affected by a covariate shift in which the marginal distributions of instances (covariates $x$) of training and testing samples $\mathrm{p}_\text{tr}(x)$ and $\mathrm{p}_\text{te}(x)$ are different but the label conditionals coincide. Existing approaches address such covariate shift by either using the ratio $\mathrm{p}_\text{te}(x)/\mathrm{p}_\text{tr}(x)$ to weight training samples (reweighted methods) or using the ratio $\mathrm{p}_\text{tr}(x)/\mathrm{p}_\text{te}(x)$ to weight testing samples (robust methods). However, the performance of such approaches can be poor under support mismatch or when the above ratios take large values. We propose a minimax risk classification (MRC) approach for covariate shift adaptation that avoids such limitations by weighting both training and testing samples. In addition, we develop effective techniques that obtain both sets of weights and generalize the conventional kernel mean matching method. We provide novel generalization bounds for our method that show a significant increase in the effective sample size compared with reweighted methods. The proposed method also achieves enhanced classification performance in both synthetic and empirical experiments.

stat.ML↗

arXiv2023

Towards human-compatible autonomous car: A study of non-verbal Turing test in automated driving with affective transition modelling

Autonomous cars are indispensable when humans go further down the hands-free route. Although existing literature highlights that the acceptance of the autonomous car will increase if it drives in a human-like manner, sparse research offers the naturalistic experience from a passenger's seat perspective to examine the humanness of current autonomous cars. The present study tested whether the AI driver could create a human-like ride experience for passengers based on 69 participants' feedback in a real-road scenario. We designed a ride experience-based version of the non-verbal Turing test for automated driving. Participants rode in autonomous cars (driven by either human or AI drivers) as a passenger and judged whether the driver was human or AI. The AI driver failed to pass our test because passengers detected the AI driver above chance. In contrast, when the human driver drove the car, the passengers' judgement was around chance. We further investigated how human passengers ascribe humanness in our test. Based on Lewin's field theory, we advanced a computational model combining signal detection theory with pre-trained language models to predict passengers' humanness rating behaviour. We employed affective transition between pre-study baseline emotions and corresponding post-stage emotions as the signal strength of our model. Results showed that the passengers' ascription of humanness would increase with the greater affective transition. Our study suggested an important role of affective transition in passengers' ascription of humanness, which might become a future direction for autonomous driving.

cs.HC↗

arXiv2023

CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data

Integration of heterogeneous and high-dimensional multi-omics data is becoming increasingly important in understanding genetic data. Each omics technique only provides a limited view of the underlying biological process and integrating heterogeneous omics layers simultaneously would lead to a more comprehensive and detailed understanding of diseases and phenotypes. However, one obstacle faced when performing multi-omics data integration is the existence of unpaired multi-omics data due to instrument sensitivity and cost. Studies may fail if certain aspects of the subjects are missing or incomplete. In this paper, we propose a deep learning method for multi-omics integration with incomplete data by Cross-omics Linked unified embedding with Contrastive Learning and Self Attention (CLCLSA). Utilizing complete multi-omics data as supervision, the model employs cross-omics autoencoders to learn the feature representation across different types of biological data. The multi-omics contrastive learning, which is used to maximize the mutual information between different types of omics, is employed before latent feature concatenation. In addition, the feature-level self-attention and omics-level self-attention are employed to dynamically identify the most informative features for multi-omics data integration. Extensive experiments were conducted on four public multi-omics datasets. The experimental results indicated that the proposed CLCLSA outperformed the state-of-the-art approaches for multi-omics data classification using incomplete multi-omics data.

cs.LG↗

arXiv2022

Discovering Customer-Service Dialog System with Semi-Supervised Learning and Coarse-to-Fine Intent Detection

Task-oriented dialog(TOD) aims to assist users in achieving specific goals through multi-turn conversation. Recently, good results have been obtained based on large pre-trained models. However, the labeled-data scarcity hinders the efficient development of TOD systems at scale. In this work, we constructed a weakly supervised dataset based on a teacher/student paradigm that leverages a large collection of unlabelled dialogues. Furthermore, we built a modular dialogue system and integrated coarse-to-fine grained classification for user intent detection. Experiments show that our method can reach the dialog goal with a higher success rate and generate more coherent responses.

cs.CL↗

arXiv2022

JAWS: Auditing Predictive Uncertainty Under Covariate Shift

We propose \textbf{JAWS}, a series of wrapper methods for distribution-free uncertainty quantification tasks under covariate shift, centered on the core method \textbf{JAW}, the \textbf{JA}ckknife+ \textbf{W}eighted with data-dependent likelihood-ratio weights. JAWS also includes computationally efficient \textbf{A}pproximations of JAW using higher-order influence functions: \textbf{JAWA}. Theoretically, we show that JAW relaxes the jackknife+'s assumption of data exchangeability to achieve the same finite-sample coverage guarantee even under covariate shift. JAWA further approaches the JAW guarantee in the limit of the sample size or the influence function order under common regularity assumptions. Moreover, we propose a general approach to repurposing predictive interval-generating methods and their guarantees to the reverse task: estimating the probability that a prediction is erroneous, based on user-specified error criteria such as a safe or acceptable tolerance threshold around the true label. We then propose \textbf{JAW-E} and \textbf{JAWA-E} as the repurposed proposed methods for this \textbf{E}rror assessment task. Practically, JAWS outperform state-of-the-art predictive inference baselines in a variety of biased real world data sets for interval-generation and error-assessment predictive uncertainty auditing tasks.

cs.LG↗

arXiv2022

A New Hip Fracture Risk Index Derived from FEA-Computed Proximal Femur Fracture Loads and Energies-to-Failure

Hip fracture risk assessment is an important but challenging task. Quantitative CT-based patient specific finite element analysis (FEA) computes the force (fracture load) to break the proximal femur in a particular loading condition. It provides different structural information about the proximal femur that can influence a subject overall fracture risk. To obtain a more robust measure of fracture risk, we used principal component analysis (PCA) to develop a global FEA computed fracture risk index that incorporates the FEA-computed yield and ultimate failure loads and energies to failure in four loading conditions (single-limb stance and impact from a fall onto the posterior, posterolateral, and lateral aspects of the greater trochanter) of 110 hip fracture subjects and 235 age and sex matched control subjects from the AGES-Reykjavik study. We found that the first PC (PC1) of the FE parameters was the only significant predictor of hip fracture. Using a logistic regression model, we determined if prediction performance for hip fracture using PC1 differed from that using FE parameters combined by stratified random resampling with respect to hip fracture status. The results showed that the average of the area under the receive operating characteristic curve (AUC) using PC1 was always higher than that using all FE parameters combined in the male subjects. The AUC of PC1 and AUC of the FE parameters combined were not significantly different than that in the female subjects or in all subjects

cs.LG↗

arXiv2022

Ambiguous Images With Human Judgments for Robust Visual Event Classification

Contemporary vision benchmarks predominantly consider tasks on which humans can achieve near-perfect performance. However, humans are frequently presented with visual data that they cannot classify with 100% certainty, and models trained on standard vision benchmarks achieve low performance when evaluated on this data. To address this issue, we introduce a procedure for creating datasets of ambiguous images and use it to produce SQUID-E ("Squidy"), a collection of noisy images extracted from videos. All images are annotated with ground truth values and a test set is annotated with human uncertainty judgments. We use this dataset to characterize human uncertainty in vision tasks and evaluate existing visual event classification models. Experimental results suggest that existing vision models are not sufficiently equipped to provide meaningful outputs for ambiguous images and that datasets of this nature can be used to assess and improve such models through model training and direct evaluation of model calibration. These findings motivate large-scale ambiguous dataset creation and further research focusing on noisy visual data.

cs.CV↗

arXiv2022

Repeated Environment Inference for Invariant Learning

We study the problem of invariant learning when the environment labels are unknown. We focus on the invariant representation notion when the Bayes optimal conditional label distribution is the same across different environments. Previous work conducts Environment Inference (EI) by maximizing the penalty term from Invariant Risk Minimization (IRM) framework. The EI step uses a reference model which focuses on spurious correlations to efficiently reach a good environment partition. However, it is not clear how to find such a reference model. In this work, we propose to repeat the EI process and retrain an ERM model on the \textit{majority} environment inferred by the previous EI step. Under mild assumptions, we find that this iterative process helps learn a representation capturing the spurious correlation better than the single step. This results in better Environment Inference and better Invariant Learning. We show that this method outperforms baselines on both synthetic and real-world datasets.

cs.LG↗