Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
problem Complexity and confounders in scRNA-seq data hamper interpretation.
method Extended Gaussian process latent variable model (GPLVM) to handle large datasets.
result Framework reconstructs latent signatures and captures disease-specific gene expression.
Statistical learning on biological data can be challenging due to confounding variables in sample collection and processing. Confounders can cause models to generalize poorly and result in inaccurate prediction performance metrics if models are not validated thoroughly. In this paper, we propose methods to control for …
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…
DCCD-CONF discovers causal graphs with unmeasured confounders.
problem Discovering causal relationships in systems with unmeasured confounders.
method Differentiable learning of nonlinear cyclic causal graphs using interventional data.
result DCCD-CONF outperforms state-of-the-art methods in causal graph recovery and confounder identification.
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
problem Determining if multimodal models learn shared biology or just confounders.
method DECAT framework classifies multimodal representations into four diagnostic scenarios using null-referenced metrics.
result DECAT detects confounders and false positives in multimodal models, improving with larger cohorts and stronger representations.
New method discovers causal relationships in confounded systems.
problem Discovering causal relationships in systems with unmeasured confounding variables.
method Differentiable algebraic constraints for continuous optimization of ADMGs.
result Effective method for causal discovery in confounded linear systems.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
Modeling correlated mutations in cancer for personalized treatment.
problem Identifying mutations for personalized cancer therapy in heterogeneous profiles.
method Proposed correlated zero-inflated negative binomial process with mixed beta-Bernoulli and variational inference.
result Identified biologically relevant correlations between somatic mutations.
In the integrative analyses of omics data, it is often of interest to extract data representation from one data type that best reflect its relations with another data type. This task is traditionally fulfilled by linear methods such as canonical correlation analysis (CCA) and partial least squares (PLS). However, infor…
The paper proposes a method to precisely decompose confounders and estimate treatment effects.
problem Estimating treatment effects from observational data with confounder identification and balancing.
method Learning decomposed representations to identify and balance confounders and non-confounders.
result The method achieves more precise treatment effect estimation than existing methods.
Causal methods for GRN inference from single-cell data often fail in real-world benchmarks.
problem Understanding when and why causal methods for GRN inference from single-cell data fail in real-world benchmarks.
method Introduced a controlled diagnostic framework to isolate and measure seven pathologies.
result Causal methods dominate in clean and structurally favorable regimes but fail in specific pathologies.
FL-Sailer enables federated learning for scATAC-seq data, reducing dimensionality and noise.
problem Privacy-preserving federated learning for ultra-high dimensional, sparse, and heterogeneous scATAC-seq data.
method FL-Sailer integrates adaptive leverage score sampling and an invariant VAE architecture.
result FL-Sailer converges to an approximate solution with bounded error, surpassing centralized methods.
Research shows continual learning challenges in confounded datasets.
problem Challenges in mitigating confounders in continual learning settings.
method Formal description of continual confounders, construction of ConCon dataset.
result Standard continual learning methods fail to ignore confounders.
Causal inference from observational data requires assumptions. These assumptions range from measuring confounders to identifying instruments. Traditionally, causal inference assumptions have focused on estimation of effects for a single treatment. In this work, we construct techniques for estimation with multiple treat…
ARMED models improve deep learning interpretability and generalize better on clustered data.
problem Clustered data leads to spurious associations and poor model fitting.
method Adversarial regularization and mixed effects subnetworks.
result ARMED models outperform conventional methods in accuracy and generalization.
Detect hidden confounding in observational data using multiple environments.
problem Detect hidden confounding in observational data.
method Theoretical framework and simulation studies to test for hidden confounding.
result The proposed procedure correctly predicts hidden confounding, especially when bias is large.
Machine learning confound removal biases results, leading to misleading predictions.
problem Common confound removal methods in machine learning lead to misleading predictions.
method Featurewise removal of confound variance by linear regression before applying ML.
result This common deconfounding approach can leak information, amplifying null or moderate effects.
KRCD detects unobserved confounders in nonlinear observational data.
problem Detecting unobserved confounders in nonlinear observational studies.
method Kernel Regression Confounder Detection (KRCD) using reproducing kernel Hilbert spaces.
result KRCD outperforms existing methods and achieves superior computational efficiency.
Study identifies conditions for proxy adjustment in confounded binary treatment outcomes.
problem Average causal effect estimation with a non-differentially mismeasured binary confounder.
method Identifies conditions for proxy adjustment in the presence of a non-differentially mismeasured binary confounder.
result Adjusting for a non-differentially mismeasured binary proxy can improve estimation of the average causal effect.
SMAI framework tests and integrates single-cell data alignability.
problem Lack of a rigorous statistical test for alignability and distortion during alignment.
method Spectral manifold alignment and inference (SMAI) framework.
result SMAI outperforms existing methods in alignability testing and integration.
New method estimates policy performance under unobserved confounding.
problem Estimating policy performance when decisions depend on unobserved variables.
method Developed worst-case bounds for robust OPE under unobserved confounding.
result Efficient procedure for computing worst-case bounds, proving statistical consistency.
Consistent estimator derived for confounding strength in observational data.
problem Estimating confounding strength in observational data is challenging due to unobserved confounders.
method Derived and adapted a consistent estimator using tools from random matrix theory.
result The original estimator is not consistent, but an adapted one is.
A new method uses randomized trials to estimate the strength of unobserved confounding.
problem Unobserved confounding compromises causal conclusions from non-randomized studies.
method Designs a statistical test to detect unobserved confounding strength and estimates a lower bound.
result Estimates an asymptotically valid lower bound on unobserved confounding strength.
This paper tackles confounding biases in data augmentation.
problem Mitigating spurious correlations and confounding variables in training data.
method Formal analysis and counterfactual data augmentation.
result Removing confounding biases leads to invariant features and better generalization.
New method recovers latent confounders from high-dimensional proxy variables.
problem Detecting latent confounders from high-dimensional proxy variables.
method Proxy Confounder Factorization (PCF) framework using ICA-PCF and GD-PCF.
result ICA-PCF recovers confounders with high correlation and low error in synthetic and real-world data.
Proposes tests to control confounding bias in predictive models.
problem Lack of non-parametric tests for confounding bias in predictive modeling.
method Partial and full confounder tests for probing null hypotheses of unconfounded and fully confounded models.
result Reveals previously unreported or hard-to-correct confounders in machine learning models.
New method tackles confounded bandit problems with dual instrumental variables.
problem Confounded contextual bandit problems where noise affects both contexts and rewards.
method Dual instrumental variable regression applied to reproducing kernel Hilbert spaces.
result Near-optimal convergence rate and computationally efficient algorithms proved.
New approach for causal inference with interdependent, time-varying latent confounders.
problem Estimating causal effects with interdependent, time-varying latent confounders.
method Variational estimation with a representer theorem and random input space.
result Demonstrates effectiveness on various temporal datasets.
Causal discovery from data affected by latent confounders is an important and difficult challenge. Causal functional model-based approaches have not been used to present variables whose relationships are affected by latent confounders, while some constraint-based methods can present them. This paper proposes a causal f…
Estimating the individual treatment effect (ITE) from observational data is essential in medicine. A central challenge in estimating the ITE is handling confounders, which are factors that affect both an intervention and its outcome. Most previous work relies on the unconfoundedness assumption, which posits that all th…
CARE improves LLM aggregation by accounting for shared confounders.
problem LLM judges' correlated errors due to shared latent confounders.
method CARE explicitly models judges' scores as true quality and confounders.
result CARE reduces aggregation error by up to 26.8% across various benchmarks.
Proposes BDCM to handle unmeasured confounders in causal inference.
problem Handling unmeasured confounders in causal inference.
method Backdoor criterion to find variables for diffusion model.
result Captures counterfactual distribution more precisely.
New methods prioritize acquiring confounding features for efficient treatment effect estimation.
problem Efficient treatment effect estimation from observational data with missing confounding information.
method Proposes two acquisition strategies: covariate balancing and reducing factual outcome error.
result Our proposed methods, especially reducing factual outcome error, improve sample efficiency for treatment effect estimation.
Valid causal inference with unobserved confounding in high-dimensional settings.
problem Estimating causal effects with unobserved confounders in high-dimensional data.
method Proposes methods to estimate causal effects with valid confidence intervals in the presence of unobserved confounders and high-dimensional nuisance models.
result Valid semiparametric inference can be obtained with unobserved confounding, and uncertainty intervals are proposed.
Spectral deconfounding improves machine learning models by reducing hidden confounding effects.
problem Machine learning models can be misled by hidden confounders, leading to unreliable predictions.
method Develops a nonlinear spectral deconfounding framework for gradient boosting that modifies boosting dynamics to slow down in confounding-aligned directions.
result Spectrally deconfounded boosting improves estimation of the target function under hidden confounding and is more scalable.
We propose a method for inferring the existence of a latent common cause ('confounder') of two observed random variables. The method assumes that the two effects of the confounder are (possibly nonlinear) functions of the confounder plus independent, additive noise. We discuss under which conditions the model is identi…
Study shows how adjusting for a binary proxy can bound causal effects.
problem Bounding causal effects with a binary confounder and proxy.
method Monotonicity assumption applied to a binary confounder and observed proxy.
result Adjusting for a proxy produces a measure of the effect between unadjusted and true measures.
Paper tackles unobserved confounding in human-AI collaborations.
problem Unobserved confounding undermines human-AI collaboration effectiveness.
method Combines sensitivity analysis from causal inference with AI-driven statistical modeling.
result Enhances robustness and reliability of collaborative outcomes.
SpaCE tackles spatial confounding in scientific studies.
problem Spatial confounding influences treatment and outcome, leading to spurious associations.
method Introduces SpaCE toolkit for benchmark datasets and tools to evaluate causal inference methods.
result Facilitates automated evaluation of machine learning and causal inference models.
Estimates causal effects with selection bias and confounding using regression.
problem Estimating causal effects in presence of selection bias and confounding.
method Two-step regression estimator (TSR) that corrects for selection bias and accounts for confounding.
result TSR estimator reduces variance and is validated in simulations.
Paper tackles backwards-compatible data adaptation for confounded covariate and label shifts.
problem Adapt covariates to predict labels confounded with covariate shifts.
method Proposes confounded shift framework based on minimizing divergence between source and target conditional distributions, conditioning on confounders.
result Demonstrates approach on synthetic and real datasets, achieving backwards-compatible data adaptation.
Deep CITs test conditional independence in images, improving brain MRI scan analysis.
problem Testing conditional independence in complex, high-dimensional variables like images.
method Combines embedding maps and nonparametric CITs for feature representations.
result Valid DNCITs for brain MRI scans and behavioral traits, confirming null results.
In this paper, we study the confounder detection problem in the linear model, where the target variable Y is predicted using its n potential causes Xn=(x1,...,xn)T. Based on an assumption of rotation invariant generating process of the model, recent study shows that the spectral measure induced by the regress…
Proposes DSW for unbiased ITE estimation with dynamic confounders.
problem Estimating ITE from dynamic observational data with time-varying confounders.
method Deep Sequential Weighting (DSW) infers hidden confounders using current treatment assignments and historical information.
result DSW generates unbiased and accurate treatment effects.
Paper uses Gaussian processes to handle shared latent confounders in causal inference.
problem Bias in causal effect estimates due to shared latent confounders.
method Hierarchical Bayesian model, Gaussian processes with structured latent confounders (GP-SLC), Monte Carlo inference algorithm.
result GP-SLC provides accurate estimates of individual treatment effects with minimal assumptions.
Study linear contextual bandits with confounded offline data, improving regret bounds.
problem Linear contextual bandits with confounded offline data.
method Construct a linear bandit algorithm that utilizes projected information.
result Proved regret bounds that improve current bounds by a factor related to visible dimensionality.
With recent advances in deep learning, neuroimaging studies increasingly rely on convolutional networks (ConvNets) to predict diagnosis based on MR images. To gain a better understanding of how a disease impacts the brain, the studies visualize the salience maps of the ConvNet highlighting voxels within the brain major…
Estimates CATE under hidden confounding, accounting for bias and ignorance.
problem Learning CATE from high-dimensional data with unobserved confounders introduces bias and ignorance.
method Parametric interval estimator that accounts for hidden confounding and underrepresented samples.
result Estimator converges to tight bounds on CATE when there may be unobserved confounding.