Many protein design applications, such as binder or enzyme design, require scaffolding a structural motif with high precision. Generative modelling paradigms based on denoising diffusion processes emerged as a leading candidate to address this motif scaffolding problem and have shown early experimental success in some cases. In the diffusion paradigm, motif scaffolding is treated as a conditional generation task, and several conditional generation protocols were proposed or imported from the Computer Vision literature. However, most of these protocols are motivated heuristically, e.g. via analogies to Langevin dynamics, and lack a unifying framework, obscuring connections between the different approaches. In this work, we unify conditional training and conditional sampling procedures under one common framework based on the mathematically well-understood Doob's h-transform. This new perspective allows us to draw connections between existing methods and propose a new variation on existing conditional training protocols. We illustrate the effectiveness of this new protocol in both, image outpainting and motif scaffolding and find that it outperforms standard methods.

This paper proposes a Bayes Net based Monte Carlo optimization for motion planning (BN-MCO). Primarily, we adjust the potential fields determined by goal and start constraints to progressively guide the sampled clusters toward the goal and start points. Then, we utilize the Gaussian mixed modal (GMM) to perform the Monte Carlo optimization, confronting these two non-convex potential fields. Moreover, KL divergence measures the bias between the true distribution determined by the fields and the proposed GMM, whose parameters are learned incrementally according to the manifold information of the bias. In this way, the Bayesian network consisting of sequential updated GMMs expands until the constraints are satisfied and the shortest path method can find a feasible path. Finally, we tune the key parameters and benchmark BN-MCO against the other 5 planners on LBR-iiwa in a bookshelf. The result shows the highest success rate and moderate solving efficiency of BN-MCO.

Robots cannot yet match humans' ability to rapidly learn the shapes of novel 3D objects and recognize them robustly despite clutter and occlusion. We present Bayes3D, an uncertainty-aware perception system for structured 3D scenes, that reports accurate posterior uncertainty over 3D object shape, pose, and scene composition in the presence of clutter and occlusion. Bayes3D delivers these capabilities via a novel hierarchical Bayesian model for 3D scenes and a GPU-accelerated coarse-to-fine sequential Monte Carlo algorithm. Quantitative experiments show that Bayes3D can learn 3D models of novel objects from just a handful of views, recognizing them more robustly and with orders of magnitude less training data than neural baselines, and tracking 3D objects faster than real time on a single GPU. We also demonstrate that Bayes3D learns complex 3D object models and accurately infers 3D scene composition when used on a Panda robot in a tabletop scenario.

Statisticians and machine learners analyze observed data by synthesizing models of those data. These models take a variety of forms, with several of the most widely used being directed graphical models, probabilistic programs, and structural causal models (SCMs). Applications of these frameworks have included cognitive modeling [7, 20], simulation-based inference [9], and model-based planning [12, 21]. Unfortunately, the richer the model class, the weaker the mathematical tools available to reason rigorously about it: SCMs built on linear equations with Gaussian noise admit easy inference, while graphical models have a clear meaning and a wide array of inference algorithms but encode a limited family of models. Probabilistic programs can encode any computably sampleable distribution, but the definition of their densities commonly relies on operational analogies with directed graphical models.

By approximating posterior distributions with weighted samples, particle filters (PFs) provide an efficient mechanism for solving non-linear sequential state estimation problems. While the effectiveness of particle filters has been recognised in various applications, their performance relies on the knowledge of dynamic models and measurement models, as well as the construction of effective proposal distributions. An emerging trend involves constructing components of particle filters using neural networks and optimising them by gradient descent, and such data-adaptive particle filtering approaches are often called differentiable particle filters. Due to the expressiveness of neural networks, differentiable particle filters are a promising computational tool for performing inference on sequential data in complex, high-dimensional tasks, such as vision-based robot localisation. In this paper, we review recent advances in differentiable particle filters and their applications. We place special emphasis on different design choices for key components of differentiable particle filters, including dynamic models, measurement models, proposal distributions, optimisation objectives, and differentiable resampling techniques.

Diffusion models have emerged as powerful tools for high-quality data generation, such as image generation. Despite its success in continuous spaces, discrete diffusion models, which apply to domains such as texts and natural languages, remain under-studied and often suffer from slow generation speed. In this paper, we propose a novel de-randomized diffusion process, which leads to an accelerated algorithm for discrete diffusion models. Our technique significantly reduces the number of function evaluations (i.e., calls to the neural network), making the sampling process much faster. Furthermore, we introduce a continuous-time (i.e., infinite-step) sampling algorithm that can provide even better sample qualities than its discrete-time (finite-step) counterpart. Extensive experiments on natural language generation and machine translation tasks demonstrate the superior performance of our method in terms of both generation speed and sample quality over existing methods for discrete diffusion models.

This article intends to systematically identify and comparatively analyze state-of-the-art supply chain (SC) forecasting strategies and technologies. A novel framework has been proposed incorporating Big Data Analytics in SC Management (problem identification, data sources, exploratory data analysis, machine-learning model training, hyperparameter tuning, performance evaluation, and optimization), forecasting effects on human-workforce, inventory, and overall SC. Initially, the need to collect data according to SC strategy and how to collect them has been discussed. The article discusses the need for different types of forecasting according to the period or SC objective. The SC KPIs and the error-measurement systems have been recommended to optimize the top-performing model. The adverse effects of phantom inventory on forecasting and the dependence of managerial decisions on the SC KPIs for determining model performance parameters and improving operations management, transparency, and planning efficiency have been illustrated. The cyclic connection within the framework introduces preprocessing optimization based on the post-process KPIs, optimizing the overall control process (inventory management, workforce determination, cost, production and capacity planning). The contribution of this research lies in the standard SC process framework proposal, recommended forecasting data analysis, forecasting effects on SC performance, machine learning algorithms optimization followed, and in shedding light on future research.

Accurate estimation of sub-surface properties like moisture content and depth of layers is crucial for applications spanning sub-surface condition monitoring, precision agriculture, and effective wildfire risk assessment. Soil in nature is often covered by overlaying surface material, making its characterization using conventional methods challenging. In addition, the estimation of the properties of the overlaying layer is crucial for applications like wildfire assessment. This study thus proposes a Bayesian model-updating-based approach for ground penetrating radar (GPR) waveform inversion to predict sub-surface properties like the moisture contents and depths of the soil layer and overlaying material accumulated above the soil. The dielectric permittivity of material layers were predicted with the proposed method, along with other parameters, including depth and electrical conductivity of layers. The proposed Bayesian model updating approach yields probabilistic estimates of these parameters that can provide information about the confidence and uncertainty related to the estimates. The methodology was evaluated for a diverse range of experimental data collected through laboratory and field investigations. Laboratory investigations included variations in soil moisture values and depth of the top layer (or overlaying material), and the field investigation included measurement of field soil moisture for sixteen days. The results demonstrated predictions consistent with time-domain reflectometry (TDR) measurements and conventional gravimetric tests. The top layer depth could also be predicted with reasonable accuracy. The proposed method provides a promising approach for uncertainty-aware sub-surface parameter estimation that can enable decision-making for risk assessment across a wide range of applications.

Epistemic emotions, such as curiosity and interest, drive the inquiry process. This study proposes a novel formulation of epistemic emotions such as curiosity and interest using two types of information gain generated by the principle of free energy minimization: Kullback-Leibler divergence(KLD) from Bayesian posterior to prior, which represents free energy reduction in recognition, and Bayesian surprise (BS), which represents the expected information gain by Bayesian prior update. By applying a Gaussian generative model with an additional uniform likelihood, we found that KLD and BS form an upward-convex function of surprise (minimized free energy and prediction error), similar to Berlyne's arousal potential functions, or the Wundt curve. We consider that the alternate maximization of BS and KLD generates an ideal inquiry cycle to approach the optimal arousal level with fluctuations in surprise, and that curiosity and interest drive to facilitate the cyclic process. We exhaustively analyzed the effects of prediction uncertainty (prior variance) and observation uncertainty (likelihood variance) on the peaks of the information gain function as optimal surprises. The results show that greater prediction uncertainty, meaning an open-minded attitude, and less observational uncertainty, meaning precise observation with attention, are expected to provide greater information gains through a greater range of exploration. The proposed mathematical framework unifies the free energy principle of the brain and the arousal potential theory to explain the Wundt curve as an information gain function and suggests an ideal inquiry process driven by epistemic emotions.

Atmospheric retrievals (AR) characterize exoplanets by estimating atmospheric parameters from observed light spectra, typically by framing the task as a Bayesian inference problem. However, traditional approaches such as nested sampling are computationally expensive, thus sparking an interest in solutions based on machine learning (ML). In this ongoing work, we first explore flow matching posterior estimation (FMPE) as a new ML-based method for AR and find that, in our case, it is more accurate than neural posterior estimation (NPE), but less accurate than nested sampling. We then combine both FMPE and NPE with importance sampling, in which case both methods outperform nested sampling in terms of accuracy and simulation efficiency. Going forward, our analysis suggests that simulation-based inference with likelihood-based importance sampling provides a framework for accurate and efficient AR that may become a valuable tool not only for the analysis of observational data from existing telescopes, but also for the development of new missions and instruments.