Develops probabilistic models for gene regulatory network inference.
problem Challenges in reconstructing gene regulatory networks from genome-wide data.
method Two complementary frameworks: PMF-GRN and GLM-Prior.
result Probabilistic inference refines regulatory estimates with quantified uncertainty.
The paper develops a scalable method to infer GRNs from sparse data.
problem Inferring complex gene regulatory networks from limited and temporally sparse data.
method Bayesian optimization and kernel-based methods to construct a Gaussian Process (GP) model.
result The method efficiently searches for the topology with the highest likelihood value.
Reconstructing the causal network in a complex dynamical system plays a crucial role in many applications, from sub-cellular biology to economic systems. Here we focus on inferring gene regulation networks (GRNs) from perturbation or gene deletion experiments. Despite their scientific merit, such perturbation experimen…
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. In t…
InfoSEM infers gene regulatory networks without GT labels, improving performance.
problem Inferring GRNs from gene expression data with high accuracy and avoiding biases.
method InfoSEM uses deep generative models with informative priors (textual gene embeddings).
result InfoSEM outperforms existing models by 38.5% across four datasets.
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.
LAGE is a systematic framework developed in Java. The motivation of LAGE is to provide a scalable and parallel solution to reconstruct Gene Regulatory Networks (GRNs) from continuous gene expression data for very large amount of genes. The basic idea of our framework is motivated by the philosophy of divideand-conquer.…
This paper is concerned with the problem of stochastic control of gene regulatory networks (GRNs) observed indirectly through noisy measurements and with uncertainty in the intervention inputs. The partial observability of the gene states and uncertainty in the intervention process are accounted for by modeling GRNs us…
Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and inconsistency between gene expression profiles and function modules, etc. It is prom…
Use of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many studies have been conducted using unsupervised methods to fulfill the task; however, such methods usually yield low prediction accuracies due to the lack of training data. In this article, we pr…
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
problem Causal inference in high-dimensional multi-omics data, especially when ignoring the hierarchical structure.
method Two-tiered divide-and-conquer strategy with ancestral conditioning sets.
result Achieves polynomial-time complexity and accurately recovers ancestral relationships.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
problem Reconstructing time-resolved regulatory effects in biological processes.
method Time-varying Network Driver Estimation (TNDE) using shared graph attention encoder and partial optimal transport.
result TNDE identifies stage-specific driver genes in mouse erythropoiesis.
Sparse GFA identifies disease factors in FTD subgroups.
problem Heterogeneity in neurological disorders hinders understanding and treatment.
method Sparse Group Factor Analysis (GFA) with regularised horseshoe priors.
result Identified latent disease factors differentially expressed in FTD subgroups.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structur…
New method identifies SDE drift and diffusion from temporal data.
problem Learning SDE parameters from temporal data, especially in noisy or incomplete data.
method Entropy-regularized optimal transport, APPEX algorithm.
result Can almost always recover drift and diffusion from temporal marginals.
Inference models are a key component in scaling variational inference to deep latent variable models, most notably as encoder networks in variational auto-encoders (VAEs). By replacing conventional optimization-based inference with a learned model, inference is amortized over data examples and therefore more computatio…
Approximate probabilistic inference algorithms are central to many fields. Examples include sequential Monte Carlo inference in robotics, variational inference in machine learning, and Markov chain Monte Carlo inference in statistics. A key problem faced by practitioners is measuring the accuracy of an approximate infe…
This work frames active inference through control as inference, offering robust control algorithms.
problem Active inference framework lacks practical sensorimotor control algorithms.
method Frame active inference through control as inference, presenting trajectory optimization as inference.
result AI may be framed as partially-observed CaI when the cost function is defined in observation states.
Simformer uses transformer models to perform flexible Bayesian inference.
problem Current simulation-based inference methods are inflexible and require fixed priors.
method Trains a probabilistic diffusion model with transformer architectures.
result Outperforms state-of-the-art methods on various benchmarks.
PE-SVI reduces SVI inference complexity by finding a suitable start point.
problem Complex posterior inference in graphical models leads to suboptimal learning.
method PE-SVI uses a pseudo-encoded start point to reduce gradient steps and step sizes.
result PE-SVI achieves the same ELBo objective as SVI with less than 1% of the required steps.
Improved Bayesian inference for neuronal ensemble inference reduces computational cost.
problem Efficient inference of neuronal ensembles from activity data.
method Modified MCMC algorithm with simulated annealing for hyperparameter control.
result Our method reduces computational cost while maintaining or improving inference accuracy.
Adding metadata abruptly changes network inference outcomes.
problem Understanding the impact of metadata on network inference.
method Investigated the effect of metadata on network inference problems.
result Metadata causes abrupt transitions in inference outcomes.
SNVI combines likelihood estimation with variational inference for efficient Bayesian inference.
problem Bayesian inference in models with intractable likelihoods.
method Sequential Neural Variational Inference (SNVI) that combines likelihood-estimation with variational inference.
result SNVI is more computationally efficient than previous algorithms without sacrificing accuracy.
Paper introduces a diagnostic for approximate inference methods.
problem Estimating errors in probabilistic inference algorithms, especially for approximate methods.
method Repeatedly simulate datasets from the prior and perform inference on each, estimating a symmetric KL-divergence.
result A diagnostic for approximate inference methods can be estimated using symmetric KL-divergence.
Probabilistic inference procedures are usually coded painstakingly from scratch, for each target model and each inference algorithm. We reduce this effort by generating inference procedures from models automatically. We make this code generation modular by decomposing inference algorithms into reusable program-to-progr…
Recent efforts on combining deep models with probabilistic graphical models are promising in providing flexible models that are also easy to interpret. We propose a variational message-passing algorithm for variational inference in such models. We make three contributions. First, we propose structured inference network…
A new method for safer statistical inference after predictions.
problem Statistical inference with pseudo-outcomes from machine learning predictions.
method Prediction De-Correlated Inference (PDC) framework.
result PDC consistently outperforms supervised methods and can adapt to any model.
Bayesian interpolants explain neural network inferences concisely.
problem Understanding neural network inferences.
method Adapting Craig interpolants for neural networks.
result Produces precise, understandable explanations.
Variational inference provides a powerful tool for approximate probabilistic in- ference on complex, structured models. Typical variational inference methods, however, require to use inference networks with computationally tractable proba- bility density functions. This largely limits the design and implementation of v…
New comparison shows differences in how value is incorporated in AIF and CAI.
problem Clarifying the relationship between Active Inference and Control-as-Inference.
method Formal comparison of AIF and CAI frameworks.
result Primary difference is how value is incorporated into generative models.
Paper shows how to infer hidden states in neural networks analytically.
problem Intractability of Bayesian inference for neural networks.
method Leverage tractable approximate Gaussian inference (TAGI) for hidden states inference.
result Demonstrates inference of hidden states through constraints for various applications.
Variational Inference shows promise for Bayesian GARCH model estimation.
problem Bayesian estimation of GARCH-family models using Monte Carlo sampling.
method Variational Inference as an alternative to Monte Carlo sampling.
result Variational Inference is a reliable and competitive method for Bayesian learning in GARCH-like models.
Post-ADC inference corrects bias in statistical inference after active data collection.
problem Bias in inference after active data collection.
method Post-ADC inference framework that corrects bias from both ADC process and data-driven target construction.
result Valid inference for data collected by SMBO methods like GP-UCB and TPE.
A new particle algorithm improves mean-field variational inference.
problem Efficiently approximating nonparametric posterior distributions in machine learning.
method Introduces PArticle VI (PAVI), a novel particle-based algorithm for nonparametric mean-field approximation.
result Obtains non-asymptotic error bounds for PArticle VI, providing the first end-to-end guarantee for particle-based MFVI.
Meta-learn Bayesian inference for task-specific BNNs using amortised inference.
problem Efficiently learning Bayesian inference for small-scale probabilistic meta-learning.
method Replace global inducing points with actual data to create a set of approximate likelihoods, train a meta-model to learn these parameters across related datasets.
result Meta-learned inference can be applied to task-specific BNNs, improving efficiency and scalability.
Bayesian method infers contextual bandit policies robustly.
problem Inference of contextual bandit policies in small sample sizes.
method Empirical likelihood for Bayesian inference.
result Accurate uncertainty measurements and policy comparison.
Exact selective inference with randomization for Gaussian regression models.
problem Exact selective inference in Gaussian regression models.
method Introduces a pivot for exact selective inference with randomization, reducing the problem to a bivariate truncated Gaussian distribution.
result Our pivot leads to exact inference and produces narrower confidence intervals than related methods.
Recent work used importance sampling ideas for better variational bounds on likelihoods. We clarify the applicability of these ideas to pure probabilistic inference, by showing the resulting Importance Weighted Variational Inference (IWVI) technique is an instance of augmented variational inference, thus identifying th…
BOED improves SBI by optimizing experimental designs and inference functions.
problem Efficiently use experimental resources for better inference on complex models.
method Link mutual information bounds between SBI and BOED, optimizing both design and inference.
result BOED improves inference in real-world simulators in epidemiology and biology.
Valid inference from data and predictions.
problem Valid statistical inference with machine learning predictions.
method Framework for valid inference using machine learning predictions.
result Valid confidence intervals without assumptions on predictions.
EFI automates statistical inference for big data.
problem Statistical inference for model parameters based on observations.
method EFI uses stochastic gradient Markov chain Monte Carlo and sparse deep neural networks.
result EFI provides higher fidelity in parameter estimation and automates the inference process.
Derives time-averaged active inference from control principles.
problem Finite-horizon or discounted-surprise problems in active inference.
method Derives infinite-horizon, average-surprise active inference from optimal control principles.
result Unified objective functional for sensorimotor control.
UA-SABI uses surrogates to speed up Bayesian inference for expensive models.
problem Inference for computationally expensive models is slow and uncertain.
method Combines surrogate modeling with Amortized Bayesian Inference (ABI) to propagate uncertainties.
result Reliable, fast, and repeated Bayesian inference for expensive models is achieved.
Deep learning enhances active inference for dynamic state spaces.
problem Limited applicability of active inference to continuous state spaces.
method Use of deep learning to approximate probability distributions for active inference.
result Active inference can be applied to continuous state spaces.
Adversarial robustness of amortized Bayesian inference is studied, showing it can be improved.
problem Adversarial robustness of amortized Bayesian inference.
method Simulation-based estimation, regularization scheme based on Fisher information.
result Adversarial robustness can be improved with a regularization scheme.
Probabilistic models can handle causal inference without special tools.
problem Confusion over necessary tools for causal inference.
method Demonstrated through concrete examples that causal questions can be answered using standard probabilistic models.
result Causal questions can be addressed using standard probabilistic modelling and inference.
New method uses EKI for efficient Bayesian inference in high-dimensional problems.
problem Efficient inference for high-dimensional posterior distributions in physics-informed neural networks.
method Ensemble Kalman Inversion (EKI) for high-dimensional posterior inference.
result EKI-based inference provides comparable uncertainty estimates to HMC-based methods but with reduced computational cost.