Chengkun Li

Chengkun Li, Aki Vehtari, Paul-Christian Bürkner et al.

Bayesian inference often faces a trade-off between computational speed and sampling accuracy. We propose an adaptive workflow that integrates rapid amortized inference with gold-standard MCMC techniques to achieve a favorable combination of both speed and accuracy when performing inference on many observed datasets. Our approach uses principled diagnostics to guide the choice of inference method for each dataset, moving along the Pareto front from fast amortized sampling via generative neural networks to slower but guaranteed-accurate MCMC when needed. By reusing computations across steps, our workflow synergizes amortized and MCMC-based inference. We demonstrate the effectiveness of this integrated approach on several synthetic and real-world problems with tens of thousands of datasets, showing efficiency gains while maintaining high posterior quality.

Bobby Huggins, Chengkun Li, Marlon Tobaben et al.

PyVBMC is a Python implementation of the Variational Bayesian Monte Carlo (VBMC) algorithm for posterior and model inference for black-box computational models (Acerbi, 2018, 2020). VBMC is an approximate inference method designed for efficient parameter estimation and model assessment when model evaluations are mildly-to-very expensive (e.g., a second or more) and/or noisy. Specifically, VBMC computes: - a flexible (non-Gaussian) approximate posterior distribution of the model parameters, from which statistics and posterior samples can be easily extracted; - an approximation of the model evidence or marginal likelihood, a metric used for Bayesian model selection. PyVBMC can be applied to any computational or statistical model with up to roughly 10-15 continuous parameters, with the only requirement that the user can provide a Python function that computes the target log likelihood of the model, or an approximation thereof (e.g., an estimate of the likelihood obtained via simulation or Monte Carlo methods). PyVBMC is particularly effective when the model takes more than about a second per evaluation, with dramatic speed-ups of 1-2 orders of magnitude when compared to traditional approximate inference methods. Extensive benchmarks on both artificial test problems and a large number of real models from the computational sciences, particularly computational and cognitive neuroscience, show that VBMC generally - and often vastly - outperforms alternative methods for sample-efficient Bayesian inference, and is applicable to both exact and simulator-based models (Acerbi, 2018, 2019, 2020). PyVBMC brings this state-of-the-art inference algorithm to Python, along with an easy-to-use Pythonic interface for running the algorithm and manipulating and visualizing its results.

Chengkun Li, Grégoire Clarté, Martin Jørgensen et al.

In applied Bayesian inference scenarios, users may have access to a large number of pre-existing model evaluations, for example from maximum-a-posteriori (MAP) optimization runs. However, traditional approximate inference techniques make little to no use of this available information. We propose the framework of post-process Bayesian inference as a means to obtain a quick posterior approximation from existing target density evaluations, with no further model calls. Within this framework, we introduce Variational Sparse Bayesian Quadrature (VSBQ), a method for post-process approximate inference for models with black-box and potentially noisy likelihoods. VSBQ reuses existing target density evaluations to build a sparse Gaussian process (GP) surrogate model of the log posterior density function. Subsequently, we leverage sparse-GP Bayesian quadrature combined with variational inference to achieve fast approximate posterior inference over the surrogate. We validate our method on challenging synthetic scenarios and real-world applications from computational neuroscience. The experiments show that VSBQ builds high-quality posterior approximations by post-processing existing optimization traces, with no further model evaluations.

Francesco Silvestrin, Chengkun Li, Luigi Acerbi

Approximate Bayesian inference for models with computationally expensive, black-box likelihoods poses a significant challenge, especially when the posterior distribution is complex. Many inference methods struggle to explore the parameter space efficiently under a limited budget of likelihood evaluations. Variational Bayesian Monte Carlo (VBMC) is a sample-efficient method that addresses this by building a local surrogate model of the log-posterior. However, its conservative exploration strategy, while promoting stability, can cause it to miss important regions of the posterior, such as distinct modes or long tails. In this work, we introduce Stacking Variational Bayesian Monte Carlo (S-VBMC), a method that overcomes this limitation by constructing a robust, global posterior approximation from multiple independent VBMC runs. Our approach merges these local approximations through a principled and inexpensive post-processing step that leverages VBMC's mixture posterior representation and per-component evidence estimates. Crucially, S-VBMC requires no additional likelihood evaluations and is naturally parallelisable, fitting seamlessly into existing inference workflows. We demonstrate its effectiveness on two synthetic problems designed to challenge VBMC's exploration and two real-world applications from computational neuroscience, showing substantial improvements in posterior approximation quality across all cases. Our code is available as a Python package at https://github.com/acerbilab/svbmc.

Jozef Marus Coldenhoff, Chengkun Li, Yurui Zhu

Sharpness-Aware Minimization (SAM) and adaptive sharpness-aware minimization (ASAM) aim to improve the model generalization. And in this project, we proposed three experiments to valid their generalization from the sharpness aware perspective. And our experiments show that sharpness aware-based optimization techniques could help to provide models with strong generalization ability. Our experiments also show that ASAM could improve the generalization performance on un-normalized data, but further research is needed to confirm this.

Yang You, Chengkun Li, Yujing Lou et al.

Visual semantic correspondence is an important topic in computer vision and could help machine understand objects in our daily life. However, most previous methods directly train on correspondences in 2D images, which is end-to-end but loses plenty of information in 3D spaces. In this paper, we propose a new method on predicting semantic correspondences by leveraging it to 3D domain and then project corresponding 3D models back to 2D domain, with their semantic labels. Our method leverages the advantages in 3D vision and can explicitly reason about objects self-occlusion and visibility. We show that our method gives comparative and even superior results on standard semantic benchmarks. We also conduct thorough and detailed experiments to analyze our network components. The code and experiments are publicly available at https://github.com/qq456cvb/SemanticTransfer.

Chengkun Li, Bobby Huggins, Petrus Mikkola et al.

Bayesian inference with computationally expensive likelihood evaluations remains a significant challenge in many scientific domains. We propose normalizing flow regression (NFR), a novel offline inference method for approximating posterior distributions. Unlike traditional surrogate approaches that require additional sampling or inference steps, NFR directly yields a tractable posterior approximation through regression on existing log-density evaluations. We introduce training techniques specifically for flow regression, such as tailored priors and likelihood functions, to achieve robust posterior and model evidence estimation. We demonstrate NFR's effectiveness on synthetic benchmarks and real-world applications from neuroscience and biology, showing superior or comparable performance to existing methods. NFR represents a promising approach for Bayesian inference when standard methods are computationally prohibitive or existing model evaluations can be recycled.

Blagoj Mitrevski, Arina Rak, Julian Schnitzler et al.

Digital note-taking is gaining popularity, offering a durable, editable, and easily indexable way of storing notes in a vectorized form, known as digital ink. However, a substantial gap remains between this way of note-taking and traditional pen-and-paper note-taking, a practice that is still favored by a vast majority. Our work InkSight, aims to bridge the gap by empowering physical note-takers to effortlessly convert their work (offline handwriting) to digital ink (online handwriting), a process we refer to as derendering. Prior research on the topic has focused on the geometric properties of images, resulting in limited generalization beyond their training domains. Our approach combines reading and writing priors, allowing training a model in the absence of large amounts of paired samples, which are difficult to obtain. To our knowledge, this is the first work that effectively derenders handwritten text in arbitrary photos with diverse visual characteristics and backgrounds. Furthermore, it generalizes beyond its training domain into simple sketches. Our human evaluation reveals that 87% of the samples produced by our model on the challenging HierText dataset are considered as a valid tracing of the input image and 67% look like a pen trajectory traced by a human.

Chengkun Li, Yuqi Tong, Kai Chen et al.

The visualization of volumetric medical data is crucial for enhancing diagnostic accuracy and improving surgical planning and education. Cinematic rendering techniques significantly enrich this process by providing high-quality visualizations that convey intricate anatomical details, thereby facilitating better understanding and decision-making in medical contexts. However, the high computing cost and low rendering speed limit the requirement of interactive visualization in practical applications. In this paper, we introduce ClipGS, an innovative Gaussian splatting framework with the clipping plane supported, for interactive cinematic visualization of volumetric medical data. To address the challenges posed by dynamic interactions, we propose a learnable truncation scheme that automatically adjusts the visibility of Gaussian primitives in response to the clipping plane. Besides, we also design an adaptive adjustment model to dynamically adjust the deformation of Gaussians and refine the rendering performance. We validate our method on five volumetric medical data (including CT and anatomical slice data), and reach an average 36.635 PSNR rendering quality with 156 FPS and 16.1 MB model size, outperforming state-of-the-art methods in rendering quality and efficiency.

Biao Gao, Yancheng Pan, Chengkun Li et al.

3D semantic segmentation is a fundamental task for robotic and autonomous driving applications. Recent works have been focused on using deep learning techniques, whereas developing fine-annotated 3D LiDAR datasets is extremely labor intensive and requires professional skills. The performance limitation caused by insufficient datasets is called data hunger problem. This research provides a comprehensive survey and experimental study on the question: are we hungry for 3D LiDAR data for semantic segmentation? The studies are conducted at three levels. First, a broad review to the main 3D LiDAR datasets is conducted, followed by a statistical analysis on three representative datasets to gain an in-depth view on the datasets' size and diversity, which are the critical factors in learning deep models. Second, a systematic review to the state-of-the-art 3D semantic segmentation is conducted, followed by experiments and cross examinations of three representative deep learning methods to find out how the size and diversity of the datasets affect deep models' performance. Finally, a systematic survey to the existing efforts to solve the data hunger problem is conducted on both methodological and dataset's viewpoints, followed by an insightful discussion of remaining problems and open questions To the best of our knowledge, this is the first work to analyze the data hunger problem for 3D semantic segmentation using deep learning techniques that are addressed in the literature review, statistical analysis, and cross-dataset and cross-algorithm experiments. We share findings and discussions, which may lead to potential topics in future works.

Yujing Lou, Yang You, Chengkun Li et al.

Semantic understanding of 3D objects is crucial in many applications such as object manipulation. However, it is hard to give a universal definition of point-level semantics that everyone would agree on. We observe that people have a consensus on semantic correspondences between two areas from different objects, but are less certain about the exact semantic meaning of each area. Therefore, we argue that by providing human labeled correspondences between different objects from the same category instead of explicit semantic labels, one can recover rich semantic information of an object. In this paper, we introduce a new dataset named CorresPondenceNet. Based on this dataset, we are able to learn dense semantic embeddings with a novel geodesic consistency loss. Accordingly, several state-of-the-art networks are evaluated on this correspondence benchmark. We further show that CorresPondenceNet could not only boost fine-grained understanding of heterogeneous objects but also cross-object registration and partial object matching.