Bayesian neural networks offer better estimates of model uncertainty compared to frequentist networks. However, inference involving Bayesian models requires multiple instantiations or sampling of the network parameters, requiring significant computational resources. Compared to traditional deep learning networks, spiking neural networks (SNNs) have the potential to reduce computational area and power, thanks to their event-driven and spike-based computational framework. Most works in literature either address frequentist SNN models or non-spiking Bayesian neural networks. In this work, we demonstrate an optimization framework for developing and implementing efficient Bayesian SNNs in hardware by additionally restricting network weights to be binary-valued to further decrease power and area consumption. We demonstrate accuracies comparable to Bayesian binary networks with full-precision Bernoulli parameters, while requiring up to $25\times$ less spikes than equivalent binary SNN implementations. We show the feasibility of the design by mapping it onto Zynq-7000, a lightweight SoC, and achieve a $6.5 \times$ improvement in GOPS/DSP while utilizing up to 30 times less power compared to the state-of-the-art.
State-of-the-art methods for Bayesian inference in state-space models are (a) conditional sequential Monte Carlo (CSMC) algorithms; (b) sophisticated 'classical' MCMC algorithms like MALA, or mGRAD from Titsias and Papaspiliopoulos (2018, arXiv:1610.09641v3 [stat.ML]). The former propose $N$ particles at each time step to exploit the model's 'decorrelation-over-time' property and thus scale favourably with the time horizon, $T$ , but break down if the dimension of the latent states, $D$, is large. The latter leverage gradient-/prior-informed local proposals to scale favourably with $D$ but exhibit sub-optimal scalability with $T$ due to a lack of model-structure exploitation. We introduce methods which combine the strengths of both approaches. The first, Particle-MALA, spreads $N$ particles locally around the current state using gradient information, thus extending MALA to $T > 1$ time steps and $N > 1$ proposals. The second, Particle-mGRAD, additionally incorporates (conditionally) Gaussian prior dynamics into the proposal, thus extending the mGRAD algorithm to $T > 1$ time steps and $N > 1$ proposals. We prove that Particle-mGRAD interpolates between CSMC and Particle-MALA, resolving the 'tuning problem' of choosing between CSMC (superior for highly informative prior dynamics) and Particle-MALA (superior for weakly informative prior dynamics). We similarly extend other 'classical' MCMC approaches like auxiliary MALA, aGRAD, and preconditioned Crank-Nicolson-Langevin (PCNL) to $T > 1$ time steps and $N > 1$ proposals. In experiments, for both highly and weakly informative prior dynamics, our methods substantially improve upon both CSMC and sophisticated 'classical' MCMC approaches.
Recent strides in the field of neural computation has seen the adoption of Winner Take All (WTA) circuits to facilitate the unification of hierarchical Bayesian inference and spiking neural networks as a neurobiologically plausible model of information processing. Current research commonly validates the performance of these networks via classification tasks, particularly of the MNIST dataset. However, researchers have not yet reached consensus about how best to translate the stochastic responses from these networks into discrete decisions, a process known as population decoding. Despite being an often underexamined part of SNNs, in this work we show that population decoding has a significanct impact on the classification performance of WTA networks. For this purpose, we apply a WTA network to the problem of cancer subtype diagnosis from multi omic data, using datasets from The Cancer Genome Atlas (TCGA). In doing so we utilise a novel implementation of gene similarity networks, a feature encoding technique based on Kohoens self organising map algorithm. We further show that the impact of selecting certain population decoding methods is amplified when facing imbalanced datasets.
We consider the problem of efficiently simulating stochastic models of chemical kinetics. The Gillespie Stochastic Simulation algorithm (SSA) is often used to simulate these models, however, in many scenarios of interest, the computational cost quickly becomes prohibitive. This is further exasperated in the Bayesian inference context when estimating parameters of chemical models, as the intractability of the likelihood requires multiple simulations of the underlying system. To deal with issues of computational complexity in this paper, we propose a novel hybrid $\tau$-leap algorithm for simulating well-mixed chemical systems. In particular, the algorithm uses $\tau$-leap when appropriate (high population densities), and SSA when necessary (low population densities, when discrete effects become non-negligible). In the intermediate regime, a combination of the two methods, which leverages the properties of the underlying Poisson formulation, is employed. As illustrated through a number of numerical experiments the hybrid $\tau$ offers significant computational savings when compared to SSA without however sacrificing the overall accuracy. This feature is particularly welcomed in the Bayesian inference context, as it allows for parameter estimation of stochastic chemical kinetics at reduced computational cost.
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do not fully understand how cell proliferation regulation impacts cell migration phenomena. Here, we present a minimal continuum model of cell migration with cell cycle dynamics, which includes density-dependent effects and hence can account for cell proliferation regulation. By combining minimal mathematical modelling, Bayesian inference, and recent experimental data, we quantify the impact of tissue crowding across different cell cycle stages in epithelial tissue expansion experiments. Our model suggests that cells sense local density and adapt cell cycle progression in response, during G1 and the combined S/G2/M phases, providing an explicit relationship between each cell cycle stage duration and local tissue density, which is consistent with several experimental observations. Finally, we compare our mathematical model predictions to different experiments studying cell cycle regulation and present a quantitative analysis on the impact of density-dependent regulation on cell migration patterns. Our work presents a systematic approach for investigating and analysing cell cycle data, providing mechanistic insights into how individual cells regulate proliferation, based on population-based experimental measurements.
We present a new Subset Simulation approach using Hamiltonian neural network-based Monte Carlo sampling for reliability analysis. The proposed strategy combines the superior sampling of the Hamiltonian Monte Carlo method with computationally efficient gradient evaluations using Hamiltonian neural networks. This combination is especially advantageous because the neural network architecture conserves the Hamiltonian, which defines the acceptance criteria of the Hamiltonian Monte Carlo sampler. Hence, this strategy achieves high acceptance rates at low computational cost. Our approach estimates small failure probabilities using Subset Simulations. However, in low-probability sample regions, the gradient evaluation is particularly challenging. The remarkable accuracy of the proposed strategy is demonstrated on different reliability problems, and its efficiency is compared to the traditional Hamiltonian Monte Carlo method. We note that this approach can reach its limitations for gradient estimations in low-probability regions of complex and high-dimensional distributions. Thus, we propose techniques to improve gradient prediction in these particular situations and enable accurate estimations of the probability of failure. The highlight of this study is the reliability analysis of a system whose parameter distributions must be inferred with Bayesian inference problems. In such a case, the Hamiltonian Monte Carlo method requires a full model evaluation for each gradient evaluation and, therefore, comes at a very high cost. However, using Hamiltonian neural networks in this framework replaces the expensive model evaluation, resulting in tremendous improvements in computational efficiency.
We consider the problem of sampling from an unknown distribution for which only a sufficiently large number of training samples are available. Such settings have recently drawn considerable interest in the context of generative modelling and Bayesian inference. In this paper, we propose a generative model combining Schr\"odinger bridges and Langevin dynamics. Schr\"odinger bridges over an appropriate reversible reference process are used to approximate the conditional transition probability from the available training samples, which is then implemented in a discrete-time reversible Langevin sampler to generate new samples. By setting the kernel bandwidth in the reference process to match the time step size used in the unadjusted Langevin algorithm, our method effectively circumvents any stability issues typically associated with the time-stepping of stiff stochastic differential equations. Moreover, we introduce a novel split-step scheme, ensuring that the generated samples remain within the convex hull of the training samples. Our framework can be naturally extended to generate conditional samples and to Bayesian inference problems. We demonstrate the performance of our proposed scheme through experiments on synthetic datasets with increasing dimensions and on a stochastic subgrid-scale parametrization conditional sampling problem as well as generating sample trajectories of a dynamical system using conditional sampling.
This article presents a general Bayesian learning framework for multi-modal groupwise image registration. The method builds on probabilistic modelling of the image generative process, where the underlying common anatomy and geometric variations of the observed images are explicitly disentangled as latent variables. Therefore, groupwise image registration is achieved via hierarchical Bayesian inference. We propose a novel hierarchical variational auto-encoding architecture to realise the inference procedure of the latent variables, where the registration parameters can be explicitly estimated in a mathematically interpretable fashion. Remarkably, this new paradigm learns groupwise image registration in an unsupervised closed-loop self-reconstruction process, sparing the burden of designing complex image-based similarity measures. The computationally efficient disentangled network architecture is also inherently scalable and flexible, allowing for groupwise registration on large-scale image groups with variable sizes. Furthermore, the inferred structural representations from multi-modal images via disentanglement learning are capable of capturing the latent anatomy of the observations with visual semantics. Extensive experiments were conducted to validate the proposed framework, including four different datasets from cardiac, brain, and abdominal medical images. The results have demonstrated the superiority of our method over conventional similarity-based approaches in terms of accuracy, efficiency, scalability, and interpretability.
Bayesian neural networks (BNNs) are a principled approach to modeling predictive uncertainties in deep learning, which are important in safety-critical applications. Since exact Bayesian inference over the weights in a BNN is intractable, various approximate inference methods exist, among which sampling methods such as Hamiltonian Monte Carlo (HMC) are often considered the gold standard. While HMC provides high-quality samples, it lacks interpretable summary statistics because its sample mean and variance is meaningless in neural networks due to permutation symmetry. In this paper, we first show that the role of permutations can be meaningfully quantified by a number of transpositions metric. We then show that the recently proposed rebasin method allows us to summarize HMC samples into a compact representation that provides a meaningful explicit uncertainty estimate for each weight in a neural network, thus unifying sampling methods with variational inference. We show that this compact representation allows us to compare trained BNNs directly in weight space across sampling methods and variational inference, and to efficiently prune neural networks trained without explicit Bayesian frameworks by exploiting uncertainty estimates from HMC.
Sequential Bayesian inference over predictive functions is a natural framework for continual learning from streams of data. However, applying it to neural networks has proved challenging in practice. Addressing the drawbacks of existing techniques, we propose an optimization objective derived by formulating continual learning as sequential function-space variational inference. In contrast to existing methods that regularize neural network parameters directly, this objective allows parameters to vary widely during training, enabling better adaptation to new tasks. Compared to objectives that directly regularize neural network predictions, the proposed objective allows for more flexible variational distributions and more effective regularization. We demonstrate that, across a range of task sequences, neural networks trained via sequential function-space variational inference achieve better predictive accuracy than networks trained with related methods while depending less on maintaining a set of representative points from previous tasks.
Reliable predictive uncertainty estimation plays an important role in enabling the deployment of neural networks to safety-critical settings. A popular approach for estimating the predictive uncertainty of neural networks is to define a prior distribution over the network parameters, infer an approximate posterior distribution, and use it to make stochastic predictions. However, explicit inference over neural network parameters makes it difficult to incorporate meaningful prior information about the data-generating process into the model. In this paper, we pursue an alternative approach. Recognizing that the primary object of interest in most settings is the distribution over functions induced by the posterior distribution over neural network parameters, we frame Bayesian inference in neural networks explicitly as inferring a posterior distribution over functions and propose a scalable function-space variational inference method that allows incorporating prior information and results in reliable predictive uncertainty estimates. We show that the proposed method leads to state-of-the-art uncertainty estimation and predictive performance on a range of prediction tasks and demonstrate that it performs well on a challenging safety-critical medical diagnosis task in which reliable uncertainty estimation is essential.
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 DAGs, but not both. In this paper we leverage the fact that it is possible to estimate the "velocity" of gene expression 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. Since our objective is to model uncertainty over discrete structures, 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.
Large language models (LLMs) can produce long, coherent passages of text, suggesting that LLMs, although trained on next-word prediction, must represent the latent structure that characterizes a document. Prior work has found that internal representations of LLMs encode one aspect of latent structure, namely syntax; here we investigate a complementary aspect, namely the document's topic structure. We motivate the hypothesis that LLMs capture topic structure by connecting LLM optimization to implicit Bayesian inference. De Finetti's theorem shows that exchangeable probability distributions can be represented as a mixture with respect to a latent generating distribution. Although text is not exchangeable at the level of syntax, exchangeability is a reasonable starting assumption for topic structure. We thus hypothesize that predicting the next token in text will lead LLMs to recover latent topic distributions. We examine this hypothesis using Latent Dirichlet Allocation (LDA), an exchangeable probabilistic topic model, as a target, and we show that the representations formed by LLMs encode both the topics used to generate synthetic data and those used to explain natural corpus data.
Control barrier functions are widely used to synthesize safety-critical controls. However, the presence of Gaussian-type noise in dynamical systems can generate unbounded signals and potentially result in severe consequences. Although research has been conducted in the field of safety-critical control for stochastic systems, in many real-world scenarios, we do not have precise knowledge about the stochastic dynamics. In this paper, we delve into the safety-critical control for stochastic systems where both the drift and diffusion components are unknown. We employ Bayesian inference as a data-driven approach to approximate the system. To be more specific, we utilize Bayesian linear regression along with the central limit theorem to estimate the drift term, and employ Bayesian inference to approximate the diffusion term. Through simulations, we verify our findings by applying them to a nonlinear dynamical model and an adaptive cruise control model.
We introduce a new variant of contextual multi-armed bandits (CMABs) called observation-augmented CMABs (OA-CMABs) wherein a robot uses extra outcome observations from an external information source, e.g. humans. In OA-CMABs, external observations are a function of context features and thus provide evidence on top of observed option outcomes to infer hidden parameters. However, if external data is error-prone, measures must be taken to preserve the correctness of inference. To this end, we derive a robust Bayesian inference process for OA-CMABs based on recently developed probabilistic semantic data association techniques, which handle complex mixture model parameter priors and hybrid discrete-continuous observation likelihoods for semantic external data sources. To cope with combined uncertainties in OA-CMABs, we also derive a new active inference algorithm for optimal option selection based on approximate expected free energy minimization. This generalizes prior work on CMAB active inference by accounting for faulty observations and non-Gaussian distributions. Results for a simulated deep space search site selection problem show that, even if incorrect semantic observations are provided externally, e.g. by scientists, efficient decision-making and robust parameter inference are still achieved in a wide variety of conditions.
Diffusion models have gained traction as powerful algorithms for synthesizing high-quality images. Central to these algorithms is the diffusion process, a set of equations which maps data to noise in a way that can significantly affect performance. In this paper, we explore whether the diffusion process can be learned from data. Our work is grounded in Bayesian inference and seeks to improve log-likelihood estimation by casting the learned diffusion process as an approximate variational posterior that yields a tighter lower bound (ELBO) on the likelihood. A widely held assumption is that the ELBO is invariant to the noise process: our work dispels this assumption and proposes multivariate learned adaptive noise (MULAN), a learned diffusion process that applies noise at different rates across an image. Specifically, our method relies on a multivariate noise schedule that is a function of the data to ensure that the ELBO is no longer invariant to the choice of the noise schedule as in previous works. Empirically, MULAN sets a new state-of-the-art in density estimation on CIFAR-10 and ImageNet and reduces the number of training steps by 50%. We provide the code, along with a blog post and video tutorial on the project page: https://s-sahoo.com/MuLAN
We consider the combinatorial volatile Gaussian process (GP) semi-bandit problem. Each round, an agent is provided a set of available base arms and must select a subset of them to maximize the long-term cumulative reward. We study the Bayesian setting and provide novel Bayesian cumulative regret bounds for three GP-based algorithms: GP-UCB, GP-BayesUCB and GP-TS. Our bounds extend previous results for GP-UCB and GP-TS to the infinite, volatile and combinatorial setting, and to the best of our knowledge, we provide the first regret bound for GP-BayesUCB. Volatile arms encompass other widely considered bandit problems such as contextual bandits. Furthermore, we employ our framework to address the challenging real-world problem of online energy-efficient navigation, where we demonstrate its effectiveness compared to the alternatives.
One of the pivotal tasks in scientific machine learning is to represent underlying dynamical systems from time series data. Many methods for such dynamics learning explicitly require the derivatives of state data, which are not directly available and can be approximated conventionally by finite differences. However, the discrete approximations of time derivatives may result in poor estimations when state data are scarce and/or corrupted by noise, thus compromising the predictiveness of the learned dynamical models. To overcome this technical hurdle, we propose a new method that learns nonlinear dynamics through a Bayesian inference of characterizing model parameters. This method leverages a Gaussian process representation of states, and constructs a likelihood function using the correlation between state data and their derivatives, yet prevents explicit evaluations of time derivatives. Through a Bayesian scheme, a probabilistic estimate of the model parameters is given by the posterior distribution, and thus a quantification is facilitated for uncertainties from noisy state data and the learning process. Specifically, we will discuss the applicability of the proposed method to several typical scenarios for dynamical systems: identification and estimation with an affine parametrization, nonlinear parametric approximation without prior knowledge, and general parameter estimation for a given dynamical system.
This paper addresses the problem of maintaining safety during training in Reinforcement Learning (RL), such that the safety constraint violations are bounded at any point during learning. In a variety of RL applications the safety of the agent is particularly important, e.g. autonomous platforms or robots that work in proximity of humans. As enforcing safety during training might severely limit the agent's exploration, we propose here a new architecture that handles the trade-off between efficient progress and safety during exploration. As the exploration progresses, we update via Bayesian inference Dirichlet-Categorical models of the transition probabilities of the Markov decision process that describes the environment dynamics. This paper proposes a way to approximate moments of belief about the risk associated to the action selection policy. We construct those approximations, and prove the convergence results. We propose a novel method for leveraging the expectation approximations to derive an approximate bound on the confidence that the risk is below a certain level. This approach can be easily interleaved with RL and we present experimental results to showcase the performance of the overall architecture.
We implement a Bayesian inference process for Neural Networks to model the time to failure of highly reliable weapon systems with interval-censored data and time-varying covariates. We analyze and benchmark our approach, LaplaceNN, on synthetic and real datasets with standard classification metrics such as Receiver Operating Characteristic (ROC) Area Under Curve (AUC) Precision-Recall (PR) AUC, and reliability curve visualizations.