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Probabilistic Methods/Bayesian Models and Methods

Van Cuong Pham, Cuong Nguyen, Trung Le, Dinh Phung, Gustavo Carneiro, Thanh-Toan Do

Bayesian Neural Networks (BNNs) offer probability distributions for model parameters, enabling uncertainty quantification in predictions. However, they often underperform compared to deterministic neural networks. Utilizing mutual learning can effectively enhance the performance of peer BNNs. In this paper, we propose a novel approach to improve BNNs performance through deep mutual learning. The proposed approaches aim to increase diversity in both network parameter distributions and feature distributions, promoting peer networks to acquire distinct features that capture different characteristics of the input, which enhances the effectiveness of mutual learning. Experimental results demonstrate significant improvements in the classification accuracy, negative log-likelihood, and expected calibration error when compared to traditional mutual learning for BNNs.

Probabilistic Methods/Bayesian Models and Methods

Alexander Immer, Emanuele Palumbo, Alexander Marx, Julia Vogt

Flexibly quantifying both irreducible aleatoric and model-dependent epistemic uncertainties plays an important role for complex regression problems. While deep neural networks in principle can provide this flexibility and learn heteroscedastic aleatoric uncertainties through non-linear functions, recent works highlight that maximizing the log likelihood objective parameterized by mean and variance can lead to compromised mean fits since the gradient are scaled by the predictive variance, and propose adjustments in line with this premise. We instead propose to use the natural parametrization of the Gaussian, which has been shown to be more stable for heteroscedastic regression based on non-linear feature maps and Gaussian processes. Further, we emphasize the significance of principled regularization of the network parameters and prediction. We therefore propose an efficient Laplace approximation for heteroscedastic neural networks that allows automatic regularization through empirical Bayes and provides epistemic uncertainties, both of which improve generalization.We showcase on a range of regression problems—including a new heteroscedastic image regression benchmark—that our methods are scalable, improve over previous approaches for heteroscedastic regression, and provide epistemic uncertainty without requiring hyperparameter tuning.

Deep Learning/Sequential Models, Time series

Samuel Dooley, Gurnoor Singh Khurana, Chirag Mohapatra, Siddartha V Naidu, Colin White

The vast majority of time-series forecasting approaches require a substantial training dataset. However, many real-life forecasting applications have very little initial observations, sometimes just 40 or fewer. Thus, the applicability of most forecasting methods is restricted in data-sparse commercial applications. While there is recent work in the setting of very limited initial data (so-called `zero-shot' forecasting), its performance is inconsistent depending on the data used for pretraining. In this work, we take a different approach and devise ForecastPFN, the first zero-shot forecasting model trained purely on a novel synthetic data distribution. ForecastPFN is a prior-data fitted network, trained to approximate Bayesian inference, which can make predictions on a new time series dataset in a single forward pass. Through extensive experiments, we show that zero-shot predictions made by ForecastPFN are more accurate and faster compared to state-of-the-art forecasting methods, even when the other methods are allowed to train on hundreds of additional in-distribution data points.

Nate Gruver, Samuel Stanton, Nathan Frey, Tim G. J. Rudner, Isidro Hotzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Wilson

A popular approach to protein design is to combine a generative model with a discriminative model for conditional sampling. The generative model samples plausible sequences while the discriminative model guides a search for sequences with high fitness. Given its broad success in conditional sampling, classifier-guided diffusion modeling is a promising foundation for protein design, leading many to develop guided diffusion models for structure with inverse folding to recover sequences. In this work, we propose diffusioN Optimized Sampling (NOS), a guidance method for discrete diffusion models that follows gradients in the hidden states of the denoising network. NOS makes it possible to perform design directly in sequence space, circumventing significant limitations of structure-based methods, including scarce data and challenging inverse design. Moreover, we use NOS to generalize LaMBO, a Bayesian optimization procedure for sequence design that facilitates multiple objectives and edit-based constraints. The resulting method, LaMBO-2, enables discrete diffusions and stronger performance with limited edits through a novel application of saliency maps. We apply LaMBO-2 to a real-world protein design task, optimizing antibodies for higher expression yield and binding affinity to several therapeutic targets under locality and developability constraints, attaining a 99\% expression rate and 40\% binding rate in exploratory in vitro experiments.

Xinran Zhu, Kaiwen Wu, Natalie Maus, Jacob Gardner, David Bindel

Variational Gaussian processes (GPs) approximate exact GP inference by using a small set of inducing points to form a sparse approximation of the true posterior, with the fidelity of the model increasing with additional inducing points. Although the approximation error in principle can be reduced through the use of more inducing points, this leads to scaling optimization challenges and computational complexity. To achieve scalability, inducing point methods typically introduce conditional independencies and then approximations to the training and test conditional distributions. In this paper, we consider an alternative approach to modifying the training and test conditionals, in which we make them more flexible. In particular, we investigate decoupling the parametric form of the predictive mean and covariance in the conditionals, and learn independent parameters for predictive mean and covariance. We derive new evidence lower bounds (ELBO) under these more flexible conditionals, and provide two concrete examples of applying the decoupled conditionals. Empirically, we find this additional flexibility leads to improved model performance on a variety of regression tasks and Bayesian optimization (BO) applications.

Probabilistic Methods

Arlind Kadra, Maciej Janowski, Martin Wistuba, Josif Grabocka

Hyperparameter optimization is an important subfield of machine learning that focuses on tuning the hyperparameters of a chosen algorithm to achieve peak performance. Recently, there has been a stream of methods that tackle the issue of hyperparameter optimization, however, most of the methods do not exploit the dominant power law nature of learning curves for Bayesian optimization. In this work, we propose Deep Power Laws (DPL), an ensemble of neural network models conditioned to yield predictions that follow a power-law scaling pattern. Our method dynamically decides which configurations to pause and train incrementally by making use of gray-box evaluations. We compare our method against 7 state-of-the-art competitors on 3 benchmarks related to tabular, image, and NLP datasets covering 59 diverse tasks. Our method achieves the best results across all benchmarks by obtaining the best any-time results compared to all competitors.

Optimization/Zero-order and Black-box Optimization

Kamil Dreczkowski, Antoine Grosnit, Haitham Bou Ammar

This paper introduces a modular framework for Mixed-variable and Combinatorial Bayesian Optimization (MCBO) to address the lack of systematic benchmarking and standardized evaluation in the field. Current MCBO papers often introduce non-diverse or non-standard benchmarks to evaluate their methods, impeding the proper assessment of different MCBO primitives and their combinations. Additionally, papers introducing a solution for a single MCBO primitive often omit benchmarking against baselines that utilize the same methods for the remaining primitives. This omission is primarily due to the significant implementation overhead involved, resulting in a lack of controlled assessments and an inability to showcase the merits of a contribution effectively.To overcome these challenges, our proposed framework enables an effortless combination of Bayesian Optimization components, and provides a diverse set of synthetic and real-world benchmarking tasks. Leveraging this flexibility, we implement 47 novel MCBO algorithms and benchmark them against seven existing MCBO solvers and five standard black-box optimization algorithms on ten tasks, conducting over 4000 experiments. Our findings reveal a superior combination of MCBO primitives outperforming existing approaches and illustrate the significance of model fit and the use of a trust region. We make our MCBO library available under the MIT license at \url{https://github.com/huawei-noah/HEBO/tree/master/MCBO}.

Applications/Language, Speech and Dialog

Jiashuo WANG, Haozhao Wang, Shichao Sun, Wenjie Li

In the quest to advance human-centric natural language generation (NLG) systems, ensuring alignment between NLG models and human preferences is crucial. For this alignment, current popular methods leverage a reinforcement learning (RL) approach with a reward model trained on feedback from humans. However, inherent disagreements due to the subjective nature of human preferences pose a significant challenge for training the reward model, resulting in a deterioration of the NLG performance. To tackle this issue, previous approaches typically rely on majority voting or averaging to consolidate multiple inconsistent preferences into a merged one. Although straightforward to understand and execute, such methods suffer from an inability to capture the nuanced degrees of disaggregation among humans and may only represent a specialized subset of individuals, thereby lacking the ability to quantitatively disclose the universality of human preferences. To address this challenge, this paper proposes a novel approach, which employs a Bayesian framework to account for the distribution of disagreements among human preferences as training a preference model, and names it as $\textbf{d-PM}$. Besides, considering the RL strategy's inefficient and complex training process over the training efficiency, we further propose utilizing the contrastive learning strategy to train the NLG model with the preference scores derived from the d-PM model. Extensive experiments on two human-centric NLG tasks, i.e., emotional support conversation and integrity ``Rule-of-Thumb'' generation, show that our method consistently exceeds previous SOTA models in both automatic and human evaluations.

Miscellaneous Aspects of Machine Learning/Transfer, Multitask and Meta-learning

Daolang Huang, Manuel Haussmann, Ulpu Remes, ST John, Grégoire Clarté, Kevin Luck, Samuel Kaski, Luigi Acerbi

Conditional Neural Processes (CNPs) are a class of metalearning models popular for combining the runtime efficiency of amortized inference with reliable uncertainty quantification. Many relevant machine learning tasks, such as in spatio-temporal modeling, Bayesian Optimization and continuous control, inherently contain equivariances – for example to translation – which the model can exploit for maximal performance. However, prior attempts to include equivariances in CNPs do not scale effectively beyond two input dimensions. In this work, we propose Relational Conditional Neural Processes (RCNPs), an effective approach to incorporate equivariances into any neural process model. Our proposed method extends the applicability and impact of equivariant neural processes to higher dimensions. We empirically demonstrate the competitive performance of RCNPs on a large array of tasks naturally containing equivariances.

Probabilistic Methods/Variational Inference

Chirag Modi, Robert Gower, Charles Margossian, Yuling Yao, David Blei, Lawrence Saul

Variational inference (VI) is a method to approximate the computationally intractable posterior distributions that arise in Bayesian statistics. Typically, VI fits a simple parametric distribution to be close to the target posterior, optimizing an appropriate objective such as the evidence lower bound (ELBO). In this work, we present a new approach to VI. Our method is based on the principle of score matching---namely, that if two distributions are equal then their score functions (i.e., gradients of the log density) are equal at every point on their support. With this principle, we develop score-matching VI, an iterative algorithm that seeks to match the scores between the variational approximation and the exact posterior. At each iteration, score-matching VI solves an inner optimization, one that minimally adjusts the current variational estimate to match the scores at a newly sampled value of the latent variables. We show that when the variational family is a Gaussian, this inner optimization enjoys a closed-form solution, which we call Gaussian score matching VI (GSM-VI). GSM-VI is a ``black box'' variational algorithm in that it only requires a differentiable joint distribution, and as such it can be applied to a wide class of models. We compare GSM-VI to black box variational inference (BBVI), which has similar requirements but instead optimizes the ELBO. We first study how GSM-VI behaves as a function of the problem dimensionality, the condition number of the target covariance matrix (when the target is Gaussian), and the degree of mismatch between the approximating and exact posterior distribution. We then study GSM-VI on a collection of real-world Bayesian inference problems from the posteriorDB database of datasets and models. We find that GSM-VI is faster than BBVI and equally or more accurate. Specifically, over a wide range of target posteriors, GSM-VI requires 10-100x fewer gradient evaluations than BBVI to obtain a comparable quality of approximation.

Probabilistic Methods/Bayesian Models and Methods

Shikai Fang, Xin Yu, Shibo Li, Zheng Wang, Mike Kirby, Shandian Zhe

Practical tensor data is often along with time information. Most existing temporal decomposition approaches estimate a set of fixed factors for the objects in each tensor mode, and hence cannot capture the temporal evolution of the objects' representation. More important, we lack an effective approach to capture such evolution from streaming data, which is common in real-world applications. To address these issues, we propose Streaming Factor Trajectory Learning (SFTL) for temporal tensor decomposition. We use Gaussian processes (GPs) to model the trajectory of factors so as to flexibly estimate their temporal evolution. To address the computational challenges in handling streaming data, we convert the GPs into a state-space prior by constructing an equivalent stochastic differential equation (SDE). We develop an efficient online filtering algorithm to estimate a decoupled running posterior of the involved factor states upon receiving new data. The decoupled estimation enables us to conduct standard Rauch-Tung-Striebel smoothing to compute the full posterior of all the trajectories in parallel, without the need for revisiting any previous data. We have shown the advantage of SFTL in both synthetic tasks and real-world applications.

Daniel Halpern, Rachel Li, Ariel Procaccia

In voting theory, when voters have ranked preferences over candidates, the celebrated Gibbard-Satterthwaite Theorem essentially rules out the existence of reasonable strategyproof methods for picking a winner. What if we weaken strategyproofness to only hold for Bayesian voters with beliefs over others' preferences? When voters believe other participants' rankings are drawn independently from a fixed distribution, the impossibility persists. However, it is quite reasonable for a voter to believe that other votes are correlated, either to each other or to their own ranking. We consider such beliefs induced by classic probabilistic models in social choice such as the Mallows, Placket-Luce, and Thurstone-Mosteller models. We single out the plurality rule (choosing the candidate ranked first most often) as a particularly promising choice as it is strategyproof for a large class of beliefs containing the specific ones we introduce. Further, we show that plurality is unique among positional scoring rules in having this property: no other scoring rule is strategyproof for beliefs induced by the Mallows model when there are a sufficient number of voters. Finally, we give examples of prominent non-scoring voting rules failing to be strategyproof on beliefs in this class, further bolstering the case for plurality.

Probabilistic Methods/Bayesian Models and Methods

Daolang Huang, Ayush Bharti, Amauri Souza, Luigi Acerbi, Samuel Kaski

Simulation-based inference (SBI) methods such as approximate Bayesian computation (ABC), synthetic likelihood, and neural posterior estimation (NPE) rely on simulating statistics to infer parameters of intractable likelihood models. However, such methods are known to yield untrustworthy and misleading inference outcomes under model misspecification, thus hindering their widespread applicability. In this work, we propose the first general approach to handle model misspecification that works across different classes of SBI methods. Leveraging the fact that the choice of statistics determines the degree of misspecification in SBI, we introduce a regularized loss function that penalizes those statistics that increase the mismatch between the data and the model. Taking NPE and ABC as use cases, we demonstrate the superior performance of our method on high-dimensional time-series models that are artificially misspecified. We also apply our method to real data from the field of radio propagation where the model is known to be misspecified. We show empirically that the method yields robust inference in misspecified scenarios, whilst still being accurate when the model is well-specified.

Deep Learning/Generative Models and Autoencoders

François Rozet, Gilles Louppe

Data assimilation, in its most comprehensive form, addresses the Bayesian inverse problem of identifying plausible state trajectories that explain noisy or incomplete observations of stochastic dynamical systems. Various approaches have been proposed to solve this problem, including particle-based and variational methods. However, most algorithms depend on the transition dynamics for inference, which becomes intractable for long time horizons or for high-dimensional systems with complex dynamics, such as oceans or atmospheres. In this work, we introduce score-based data assimilation for trajectory inference. We learn a score-based generative model of state trajectories based on the key insight that the score of an arbitrarily long trajectory can be decomposed into a series of scores over short segments. After training, inference is carried out using the score model, in a non-autoregressive manner by generating all states simultaneously. Quite distinctively, we decouple the observation model from the training procedure and use it only at inference to guide the generative process, which enables a wide range of zero-shot observation scenarios. We present theoretical and empirical evidence supporting the effectiveness of our method.

Deep Learning/Generative Models and Autoencoders

Maciej Falkiewicz, Naoya Takeishi, Imahn Shekhzadeh, Antoine Wehenkel, Arnaud Delaunoy, Gilles Louppe, Alexandros Kalousis

Bayesian inference allows expressing the uncertainty of posterior belief under a probabilistic model given prior information and the likelihood of the evidence. Predominantly, the likelihood function is only implicitly established by a simulator posing the need for simulation-based inference (SBI). However, the existing algorithms can yield overconfident posteriors (Hermans *et al.*, 2022) defeating the whole purpose of credibility if the uncertainty quantification is inaccurate. We propose to include a calibration term directly into the training objective of the neural model in selected amortized SBI techniques. By introducing a relaxation of the classical formulation of calibration error we enable end-to-end backpropagation. The proposed method is not tied to any particular neural model and brings moderate computational overhead compared to the profits it introduces. It is directly applicable to existing computational pipelines allowing reliable black-box posterior inference. We empirically show on six benchmark problems that the proposed method achieves competitive or better results in terms of coverage and expected posterior density than the previously existing approaches.

Probabilistic Methods/Bayesian Models and Methods

Florian Seligmann, Philipp Becker, Michael Volpp, Gerhard Neumann

Bayesian deep learning (BDL) is a promising approach to achieve well-calibrated predictions on distribution-shifted data. Nevertheless, there exists no large-scale survey that evaluates recent SOTA methods on diverse, realistic, and challenging benchmark tasks in a systematic manner. To provide a clear picture of the current state of BDL research, we evaluate modern BDL algorithms on real-world datasets from the WILDS collection containing challenging classification and regression tasks, with a focus on generalization capability and calibration under distribution shift. We compare the algorithms on a wide range of large, convolutional and transformer-based neural network architectures. In particular, we investigate a signed version of the expected calibration error that reveals whether the methods are over- or underconfident, providing further insight into the behavior of the methods. Further, we provide the first systematic evaluation of BDL for fine-tuning large pre-trained models, where training from scratch is prohibitively expensive. Finally, given the recent success of Deep Ensembles, we extend popular single-mode posterior approximations to multiple modes by the use of ensembles. While we find that ensembling single-mode approximations generally improves the generalization capability and calibration of the models by a significant margin, we also identify a failure mode of ensembles when finetuning large transformer-based language models. In this setting, variational inference based approaches such as last-layer Bayes By Backprop outperform other methods in terms of accuracy by a large margin, while modern approximate inference algorithms such as SWAG achieve the best calibration.

Applications/Genetics, Cell Biology, etc

Takahiro Mimori, Michiaki Hamada

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.

Probabilistic Methods/Bayesian Models and Methods

Shuyi Li, Michael O'Connor, Shiwei Lan

Regularization is one of the most fundamental topics in optimization, statistics and machine learning. To get sparsity in estimating a parameter $u\in\mathbb{R}^d$, an $\ell_q$ penalty term, $\Vert u\Vert_q$, is usually added to the objective function. What is the probabilistic distribution corresponding to such $\ell_q$ penalty? What is the \emph{correct} stochastic process corresponding to $\Vert u\Vert_q$ when we model functions $u\in L^q$? This is important for statistically modeling high-dimensional objects such as images, with penalty to preserve certainty properties, e.g. edges in the image.In this work, we generalize the $q$-exponential distribution (with density proportional to) $\exp{(- \frac{1}{2}|u|^q)}$ to a stochastic process named \emph{$Q$-exponential (Q-EP) process} that corresponds to the $L_q$ regularization of functions. The key step is to specify consistent multivariate $q$-exponential distributions by choosing from a large family of elliptic contour distributions. The work is closely related to Besov process which is usually defined in terms of series. Q-EP can be regarded as a definition of Besov process with explicit probabilistic formulation, direct control on the correlation strength, and tractable prediction formula. From the Bayesian perspective, Q-EP provides a flexible prior on functions with sharper penalty ($q<2$) than the commonly used Gaussian process (GP, $q=2$).We compare GP, Besov and Q-EP in modeling functional data, reconstructing images and solving inverse problems and demonstrate the advantage of our proposed methodology.

Social Aspects/Accountability, Transparency and Interpretability

Zi Wang, Alexander Ku, Jason Baldridge, Tom Griffiths, Been Kim

Understanding which concepts models can and cannot represent has been fundamental to many tasks: from effective and responsible use of models to detecting out of distribution data. We introduce Gaussian process probes (GPP), a unified and simple framework for probing and measuring uncertainty about concepts represented by models. As a Bayesian extension of linear probing methods, GPP asks what kind of distribution over classifiers (of concepts) is induced by the model. This distribution can be used to measure both what the model represents and how confident the probe is about what the model represents. GPP can be applied to any pre-trained model with vector representations of inputs (e.g., activations). It does not require access to training data, gradients, or the architecture. We validate GPP on datasets containing both synthetic and real images. Our experiments show it can (1) probe a model's representations of concepts even with a very small number of examples, (2) accurately measure both epistemic uncertainty (how confident the probe is) and aleatory uncertainty (how fuzzy the concepts are to the model), and (3) detect out of distribution data using those uncertainty measures as well as classic methods do. By using Gaussian processes to expand what probing can offer, GPP provides a data-efficient, versatile and uncertainty-aware tool for understanding and evaluating the capabilities of machine learning models.

Applications/Genetics, Cell Biology, etc

Lazar Atanackovic, Alexander Tong, Bo Wang, Leo J Lee, Yoshua Bengio, Jason Hartford

One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise so for typical sample sizes, there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over directed acyclic graphs, but not both. In this paper we leverage the fact that it is possible to estimate the ``velocity'' of the expression of a gene with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. We leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.