Computer simulations have long presented the exciting possibility of scientific insight into complex real-world processes. Despite the power of modern computing, however, it remains challenging to systematically perform inference under simulation models. This has led to the rise of simulation-based inference (SBI), a class of machine learning-enabled techniques for approaching inverse problems with stochastic simulators. Many such methods, however, require large numbers of simulation samples and face difficulty scaling to high-dimensional settings, often making inference prohibitive under resource-intensive simulators. To mitigate these drawbacks, we introduce active sequential neural posterior estimation (ASNPE). ASNPE brings an active learning scheme into the inference loop to estimate the utility of simulation parameter candidates to the underlying probabilistic model. The proposed acquisition scheme is easily integrated into existing posterior estimation pipelines, allowing for improved sample efficiency with low computational overhead. We further demonstrate the effectiveness of the proposed method in the travel demand calibration setting, a high-dimensional inverse problem commonly requiring computationally expensive traffic simulators. Our method outperforms well-tuned benchmarks and state-of-the-art posterior estimation methods on a large-scale real-world traffic network, as well as demonstrates a performance advantage over non-active counterparts on a suite of SBI benchmark environments.

Augmenting a smooth cost function with an $\ell_1$ penalty allows analysts to efficiently conduct estimation and variable selection simultaneously in sophisticated models and can be efficiently implemented using proximal gradient methods. However, one drawback of the $\ell_1$ penalty is bias: nonzero parameters are underestimated in magnitude, motivating techniques such as the Adaptive Lasso which endow each parameter with its own penalty coefficient. But it's not clear how these parameter-specific penalties should be set in complex models. In this article, we study the approach of treating the penalty coefficients as additional decision variables to be learned in a \textit{Maximum a Posteriori} manner, developing a proximal gradient approach to joint optimization of these together with the parameters of any differentiable cost function. Beyond reducing bias in estimates, this procedure can also encourage arbitrary sparsity structure via a prior on the penalty coefficients. We compare our method to implementations of specific sparsity structures for non-Gaussian regression on synthetic and real datasets, finding our more general method to be competitive in terms of both speed and accuracy. We then consider nonlinear models for two case studies: COVID-19 vaccination behavior and international refugee movement, highlighting the applicability of this approach to complex problems and intricate sparsity structures.

Understanding how changes in explanatory features affect the unconditional distribution of the outcome is important in many applications. However, existing black-box predictive models are not readily suited for analyzing such questions. In this work, we develop an approximation method to compute the feature importance curves relevant to the unconditional distribution of outcomes, while leveraging the power of pre-trained black-box predictive models. The feature importance curves measure the changes across quantiles of outcome distribution given an external impact of change in the explanatory features. Through extensive numerical experiments and real data examples, we demonstrate that our approximation method produces sparse and faithful results, and is computationally efficient.

With the advent of diffusion models, new proteins can be generated at an unprecedented rate. The \textit{motif scaffolding problem} requires steering this generative process to yield proteins with a desirable functional substructure -- a motif. While models have been trained to take the motif as conditional input, recent techniques in diffusion posterior sampling can be leveraged as zero-shot alternatives whose approximations can be corrected with sequential Monte Carlo (SMC) algorithms. In this work, we introduce a new set of guidance potentials to describe and solve scaffolding tasks by adapting SMC-aided diffusion posterior samplers with an unconditional model, Genie, acting as a prior. Against established benchmarks, we successfully scaffold several single-motif and multi-motif problems. The latter is possible by pairing reconstruction guidance with $\mathrm{SE}(3)$-invariant potentials. In the single-motif case, we find these potentials perform comparably to the conventional masking approach and that reconstruction guidance outperforms replacement methods when aided with SMC. We additionally consider a guidance potential for point symmetry constraints and produce designable internally symmetric monomers with our setup. Overall, this work highlights the capabilities and areas for improvement of zero-shot posterior samplers in motif scaffolding tasks. Code is available at: https://github.com/matsagad/mres-project

This manuscript gives a big-picture, up-to-date overview of the field of (deep) reinforcement learning and sequential decision making, covering value-based RL, policy-gradient methods, model-based methods, and various other topics (including a very brief discussion of RL+LLMs).

Understanding the effects of quarantine policies in populations with underlying social networks is crucial for public health, yet most causal inference methods fail here due to their assumption of independent individuals. We introduce DeepNetTMLE, a deep-learning-enhanced Targeted Maximum Likelihood Estimation (TMLE) method designed to estimate time-sensitive treatment effects in observational data. DeepNetTMLE mitigates bias from time-varying confounders under general interference by incorporating a temporal module and domain adversarial training to build intervention-invariant representations. This process removes associations between current treatments and historical variables, while the targeting step maintains the bias-variance trade-off, enhancing the reliability of counterfactual predictions. Using simulations of a ``Susceptible-Infected-Recovered'' model with varied quarantine coverages, we show that DeepNetTMLE achieves lower bias and more precise confidence intervals in counterfactual estimates, enabling optimal quarantine recommendations within budget constraints, surpassing state-of-the-art methods.

Circuits based on sum-product structure have become a ubiquitous representation to compactly encode knowledge, from Boolean functions to probability distributions. By imposing constraints on the structure of such circuits, certain inference queries become tractable, such as model counting and most probable configuration. Recent works have explored analyzing probabilistic and causal inference queries as compositions of basic operators to derive tractability conditions. In this paper, we take an algebraic perspective for compositional inference, and show that a large class of queries - including marginal MAP, probabilistic answer set programming inference, and causal backdoor adjustment - correspond to a combination of basic operators over semirings: aggregation, product, and elementwise mapping. Using this framework, we uncover simple and general sufficient conditions for tractable composition of these operators, in terms of circuit properties (e.g., marginal determinism, compatibility) and conditions on the elementwise mappings. Applying our analysis, we derive novel tractability conditions for many such compositional queries. Our results unify tractability conditions for existing problems on circuits, while providing a blueprint for analysing novel compositional inference queries.

Generative modeling for tabular data has recently gained significant attention in the Deep Learning domain. Its objective is to estimate the underlying distribution of the data. However, estimating the underlying distribution of tabular data has its unique challenges. Specifically, this data modality is composed of mixed types of features, making it a non-trivial task for a model to learn intra-relationships between them. One approach to address mixture is to embed each feature into a continuous matrix via tokenization, while a solution to capture intra-relationships between variables is via the transformer architecture. In this work, we empirically investigate the potential of using embedding representations on tabular data generation, utilizing tensor contraction layers and transformers to model the underlying distribution of tabular data within Variational Autoencoders. Specifically, we compare four architectural approaches: a baseline VAE model, two variants that focus on tensor contraction layers and transformers respectively, and a hybrid model that integrates both techniques. Our empirical study, conducted across multiple datasets from the OpenML CC18 suite, compares models over density estimation and Machine Learning efficiency metrics. The main takeaway from our results is that leveraging embedding representations with the help of tensor contraction layers improves density estimation metrics, albeit maintaining competitive performance in terms of machine learning efficiency.

We propose a novel method for measuring the discrepancy between a set of samples and a desired posterior distribution for Bayesian inference. Classical methods for assessing sample quality like the effective sample size are not appropriate for scalable Bayesian sampling algorithms, such as stochastic gradient Langevin dynamics, that are asymptotically biased. Instead, the gold standard is to use the kernel Stein Discrepancy (KSD), which is itself not scalable given its quadratic cost in the number of samples. The KSD and its faster extensions also typically suffer from the curse-of-dimensionality and can require extensive tuning. To address these limitations, we develop the polynomial Stein discrepancy (PSD) and an associated goodness-of-fit test. While the new test is not fully convergence-determining, we prove that it detects differences in the first r moments in the Bernstein-von Mises limit. We empirically show that the test has higher power than its competitors in several examples, and at a lower computational cost. Finally, we demonstrate that the PSD can assist practitioners to select hyper-parameters of Bayesian sampling algorithms more efficiently than competitors.

Fake news on social media platforms poses a significant threat to societal systems, underscoring the urgent need for advanced detection methods. The existing detection methods can be divided into machine intelligence-based, crowd intelligence-based, and hybrid intelligence-based methods. Among them, hybrid intelligence-based methods achieve the best performance but fail to consider the reliability issue in detection. In light of this, we propose a novel Reliability Aware Hybrid Intelligence (RAHI) method for fake news detection. Our method comprises three integral modules. The first module employs a Bayesian deep learning model to capture the inherent reliability within machine intelligence. The second module uses an Item Response Theory (IRT)-based user response aggregation to account for the reliability in crowd intelligence. The third module introduces a new distribution fusion mechanism, which takes the distributions derived from both machine and crowd intelligence as input, and outputs a fused distribution that provides predictions along with the associated reliability. The experiments on the Weibo dataset demonstrate the advantages of our method. This study contributes to the research field with a novel RAHI-based method, and the code is shared at https://github.com/Kangwei-g/RAHI. This study has practical implications for three key stakeholders: internet users, online platform managers, and the government.