论文检索

Reinforcement Learning · Everything Else

Xue Yan, Yan Song, Xidong Feng, Mengyue Yang, Haifeng Zhang, Haitham Bou Ammar, Jun Wang

In sequential decision-making (SDM) tasks, methods like reinforcement learning (RL) and heuristic search have made notable advances in specific cases. However, they often require extensive exploration and face challenges in generalizing across diverse environments due to their limited grasp of the underlying decision dynamics. In contrast, large language models (LLMs) have recently emerged as powerful general-purpose tools, due to their capacity to maintain vast amounts of domain-specific knowledge. To harness this rich prior knowledge for efficiently solving complex SDM tasks, we propose treating LLMs as prior action distributions and integrating them into RL frameworks through Bayesian inference methods, making use of variational inference and direct posterior sampling. The proposed approaches facilitate the seamless incorporation of fixed LLM priors into both policy-based and value-based RL frameworks. Our experiments show that incorporating LLM-based action priors significantly reduces exploration and optimization complexity, substantially improving sample efficiency compared to traditional RL techniques, e.g., using LLM priors decreases the number of required samples by over 90\% in offline learning scenarios.

Applications · Genetics, Cell Biology, Health, etc

Ziwei Yang, Zheng Chen, XIN LIU, Rikuto Kotoge, Peng Chen, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts.

Probabilistic Methods · Variational Inference

Marcello Negri, Jonathan Aellen, Volker Roth

Normalizing Flows (NFs) are powerful and efficient models for density estimation. When modeling densities on manifolds, NFs can be generalized to injective flows but the Jacobian determinant becomes computationally prohibitive. Current approaches either consider bounds on the log-likelihood or rely on some approximations of the Jacobian determinant. In contrast, we propose injective flows for star-like manifolds and show that for such manifolds we can compute the Jacobian determinant exactly and efficiently. This aspect is particularly relevant for variational inference settings, where no samples are available and only some unnormalized target is known. Among many, we showcase the relevance of modeling densities on star-like manifolds in two settings. Firstly, we introduce a novel Objective Bayesian approach for penalized likelihood models by interpreting level-sets of the penalty as star-like manifolds. Secondly, we consider probabilistic mixing models and introduce a general method for variational inference by defining the posterior of mixture weights on the probability simplex.

Probabilistic Methods · Variational Inference

Zhanfeng Mo, Haosen Shi, Sinno Jialin Pan

Neural pruning aims to compress and accelerate deep neural networks by identifying the optimal subnetwork within a specified sparsity budget. In this work, we study how to gradually sparsify the unpruned dense model to the target sparsity level with minimal performance drop. Specifically, we analyze the evolution of the population of optimal subnetworks under continuous sparsity increments from a thermodynamic perspective. We first reformulate neural pruning as an expected loss minimization problem over the mask distributions. Then, we establish an effective approximation for the sparsity evolution of the optimal mask distribution, termed the **S**parsity Evolutionary **F**okker-**P**lanck-**K**olmogorov Equation (**SFPK**), which provides closed-form, mathematically tractable guidance on distributional transitions for minimizing the expected loss under an infinitesimal sparsity increment. On top of that, we propose SFPK-pruner, a particle simulation-based probabilistic pruning method, to sample performant masks with desired sparsity from the destination distribution of SFPK. In theory, we establish the convergence guarantee for the proposed SFPK-pruner. Our SFPK-pruner exhibits competitive performance in various pruning scenarios. The code is available on https://github.com/mzf666/SFPK-main.

Deep Learning · Generative Models and Autoencoders

Xin Gao, Jian Pu

Multi-View Representation Learning (MVRL) aims to derive a unified representation from multi-view data by leveraging shared and complementary information across views. However, when views are irregularly missing, the incomplete data can lead to representations that lack sufficiency and consistency. To address this, we propose Multi-View Permutation of Variational Auto-Encoders (MVP), which excavates invariant relationships between views in incomplete data. MVP establishes inter-view correspondences in the latent space of Variational Auto-Encoders, enabling the inference of missing views and the aggregation of more sufficient information. To derive a valid Evidence Lower Bound (ELBO) for learning, we apply permutations to randomly reorder variables for cross-view generation and then partition them by views to maintain invariant meanings under permutations. Additionally, we enhance consistency by introducing an informational prior with cyclic permutations of posteriors, which turns the regularization term into a similarity measure across distributions. We demonstrate the effectiveness of our approach on seven diverse datasets with varying missing ratios, achieving superior performance in multi-view clustering and generation tasks.

Probabilistic Methods · Bayesian Models and Methods

Ola Rønning, Eric Nalisnick, Christophe Ley, Padhraic Smyth, Thomas Hamelryck

Stein variational gradient descent (SVGD) (Liu & Wang, 2016) performs approximate Bayesian inference by representing the posterior with a set of particles.However, SVGD suffers from variance collapse, i.e. poor predictions due to underestimating uncertainty (Ba et al., 2021), even for moderately-dimensional modelssuch as small Bayesian neural networks (BNNs). To address this issue, we generalize SVGD by letting each particle parameterize a component distribution ina mixture model. Our method, Stein Mixture Inference (SMI), optimizes a lowerbound to the evidence (ELBO) and introduces user-specified guides parameterizedby particles. SMI extends the Nonlinear SVGD framework (Wang & Liu, 2019) tothe case of variational Bayes. SMI effectively avoids variance collapse, judging bya previously described test developed for this purpose, and performs well on standard data sets. In addition, SMI requires considerably fewer particles than SVGDto accurately estimate uncertainty for small BNNs. The synergistic combination ofNSVGD, ELBO optimization and user-specified guides establishes a promisingapproach towards variational Bayesian inference in the case of tall and wide data.

Optimization · Optimization and Learning under Uncertainty

Dan Steinberg, Rafael Oliveira, Cheng Soon Ong, Edwin Bonilla

We develop VSD, a method for conditioning a generative model of discrete, combinatorial designs on a rare desired class by efficiently evaluating a black-box (e.g. experiment, simulation) in a batch sequential manner. We call this task active generation; we formalize active generation's requirements and desiderata, and formulate a solution via variational inference. VSD uses off-the-shelf gradient based optimization routines, can learn powerful generative models for desirable designs, and can take advantage of scalable predictive models. We derive asymptotic convergence rates for learning the true conditional generative distribution of designs with certain configurations of our method. After illustrating the generative model on images, we empirically demonstrate that VSD can outperform existing baseline methods on a set of real sequence-design problems in various protein and DNA/RNA engineering tasks.

Applications · Robotics

Priya Sundaresan, Hengyuan Hu, Quan Vuong, Jeannette Bohg, Dorsa Sadigh

While imitation learning (IL) offers a promising framework for teaching robots various behaviors, learning complex tasks remains challenging. Existing IL policies struggle to generalize effectively across visual and spatial variations even for simple tasks. In this work, we introduce **SPHINX**: **S**alient **P**oint-based **H**ybrid **I**mitatio**N** and e**X**ecution, a flexible IL policy that leverages multimodal observations (point clouds and wrist images), along with a hybrid action space of low-frequency, sparse waypoints and high-frequency, dense end effector movements. Given 3D point cloud observations, SPHINX learns to infer task-relevant points within a point cloud, or *salient points*, which support spatial generalization by focusing on semantically meaningful features. These salient points serve as anchor points to predict waypoints for long-range movement, such as reaching target poses in free-space. Once near a salient point, SPHINX learns to switch to predicting dense end-effector movements given close-up wrist images for precise phases of a task. By exploiting the strengths of different input modalities and action representations for different manipulation phases, SPHINX tackles complex tasks in a sample-efficient, generalizable manner. Our method achieves **86.7%** success across 4 real-world and 2 simulated tasks, outperforming the next best state-of-the-art IL baseline by **41.1%** on average across **440** real world trials. SPHINX additionally generalizes to novel viewpoints, visual distractors, spatial arrangements, and execution speeds with a **1.7x** speedup over the most competitive baseline. Our website (http://sphinx-manip.github.io) provides open-sourced code for data collection, training, and evaluation, along with supplementary videos.

Theory · Probabilistic Methods

Vincent Plassier, Alexander Fishkov, Mohsen Guizani, Maxim Panov, Eric Moulines

We develop a new method for generating prediction sets that combines the flexibility of conformal methods with an estimate of the conditional distribution $\textup{P}_{Y \mid X}$. Existing methods, such as conformalized quantile regression and probabilistic conformal prediction, usually provide only a marginal coverage guarantee. In contrast, our approach extends these frameworks to achieve approximately conditional coverage, which is crucial for many practical applications. Our prediction sets adapt to the behavior of the predictive distribution, making them effective even under high heteroscedasticity. While exact conditional guarantees are infeasible without assumptions on the underlying data distribution, we derive non-asymptotic bounds that depend on the total variation distance of the conditional distribution and its estimate. Using extensive simulations, we show that our method consistently outperforms existing approaches in terms of conditional coverage, leading to more reliable statistical inference in a variety of applications.

Probabilistic Methods · Variational Inference

Hyungi Lee, Seungyoo Lee, Juho Lee

The success of deep learning requires large datasets and extensive training, which can create significant computational challenges. To address these challenges, pseudo-coresets, small learnable datasets that mimic the entire data, have been proposed. Bayesian Neural Networks, which offer predictive uncertainty and probabilistic interpretation for deep neural networks, also face issues with large-scale datasets due to their high-dimensional parameter space. Prior works on Bayesian Pseudo-Coresets (BPC) attempt to reduce the computational load for computing weight posterior distribution by a small number of pseudo-coresets but suffer from memory inefficiency during BPC training and sub-optimal results. To overcome these limitations, we propose Variational Bayesian Pseudo-Coreset (VBPC), a novel approach that utilizes variational inference to efficiently approximate the posterior distribution, reducing memory usage and computational costs while improving performance across benchmark datasets.

Probabilistic Methods · Bayesian Models and Methods

Chukwudi Paul Obite, Zhi Chang, Keyan Wu, Shiwei Lan

The effectiveness of statistical and machine learning methods depends on how well data features are characterized. Developing informative and interpretable latent representations with controlled complexity is essential for visualizing data structure and for facilitating efficient model building through dimensionality reduction. Latent variable models, such as Gaussian Process Latent Variable Models (GP-LVM), have become popular for learning complex, nonlinear representations as alternatives to Principal Component Analysis (PCA). In this paper, we propose a novel class of latent variable models based on the recently introduced Q-exponential process (QEP), which generalizes GP-LVM with a tunable complexity parameter, $q>0$. Our approach, the \emph{Q-exponential Process Latent Variable Model (QEP-LVM)}, subsumes GP-LVM as a special case when $q=2$, offering greater flexibility in managing representation complexity while enhancing interpretability. To ensure scalability, we incorporate sparse variational inference within a Bayesian training framework. We establish connections between QEP-LVM and probabilistic PCA, demonstrating its superior performance through experiments on datasets such as the Swiss roll, oil flow, and handwritten digits.

Probabilistic Methods · Variational Inference

Daniel Ward, Mark Beaumont, Matteo Fasiolo

Estimating a distribution given access to its unnormalized density is pivotal in Bayesian inference, where the posterior is generally known only up to an unknown normalizing constant. Variational inference and Markov chain Monte Carlo methods are the predominant tools for this task; however, both are often challenging to apply reliably, particularly when the posterior has complex geometry. Here, we introduce Soft Contrastive Variational Inference (SoftCVI), which allows a family of variational objectives to be derived through a contrastive estimation framework. The approach parameterizes a classifier in terms of a variational distribution, reframing the inference task as a contrastive estimation problem aiming to identify a single true posterior sample among a set of samples. Despite this framing, we do not require positive or negative samples, but rather learn by sampling the variational distribution and computing ground truth soft classification labels from the unnormalized posterior itself. The objectives have zero variance gradient when the variational approximation is exact, without the need for specialized gradient estimators. We empirically investigate the performance on a variety of Bayesian inference tasks, using both simple (e.g. normal) and expressive (normalizing flow) variational distributions. We find that SoftCVI can be used to form objectives which are stable to train and mass-covering, frequently outperforming inference with other variational approaches.

Probabilistic Methods · Variational Inference

Sayan Banerjee, Krishna Balasubramanian, PROMIT GHOSAL

We provide finite-particle convergence rates for the Stein Variational Gradient Descent (SVGD) algorithm in the Kernelized Stein Discrepancy ($\KSD$) and Wasserstein-2 metrics. Our key insight is that the time derivative of the relative entropy between the joint density of $N$ particle locations and the $N$-fold product target measure, starting from a regular initial distribution, splits into a dominant 'negative part' proportional to $N$ times the expected $\KSD^2$ and a smaller 'positive part'. This observation leads to $\KSD$ rates of order $1/\sqrt{N}$, in both continuous and discrete time, providing a near optimal (in the sense of matching the corresponding i.i.d. rates) double exponential improvement over the recent result by~\cite{shi2024finite}. Under mild assumptions on the kernel and potential, these bounds also grow polynomially in the dimension $d$. By adding a bilinear component to the kernel, the above approach is used to further obtain Wasserstein-2 convergence in continuous time. For the case of `bilinear + Mat\'ern' kernels, we derive Wasserstein-2 rates that exhibit a curse-of-dimensionality similar to the i.i.d. setting. We also obtain marginal convergence and long-time propagation of chaos results for the time-averaged particle laws.

Probabilistic Methods · Variational Inference

Charles Dawson, Van Tran, Max Li, Chuchu Fan

Increased deployment of autonomous systems in fields like transportation and robotics have seen a corresponding increase in safety-critical failures. These failures can be difficult to model and debug due to the relative lack of data: compared to tens of thousands of examples from normal operations, we may have only seconds of data leading up to the failure. This scarcity makes it challenging to train generative models of rare failure events, as existing methods risk either overfitting to noise in the limited failure dataset or underfitting due to an overly strong prior. We address this challenge with CalNF, or calibrated normalizing flows, a self-regularized framework for posterior learning from limited data. CalNF achieves state-of-the-art performance on data-limited failure modeling and inverse problems and enables a first-of-a-kind case study into the root causes of the 2022 Southwest Airlines scheduling crisis.

Applications · Genetics, Cell Biology, Health, etc

Sichen Zhu, Yuchen Zhu, Molei Tao, Peng Qiu

Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and eosin (H\&E) stained histology images to spatially resolved gene expressions. ST is a time-consuming, expensive yet powerful experimental technique that provides new opportunities to understand cancer mechanisms at a fine-grained molecular level, which is critical for uncovering new approaches for disease diagnosis and treatments. Here, we present $\textbf{Stem}$ ($\underline{\textbf{S}}$pa$\underline{\textbf{T}}$ially resolved gene $\underline{\textbf{E}}$xpression inference with diffusion $\underline{\textbf{M}}$odel), a novel computational tool that leverages a conditional diffusion generative model to enable in silico gene expression inference from H&E stained images. Through better capturing the inherent stochasticity and heterogeneity in ST data, $\textbf{Stem}$ achieves state-of-the-art performance on spatial gene expression prediction and generates biologically meaningful gene profiles for new H&E stained images at test time. We evaluate the proposed algorithm on datasets with various tissue sources and sequencing platforms, where it demonstrates clear improvement over existing approaches. $\textbf{Stem}$ generates high-fidelity gene expression predictions that share similar gene variation levels as ground truth data, suggesting that our method preserves the underlying biological heterogeneity. Our proposed pipeline opens up the possibility of analyzing existing, easily accessible H&E stained histology images from a genomics point of view without physically performing gene expression profiling and empowers potential biological discovery from H&E stained histology images. Code is available at: https://github.com/SichenZhu/Stem.

Deep Learning · Generative Models and Autoencoders

Valerii Iakovlev, Harri Lähdesmäki

Spatiotemporal dynamics models are fundamental for various domains, from heat propagation in materials to oceanic and atmospheric flows. However, currently available neural network-based spatiotemporal modeling approaches fall short when faced with data that is collected randomly over time and space, as is often the case with sensor networks in real-world applications like crowdsourced earthquake detection or pollution monitoring. In response, we developed a new method that can effectively learn spatiotemporal dynamics from such point process observations. Our model integrates techniques from neural differential equations, neural point processes, implicit neural representations and amortized variational inference to model both the dynamics of the system and the probabilistic locations and timings of observations. It outperforms existing methods on challenging spatiotemporal datasets by offering substantial improvements in predictive accuracy and computational efficiency, making it a useful tool for modeling and understanding complex dynamical systems observed under realistic, unconstrained conditions.

Probabilistic Methods · Monte Carlo and Sampling Methods

Byoungwoo Park, Hyungi Lee, Juho Lee

Many real-world datasets, such as healthcare, climate, and economics, are often collected as irregular time series, which poses challenges for accurate modeling. In this paper, we propose the Amortized Control of continuous State Space Model (ACSSM) for continuous dynamical modeling of time series for irregular and discrete observations. We first present a multi-marginal Doob's $h$-transform to construct a continuous dynamical system conditioned on these irregular observations. Following this, we introduce a variational inference algorithm with a tight evidence lower bound (ELBO), leveraging stochastic optimal control (SOC) theory to approximate the intractable Doob's $h$-transform and simulate the conditioned dynamics. To improve efficiency and scalability during both training and inference, ACSSM leverages auxiliary variable to flexibly parameterize the latent dynamics and amortized control. Additionally, it incorporates a simulation-free latent dynamics framework and a transformer-based data assimilation scheme, facilitating parallel inference of the latent states and ELBO computation. Through empirical evaluations across a variety of real-world datasets, ACSSM demonstrates superior performance in tasks such as classification, regression, interpolation, and extrapolation, while maintaining computational efficiency.

Probabilistic Methods · Monte Carlo and Sampling Methods

Byoungwoo Park, Hyungi Lee, Juho Lee

Many real-world datasets, such as healthcare, climate, and economics, are often collected as irregular time series, which poses challenges for accurate modeling. In this paper, we propose the Amortized Control of continuous State Space Model (ACSSM) for continuous dynamical modeling of time series for irregular and discrete observations. We first present a multi-marginal Doob's $h$-transform to construct a continuous dynamical system conditioned on these irregular observations. Following this, we introduce a variational inference algorithm with a tight evidence lower bound (ELBO), leveraging stochastic optimal control (SOC) theory to approximate the intractable Doob's $h$-transform and simulate the conditioned dynamics. To improve efficiency and scalability during both training and inference, ACSSM leverages auxiliary variable to flexibly parameterize the latent dynamics and amortized control. Additionally, it incorporates a simulation-free latent dynamics framework and a transformer-based data assimilation scheme, facilitating parallel inference of the latent states and ELBO computation. Through empirical evaluations across a variety of real-world datasets, ACSSM demonstrates superior performance in tasks such as classification, regression, interpolation, and extrapolation, while maintaining computational efficiency.

Probabilistic Methods · Monte Carlo and Sampling Methods

Emanuel Sommer, Jakob Robnik, Giorgi Nozadze, Uros Seljak, David Rügamer

Despite recent advances, sampling-based inference for Bayesian Neural Networks (BNNs) remains a significant challenge in probabilistic deep learning. While sampling-based approaches do not require a variational distribution assumption, current state-of-the-art samplers still struggle to navigate the complex and highly multimodal posteriors of BNNs. As a consequence, sampling still requires considerably longer inference times than non-Bayesian methods even for small neural networks, despite recent advances in making software implementations more efficient. Besides the difficulty of finding high-probability regions, the time until samplers provide sufficient exploration of these areas remains unpredictable. To tackle these challenges, we introduce an ensembling approach that leverages strategies from optimization and a recently proposed sampler called Microcanonical Langevin Monte Carlo (MCLMC) for efficient, robust and predictable sampling performance. Compared to approaches based on the state-of-the-art No-U-Turn Sampler, our approach delivers substantial speedups up to an order of magnitude, while maintaining or improving predictive performance and uncertainty quantification across diverse tasks and data modalities. The suggested Microcanonical Langevin Ensembles and modifications to MCLMC additionally enhance the method's predictability in resource requirements, facilitating easier parallelization. All in all, the proposed method offers a promising direction for practical, scalable inference for BNNs.

Deep Learning · Large Language Models

Wen-Ding Li, Keya Hu, Carter Larsen, Yuqing Wu, Simon Alford, Caleb Woo, Spencer Dunn, Hao Tang, Wei-Long Zheng, Yewen Pu 等

When learning an input-output mapping from very few examples, is it better to first infer a latent function that explains the examples, or is it better to directly predict new test outputs, e.g. using a neural network? We study this question on ARC by training neural models for \emph{induction} (inferring latent functions) and \emph{transduction} (directly predicting the test output for a given test input). We train on synthetically generated variations of Python programs that solve ARC training tasks. We find inductive and transductive models solve different kinds of test problems, despite having the same training problems and sharing the same neural architecture: Inductive program synthesis excels at precise computations, and at composing multiple concepts, while transduction succeeds on fuzzier perceptual concepts. Ensembling them approaches human-level performance on ARC.