Kaiwen Wu

Bo Peng, Kaiwen Wu, Sirui Chen et al. · tencent-ai

Causal discovery from observational data remains challenging due to the fundamental limitations of purely statistical methods, such as statistical distinguishability within equivalence classes and sensitivity to finite sample sizes. While large language models (LLMs) offer a promising source of domain knowledge to complement statistical inference, existing LLM-augmented methods are vulnerable to LLM errors and incur high token costs. Moreover, reliance on a single data-centric algorithm can make results sensitive to algorithm-specific biases. To address these limitations, we propose CauTion, a framework that reliably integrates LLM domain knowledge into an ensemble of statistical causal discovery algorithms through consensus filtering and LLM reliability estimation. CauTion proceeds in three stages. First, an algorithm ensemble utilizes a consensus voting to resolve up to 96% of edges on which algorithms agree, achieving near-perfect accuracy on the filtered consensus edges. Second, a trust-calibrated arbitration mechanism estimates the relative reliability of the LLM and the algorithms via an annotation-free trust calibration procedure, which is then utilized to govern a trust-weighted voting process that restricts LLM arbitration exclusively to edges with unreliable algorithmic evidence. Third, a cycle repair step is applied to guarantee the final causal graph is validly acyclic. Experiments on six datasets demonstrate that CauTion consistently outperforms both data-centric and LLM-augmented baselines, with larger gains on larger graphs and strong robustness to LLM errors. Code is available at https://github.com/OpenCausaLab/CauTion.

Quan Nguyen, Kaiwen Wu, Jacob R. Gardner et al.

Local optimization presents a promising approach to expensive, high-dimensional black-box optimization by sidestepping the need to globally explore the search space. For objective functions whose gradient cannot be evaluated directly, Bayesian optimization offers one solution -- we construct a probabilistic model of the objective, design a policy to learn about the gradient at the current location, and use the resulting information to navigate the objective landscape. Previous work has realized this scheme by minimizing the variance in the estimate of the gradient, then moving in the direction of the expected gradient. In this paper, we re-examine and refine this approach. We demonstrate that, surprisingly, the expected value of the gradient is not always the direction maximizing the probability of descent, and in fact, these directions may be nearly orthogonal. This observation then inspires an elegant optimization scheme seeking to maximize the probability of descent while moving in the direction of most-probable descent. Experiments on both synthetic and real-world objectives show that our method outperforms previous realizations of this optimization scheme and is competitive against other, significantly more complicated baselines.

Natalie Maus, Kaiwen Wu, David Eriksson et al.

Bayesian optimization (BO) is a popular approach for sample-efficient optimization of black-box objective functions. While BO has been successfully applied to a wide range of scientific applications, traditional approaches to single-objective BO only seek to find a single best solution. This can be a significant limitation in situations where solutions may later turn out to be intractable. For example, a designed molecule may turn out to violate constraints that can only be reasonably evaluated after the optimization process has concluded. To address this issue, we propose Rank-Ordered Bayesian Optimization with Trust-regions (ROBOT) which aims to find a portfolio of high-performing solutions that are diverse according to a user-specified diversity metric. We evaluate ROBOT on several real-world applications and show that it can discover large sets of high-performing diverse solutions while requiring few additional function evaluations compared to finding a single best solution.

Kaiwen Wu, Jonathan Wenger, Haydn Jones et al.

Training and inference in Gaussian processes (GPs) require solving linear systems with $n\times n$ kernel matrices. To address the prohibitive $\mathcal{O}(n^3)$ time complexity, recent work has employed fast iterative methods, like conjugate gradients (CG). However, as datasets increase in magnitude, the kernel matrices become increasingly ill-conditioned and still require $\mathcal{O}(n^2)$ space without partitioning. Thus, while CG increases the size of datasets GPs can be trained on, modern datasets reach scales beyond its applicability. In this work, we propose an iterative method which only accesses subblocks of the kernel matrix, effectively enabling mini-batching. Our algorithm, based on alternating projection, has $\mathcal{O}(n)$ per-iteration time and space complexity, solving many of the practical challenges of scaling GPs to very large datasets. Theoretically, we prove the method enjoys linear convergence. Empirically, we demonstrate its fast convergence in practice and robustness to ill-conditioning. On large-scale benchmark datasets with up to four million data points, our approach accelerates GP training and inference by speed-up factors up to $27\times$ and $72 \times$, respectively, compared to CG.

Kyurae Kim, Kaiwen Wu, Jisu Oh et al.

Understanding the gradient variance of black-box variational inference (BBVI) is a crucial step for establishing its convergence and developing algorithmic improvements. However, existing studies have yet to show that the gradient variance of BBVI satisfies the conditions used to study the convergence of stochastic gradient descent (SGD), the workhorse of BBVI. In this work, we show that BBVI satisfies a matching bound corresponding to the $ABC$ condition used in the SGD literature when applied to smooth and quadratically-growing log-likelihoods. Our results generalize to nonlinear covariance parameterizations widely used in the practice of BBVI. Furthermore, we show that the variance of the mean-field parameterization has provably superior dimensional dependence.

Haydn Jones, Yimeng Zeng, Alden Rose et al.

Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks -- blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions -- Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard -- e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

Kaiwen Wu, Jacob R. Gardner

Elliptical slice sampling, when adapted to linearly truncated multivariate normal distributions, is a rejection-free Markov chain Monte Carlo method. At its core, it requires analytically constructing an ellipse-polytope intersection. The main novelty of this paper is an algorithm that computes this intersection in $\mathcal{O}(m \log m)$ time, where $m$ is the number of linear inequality constraints representing the polytope. We show that an implementation based on this algorithm enhances numerical stability, speeds up running time, and is easy to parallelize for launching multiple Markov chains.

Kaiwen Wu, Jacob R. Gardner

The knowledge gradient is a popular acquisition function in Bayesian optimization (BO) for optimizing black-box objectives with noisy function evaluations. Many practical settings, however, allow only pairwise comparison queries, yielding a preferential BO problem where direct function evaluations are unavailable. Extending the knowledge gradient to preferential BO is hindered by its computational challenge. At its core, the look-ahead step in the preferential setting requires computing a non-Gaussian posterior, which was previously considered intractable. In this paper, we address this challenge by deriving an exact and analytical knowledge gradient for preferential BO. We show that the exact knowledge gradient performs strongly on a suite of benchmark problems, often outperforming existing acquisition functions. In addition, we also present a case study illustrating the limitation of the knowledge gradient in certain scenarios.

Guojun Zhang, Kaiwen Wu, Pascal Poupart et al.

Differential games, in particular two-player sequential zero-sum games (a.k.a. minimax optimization), have been an important modeling tool in applied science and received renewed interest in machine learning due to many recent applications, such as adversarial training, generative models and reinforcement learning. However, existing theory mostly focuses on convex-concave functions with few exceptions. In this work, we propose two novel Newton-type algorithms for nonconvex-nonconcave minimax optimization. We prove their local convergence at strict local minimax points, which are surrogates of global solutions. We argue that our Newton-type algorithms nicely complement existing ones in that (a) they converge faster to strict local minimax points; (b) they are much more effective when the problem is ill-conditioned; (c) their computational complexity remains similar. We verify the effectiveness of our Newton-type algorithms through experiments on training GANs which are intrinsically nonconvex and ill-conditioned. Our code is available at https://github.com/watml/min-max-2nd-order.

Jonathan Wenger, Kaiwen Wu, Philipp Hennig et al.

Model selection in Gaussian processes scales prohibitively with the size of the training dataset, both in time and memory. While many approximations exist, all incur inevitable approximation error. Recent work accounts for this error in the form of computational uncertainty, which enables -- at the cost of quadratic complexity -- an explicit tradeoff between computation and precision. Here we extend this development to model selection, which requires significant enhancements to the existing approach, including linear-time scaling in the size of the dataset. We propose a novel training loss for hyperparameter optimization and demonstrate empirically that the resulting method can outperform SGPR, CGGP and SVGP, state-of-the-art methods for GP model selection, on medium to large-scale datasets. Our experiments show that model selection for computation-aware GPs trained on 1.8 million data points can be done within a few hours on a single GPU. As a result of this work, Gaussian processes can be trained on large-scale datasets without significantly compromising their ability to quantify uncertainty -- a fundamental prerequisite for optimal decision-making.

Kaiwen Wu, Craig Sanders, Benjamin Letham et al.

Gaussian processes (GPs) are powerful models for human-in-the-loop experiments due to their flexibility and well-calibrated uncertainty. However, GPs modeling human responses typically ignore auxiliary information, including a priori domain expertise and non-task performance information like user confidence ratings. We propose mixed likelihood variational GPs to leverage auxiliary information, which combine multiple likelihoods in a single evidence lower bound to model multiple types of data. We demonstrate the benefits of mixing likelihoods in three real-world experiments with human participants. First, we use mixed likelihood training to impose prior knowledge constraints in GP classifiers, which accelerates active learning in a visual perception task where users are asked to identify geometric errors resulting from camera position errors in virtual reality. Second, we show that leveraging Likert scale confidence ratings by mixed likelihood training improves model fitting for haptic perception of surface roughness. Lastly, we show that Likert scale confidence ratings improve human preference learning in robot gait optimization. The modeling performance improvements found using our framework across this diverse set of applications illustrates the benefits of incorporating auxiliary information into active learning and preference learning by using mixed likelihoods to jointly model multiple inputs.

Kaiwen Wu, Jacob R. Gardner

Stochastic natural gradient variational inference (NGVI) is a popular posterior inference method with applications in various probabilistic models. Despite its wide usage, little is known about the non-asymptotic convergence rate in the \emph{stochastic} setting. We aim to lessen this gap and provide a better understanding. For conjugate likelihoods, we prove the first $\mathcal{O}(\frac{1}{T})$ non-asymptotic convergence rate of stochastic NGVI. The complexity is no worse than stochastic gradient descent (\aka black-box variational inference) and the rate likely has better constant dependency that leads to faster convergence in practice. For non-conjugate likelihoods, we show that stochastic NGVI with the canonical parameterization implicitly optimizes a non-convex objective. Thus, a global convergence rate of $\mathcal{O}(\frac{1}{T})$ is unlikely without some significant new understanding of optimizing the ELBO using natural gradients.

Kaiwen Wu, Kyurae Kim, Roman Garnett et al.

A recent development in Bayesian optimization is the use of local optimization strategies, which can deliver strong empirical performance on high-dimensional problems compared to traditional global strategies. The "folk wisdom" in the literature is that the focus on local optimization sidesteps the curse of dimensionality; however, little is known concretely about the expected behavior or convergence of Bayesian local optimization routines. We first study the behavior of the local approach, and find that the statistics of individual local solutions of Gaussian process sample paths are surprisingly good compared to what we would expect to recover from global methods. We then present the first rigorous analysis of such a Bayesian local optimization algorithm recently proposed by Müller et al. (2021), and derive convergence rates in both the noisy and noiseless settings.

Kyurae Kim, Jisu Oh, Kaiwen Wu et al.

We provide the first convergence guarantee for full black-box variational inference (BBVI), also known as Monte Carlo variational inference. While preliminary investigations worked on simplified versions of BBVI (e.g., bounded domain, bounded support, only optimizing for the scale, and such), our setup does not need any such algorithmic modifications. Our results hold for log-smooth posterior densities with and without strong log-concavity and the location-scale variational family. Also, our analysis reveals that certain algorithm design choices commonly employed in practice, particularly, nonlinear parameterizations of the scale of the variational approximation, can result in suboptimal convergence rates. Fortunately, running BBVI with proximal stochastic gradient descent fixes these limitations, and thus achieves the strongest known convergence rate guarantees. We evaluate this theoretical insight by comparing proximal SGD against other standard implementations of BBVI on large-scale Bayesian inference problems.

Kaiwen Wu, Allen Houze Wang, Yaoliang Yu

Deep models, while being extremely flexible and accurate, are surprisingly vulnerable to "small, imperceptible" perturbations known as adversarial attacks. While the majority of existing attacks focus on measuring perturbations under the $\ell_p$ metric, Wasserstein distance, which takes geometry in pixel space into account, has long been known to be a suitable metric for measuring image quality and has recently risen as a compelling alternative to the $\ell_p$ metric in adversarial attacks. However, constructing an effective attack under the Wasserstein metric is computationally much more challenging and calls for better optimization algorithms. We address this gap in two ways: (a) we develop an exact yet efficient projection operator to enable a stronger projected gradient attack; (b) we show that the Frank-Wolfe method equipped with a suitable linear minimization oracle works extremely fast under Wasserstein constraints. Our algorithms not only converge faster but also generate much stronger attacks. For instance, we decrease the accuracy of a residual network on CIFAR-10 to $3.4\%$ within a Wasserstein perturbation ball of radius $0.005$, in contrast to $65.6\%$ using the previous Wasserstein attack based on an \emph{approximate} projection operator. Furthermore, employing our stronger attacks in adversarial training significantly improves the robustness of adversarially trained models.

Kaiwen Wu, Yaoliang Yu

Deep models, while being extremely versatile and accurate, are vulnerable to adversarial attacks: slight perturbations that are imperceptible to humans can completely flip the prediction of deep models. Many attack and defense mechanisms have been proposed, although a satisfying solution still largely remains elusive. In this work, we give strong evidence that during training, deep models maximize the minimum margin in order to achieve high accuracy, but at the same time decrease the \emph{average} margin hence hurting robustness. Our empirical results highlight an intrinsic trade-off between accuracy and robustness for current deep model training. To further address this issue, we propose a new regularizer to explicitly promote average margin, and we verify through extensive experiments that it does lead to better robustness. Our regularized objective remains Fisher-consistent, hence asymptotically can still recover the Bayes optimal classifier.

Borislav Mavrin, Shangtong Zhang, Hengshuai Yao et al.

In distributional reinforcement learning (RL), the estimated distribution of value function models both the parametric and intrinsic uncertainties. We propose a novel and efficient exploration method for deep RL that has two components. The first is a decaying schedule to suppress the intrinsic uncertainty. The second is an exploration bonus calculated from the upper quantiles of the learned distribution. In Atari 2600 games, our method outperforms QR-DQN in 12 out of 14 hard games (achieving 483 \% average gain across 49 games in cumulative rewards over QR-DQN with a big win in Venture). We also compared our algorithm with QR-DQN in a challenging 3D driving simulator (CARLA). Results show that our algorithm achieves near-optimal safety rewards twice faster than QRDQN.