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Miscellaneous Aspects of Machine Learning · Causality

HAOYUE DAI, Ignavier Ng, Gongxu Luo, Peter Spirtes, Petar Stojanov, Kun Zhang

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

Deep Learning · Large Language Models

Zecheng Tang, Chenfei Wu, Juntao Li, Nan Duan

Graphic layout generation, a growing research field, plays a significant role in user engagement and information perception. Existing methods primarily treat layout generation as a numerical optimization task, focusing on quantitative aspects while overlooking the semantic information of layout, such as the relationship between each layout element. In this paper, we propose LayoutNUWA, the first model that treats layout generation as a code generation task to enhance semantic information and harness the hidden layout expertise of large language models~(LLMs). Concretely, we develop a Code Instruct Tuning (CIT) approach comprising three interconnected modules: 1) the Code Initialization (CI) module quantifies the numerical conditions and initializes them as HTML code with strategically placed masks; 2) the Code Completion (CC) module employs the formatting knowledge of LLMs to fill in the masked portions within the HTML code; 3) the Code Rendering (CR) module transforms the completed code into the final layout output, ensuring a highly interpretable and transparent layout generation procedure that directly maps code to a visualized layout. We attain significant state-of-the-art performance (even over 50\% improvements compared to previous works) on multiple datasets, showcasing the strong capabilities of LayoutNUWA.

Probabilistic Methods · Graphical Models

Jonas Seng, Matej Zečević, Devendra Singh Dhami, Kristian Kersting

Structure learning is a crucial task in science, especially in fields such as medicine and biology, where the wrong identification of (in)dependencies among random variables can have significant implications. The primary objective of structure learning is to learn a Directed Acyclic Graph (DAG) that represents the underlying probability distribution of the data. Many prominent DAG learners rely on least square losses or log-likelihood losses for optimization. It is well-known from regression models that least square losses are heavily influenced by the scale of the variables. Recently it has been demonstrated that the scale of data also affects performance of structure learning algorithms, though with a strong focus on linear 2-node systems and simulated data. Moving beyond these results, we provide conditions under which square-based losses are minimal for wrong DAGs in $d$-dimensional cases. Furthermore, we also show that scale can impair performance of structure learners if relations among variables are non-linear for both square based and log-likelihood based losses. We confirm our theoretical findings through extensive experiments on synthetic and real-world data.

Applications · Computer Vision

Wenlong Liu, Tianyu Yang, Yuhan Wang, Qizhi Yu, Lei Zhang

This work studies the problem of panoptic symbol spotting, which is to spot and parse both countable object instances (windows, doors, tables, etc.) and uncountable stuff (wall, railing, etc.) from computer-aided design (CAD) drawings. Existing methods typically involve either rasterizing the vector graphics into images and using image-based methods for symbol spotting, or directly building graphs and using graph neural networks for symbol recognition. In this paper, we take a different approach, which treats graphic primitives as a set of 2D points that are locally connected and use point cloud segmentation methods to tackle it. Specifically, we utilize a point transformer to extract the primitive features and append a mask2former-like spotting head to predict the final output. To better use the local connection information of primitives and enhance their discriminability, we further propose the attention with connection module (ACM) and contrastive connection learning scheme (CCL). Finally, we propose a KNN interpolation mechanism for the mask attention module of the spotting head to better handle primitive mask downsampling, which is primitive-level in contrast to pixel-level for the image. Our approach, named SymPoint, is simple yet effective, outperforming recent state-of-the-art method GAT-CADNet by an absolute increase of 9.6% PQ and 10.4% RQ on the FloorPlanCAD dataset. The source code and models will be available at \url{https://github.com/nicehuster/SymPoint}.

Applications · Health

Raphael Poulain, Rahmatollah Beheshti

Following the success of transformer-based methods across various machine learning applications, their adoption for healthcare predictive tasks using electronic health records (EHRs) has also expanded extensively. Similarly, graph-based methods have been shown to be very effective in capturing inherent graph-type relationships in EHRs, leading to improved downstream performance. Although integrating these two families of approaches seems like a natural next step, in practice, creating such a design is challenging and has not been done. This is partly due to known EHR problems, such as high sparsity, making extracting meaningful temporal representations of medical visits challenging. In this study, we propose GT-BEHRT, a new approach that leverages temporal visit embeddings extracted from a graph transformer and uses a BERT-based model to obtain more robust patient representations, especially on longer EHR sequences. The graph-based approach allows GT-BEHRT to implicitly capture the intrinsic graphical relationships between medical observations, while the BERT model extracts the temporal relationships between visits, loosely mimicking the clinicians' decision-making process. As part of our method, we also present a two-step pre-training strategy for learning better graphical and temporal representations. Our proposed method achieves state-of-the-art performance in a variety of standard medical predictive tasks, demonstrating the versatility of our approach.

Social Aspects · Accountability, Transparency and Interpretability

Xu Zheng, Farhad Shirani, Tianchun Wang, Wei Cheng, Zhuomin Chen, Haifeng Chen, Hua Wei, Dongsheng Luo

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes --- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including $Fid_+$, $Fid_-$, and $Fid_\Delta$. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics.

Deep Learning · Large Language Models

Jonas Belouadi, Anne Lauscher, Steffen Eger

Generating bitmap graphics from text has gained considerable attention, yet for scientific figures, vector graphics are often preferred. Given that vector graphics are typically encoded using low-level graphics primitives, generating them directly is difficult. To address this, we propose the use of TikZ, a well-known abstract graphics language that can be compiled to vector graphics, as an intermediate representation of scientific figures. TikZ offers human-oriented, high-level commands, thereby facilitating conditional language modeling with any large language model. To this end, we introduce DaTikZ the first large-scale TikZ dataset, consisting of 120k TikZ drawings aligned with captions. We fine-tune LLaMA on DaTikZ, as well as our new model CLiMA, which augments LLaMA with multimodal CLIP embeddings. In both human and automatic evaluation, CLiMA and LLaMA outperform commercial GPT-4 and Claude 2 in terms of similarity to human-created figures, with CLiMA additionally improving text-image alignment. Our detailed analysis shows that all models generalize well and are not susceptible to memorization. GPT-4 and Claude 2, however, tend to generate more simplistic figures compared to both humans and our models. We make our framework, AutomaTikZ, along with model weights and datasets, publicly available.

Miscellaneous Aspects of Machine Learning · Causality

Xiuchuan Li, Kun Zhang, Tongliang Liu

Traditional causal discovery approaches typically assume the absence of latent variables, a simplification that often does not align with real-world situations. Recently, there has been a surge of causal discovery methods that explicitly consider latent variables. While some works aim to reveal causal relations between observed variables in the presence of latent variables, others seek to identify latent variables and recover the causal structure over them. The latter typically entail strong distributional and graphical assumptions, such as the non-Gaussianity, purity, and two-pure-children assumption. In this paper, we endeavor to recover the whole causal structure involving both latent and observed variables under milder assumptions. We formulate two cases, one allows entirely arbitrary distribution and requires only one pure child per latent variable, and the other requires no pure child and imposes the non-Gaussianity requirement on only a subset of variables, and they both avoid the purity assumption. We prove the identifiability of linear latent variable models in both cases, and our constructive proof leads to theoretically sound and computationally efficient algorithms.

Zhen Liu, Yao Feng, Yuliang Xiu, Weiyang Liu, Liam Paull, Michael J Black, Bernhard Schoelkopf

The creation of photorealistic virtual worlds requires the accurate modeling of 3D surface geometry for a wide range of objects. For this, meshes are appealing since they enable 1) fast physics-based rendering with realistic material and lighting, 2) physical simulation, and 3) are memory-efficient for modern graphics pipelines. Recent work on reconstructing and statistically modeling 3D shape, however, has critiqued meshes as being topologically inflexible. To capture a wide range of object shapes, any 3D representation must be able to model solid, watertight, shapes as well as thin, open, surfaces. Recent work has focused on the former, and methods for reconstructing open surfaces do not support fast reconstruction with material and lighting or unconditional generative modelling. Inspired by the observation that open surfaces can be seen as islands floating on watertight surfaces, we parametrize open surfaces by defining a manifold signed distance field on watertight templates. With this parametrization, we further develop a grid-based and differentiable representation that parametrizes both watertight and non-watertight meshes of arbitrary topology. Our new representation, called Ghost-on-the-Shell (G-Shell), enables two important applications: differentiable rasterization-based reconstruction from multiview images and generative modelling of non-watertight meshes. We empirically demonstrate that G-Shell achieves state-of-the-art performance on non-watertight mesh reconstruction and generation tasks, while also performing effectively for watertight meshes.

Optimization · Sampling and Optimization

Nick Richardson, Deniz Oktay, Yaniv Ovadia, James Bowden, Ryan P Adams

Integrals with discontinuous integrands are ubiquitous, arising from discrete structure in applications like topology optimization, graphics, and computational geometry. These integrals are often part of a forward model in an inverse problem where it is necessary to reason backwards about the parameters, ideally using gradient-based optimization. Monte Carlo methods are widely used to estimate the value of integrals, but this results in a non-differentiable approximation that is amenable to neither conventional automatic differentiation nor reparameterization-based gradient methods. This significantly disrupts efforts to integrate machine learning methods in areas that exhibit these discontinuities: physical simulation and robotics, design, graphics, and computational geometry. Although bespoke domain-specific techniques can handle special cases, a general methodology to wield automatic differentiation in these discrete contexts is wanting. We introduce a differentiable variant of the simple Monte Carlo estimator which samples line segments rather than points from the domain. We justify our estimator analytically as conditional Monte Carlo and demonstrate the diverse functionality of the method as applied to image stylization, topology optimization, and computational geometry.

Probabilistic Methods · Graphical Models

Anji Liu, Mathias Niepert, Guy Van den Broeck

Diffusion models are the current state of the art for generating photorealistic images. Controlling the sampling process for constrained image generation tasks such as inpainting, however, remains challenging since exact conditioning on such constraints is intractable. While existing methods use various techniques to approximate the constrained posterior, this paper proposes to exploit the ability of Tractable Probabilistic Models (TPMs) to exactly and efficiently compute the constrained posterior, and to leverage this signal to steer the denoising process of diffusion models. Specifically, this paper adopts a class of expressive TPMs termed Probabilistic Circuits (PCs). Building upon prior advances, we further scale up PCs and make them capable of guiding the image generation process of diffusion models. Empirical results suggest that our approach can consistently improve the overall quality and semantic coherence of inpainted images across three natural image datasets (i.e., CelebA-HQ, ImageNet, and LSUN) with only ~10% additional computational overhead brought by the TPM. Further, with the help of an image encoder and decoder, our method can readily accept semantic constraints on specific regions of the image, which opens up the potential for more controlled image generation tasks. In addition to proposing a new framework for constrained image generation, this paper highlights the benefit of more tractable models and motivates the development of expressive TPMs.

Deep Learning · Graph Neural Networks

Tuo Xu, Lei Zou

Designing expressive Graph Neural Networks (GNNs) is an important topic in graph machine learning fields. Despite the existence of numerous approaches proposed to enhance GNNs based on Weisfeiler-Lehman (WL) tests, what GNNs can and cannot learn still lacks a deeper understanding. This paper adopts a fundamentally different approach to examine the expressive power of GNNs from a probabilistic perspective. By establishing connections between GNNs' predictions and the central inference problems of probabilistic graphical models (PGMs), we can analyze previous GNN variants with a novel hierarchical framework and gain new insights into their node-level and link-level behaviors. Additionally, we introduce novel methods that can provably enhance GNNs' ability to capture complex dependencies and make complex predictions. Experiments on both synthetic and real-world datasets demonstrate the effectiveness of our approaches.

Jiarong Liu, Yifan Zhong, Siyi Hu, Haobo Fu, QIANG FU, Xiaojun Chang, Yaodong Yang

*Multi-agent reinforcement learning* (MARL) has been shown effective for cooperative games in recent years. However, existing state-of-the-art methods face challenges related to sample complexity, training instability, and the risk of converging to a suboptimal Nash Equilibrium. In this paper, we propose a unified framework for learning \emph{stochastic} policies to resolve these issues. We embed cooperative MARL problems into probabilistic graphical models, from which we derive the maximum entropy (MaxEnt) objective for MARL. Based on the MaxEnt framework, we propose *Heterogeneous-Agent Soft Actor-Critic* (HASAC) algorithm. Theoretically, we prove the monotonic improvement and convergence to *quantal response equilibrium* (QRE) properties of HASAC. Furthermore, we generalize a unified template for MaxEnt algorithmic design named *Maximum Entropy Heterogeneous-Agent Mirror Learning* (MEHAML), which provides any induced method with the same guarantees as HASAC. We evaluate HASAC on six benchmarks: Bi-DexHands, Multi-Agent MuJoCo, StarCraft Multi-Agent Challenge, Google Research Football, Multi-Agent Particle Environment, and Light Aircraft Game. Results show that HASAC consistently outperforms strong baselines, exhibiting better sample efficiency, robustness, and sufficient exploration.

Deep Learning · Generative Models and Autoencoders

Jian Chen, Ruiyi Zhang, Yufan Zhou, Changyou Chen

Controllable layout generation refers to the process of creating a plausible visual arrangement of elements within a graphic design (*e.g.*, document and web designs) with constraints representing design intentions. Although recent diffusion-based models have achieved state-of-the-art FID scores, they tend to exhibit more pronounced misalignment compared to earlier transformer-based models. In this work, we propose the **LA**yout **C**onstraint diffusion mod**E**l (LACE), a unified model to handle a broad range of layout generation tasks, such as arranging elements with specified attributes and refining or completing a coarse layout design. The model is based on continuous diffusion models. Compared with existing methods that use discrete diffusion models, continuous state-space design can enable the incorporation of continuous aesthetic constraint functions in training more naturally. For conditional generation, we propose injecting layout conditions in the form of masks or gradient guidance during inference. Empirical results show that LACE produces high-quality layouts and outperforms existing state-of-the-art baselines. We will release our source code and model checkpoints.

Applications · Computer Vision

Xindi Yang, Zeke Xie, Xiong Zhou, Boyu Liu, Buhua Liu, Yi Liu, Haoran Wang, YUNFENG CAI, Mingming Sun

Neural field methods have seen great progress in various long-standing tasks in computer vision and computer graphics, including novel view synthesis and geometry reconstruction. As existing neural field methods try to predict some coordinate-based continuous target values, such as RGB for Neural Radiance Field (NeRF), all of these methods are regression models and are optimized by some regression loss. However, are regression models really better than classification models for neural field methods? In this work, we try to visit this very fundamental but overlooked question for neural fields from a machine learning perspective. We successfully propose a novel Neural Field Classifier (NFC) framework which formulates existing neural field methods as classification tasks rather than regression tasks. The proposed NFC can easily transform arbitrary Neural Field Regressor (NFR) into its classification variant via employing a novel Target Encoding module and optimizing a classification loss. By encoding a continuous regression target into a high-dimensional discrete encoding, we naturally formulate a multi-label classification task. Extensive experiments demonstrate the impressive effectiveness of NFC at the nearly free extra computational costs. Moreover, NFC also shows robustness to sparse inputs, corrupted images, and dynamic scenes.

Probabilistic Methods · Gaussian Processes

Yijue Dai, Wenzhong Yan, Feng Yin

Integrating information while recognizing dependence from multiple data sources and enhancing the predictive performance of the multi-output regression are challenging tasks. Multioutput Gaussian Process (MOGP) methods offer outstanding solutions with tractable predictions and uncertainty quantification. However, their practical applications are hindered by high computational complexity and storage demand. Additionally, there exist model mismatches in existing MOGP models when dealing with non-Gaussian data. To improve the model representation ability in terms of flexibility, optimality, and scalability, this paper introduces a novel multi-output regression framework, termed Graphical MOGP (GMOGP), which is empowered by: (i) Generating flexible Gaussian process priors consolidated from dentified parents, (ii) providing dependent processes with attention-based graphical representations, and (iii) achieving Pareto optimal solutions of kernel hyperparameters via a distributed learning framework. Numerical results confirm that the proposed GMOGP significantly outperforms state-of-the-art MOGP alternatives in predictive performance, as well as in time and memory efficiency, across various synthetic and real datasets.

Deep Learning · Generative Models and Autoencoders

Sigal Raab, Inbal Leibovitch, Guy Tevet, Moab Arar, Amit Bermano, Daniel Cohen-Or

Synthesizing realistic animations of humans, animals, and even imaginary creatures, has long been a goal for artists and computer graphics professionals. Compared to the imaging domain, which is rich with large available datasets, the number of data instances for the motion domain is limited, particularly for the animation of animals and exotic creatures (e.g., dragons), which have unique skeletons and motion patterns. In this work, we introduce SinMDM, a Single Motion Diffusion Model. It is designed to learn the internal motifs of a single motion sequence with arbitrary topology and synthesize a variety of motions of arbitrary length that remain faithful to the learned motifs. We harness the power of diffusion models and present a denoising network explicitly designed for the task of learning from a single input motion. SinMDM is crafted as a lightweight architecture, which avoids overfitting by using a shallow network with local attention layers that narrow the receptive field and encourage motion diversity. Our work applies to multiple contexts, including spatial and temporal in-betweening, motion expansion, style transfer, and crowd animation. Our results show that SinMDM outperforms existing methods both qualitatively and quantitatively. Moreover, while prior network-based approaches require additional training for different applications, SinMDM supports these applications during inference. Our project page, which includes links to the code and trained models, is accessible at https://sinmdm.github.io/SinMDM-page.

Miscellaneous Aspects of Machine Learning · Everything Else

Francisco Andrade, Gabriel Peyré, Clarice Poon

Optimal Transport is a useful metric to compare probability distributions and to compute a pairing given a ground cost. Its entropic regularization variant (eOT) is crucial to have fast algorithms and reflect fuzzy/noisy matchings. This work focuses on Inverse Optimal Transport (iOT), the problem of inferring the ground cost from samples drawn from a coupling that solves an eOT problem. It is a relevant problem that can be used to infer unobserved/missing links, and to obtain meaningful information about the structure of the ground cost yielding the pairing. On one side, iOT benefits from convexity, but on the other side, being ill-posed, it requires regularization to handle the sampling noise. This work presents an in-depth theoretical study of the $\ell_1$ regularization to model for instance Euclidean costs with sparse interactions between features. Specifically, we derive a sufficient condition for the robust recovery of the sparsity of the ground cost that can be seen as a far reaching generalization of the Lasso’s celebrated ``Irrepresentability Condition’’. To provide additional insight into this condition (consequently on the types of recoverable costs) we work out in detail the Gaussian case. Surprisingly, varying the entropic regularizer provides evidence that the Gaussian iOT interpolates between a graphical Lasso and a classical Lasso, thereby establishing a connection between iOT and graph estimation, an important problem in ML.

Zhipeng Cai, Matthias Müller

Novel view synthesis aims to render unseen views given a set of calibrated images. In practical applications, the coverage, appearance or geometry of the scene may change over time, with new images continuously being captured. Efficiently incorporating such continuous change is an open challenge. Standard NeRF benchmarks only involve scene coverage expansion. To study other practical scene changes, we propose a new dataset, World Across Time (WAT), consisting of scenes that change in appearance and geometry over time. We also propose a simple yet effective method, CLNeRF, which introduces continual learning (CL) to Neural Radiance Fields (NeRFs). CLNeRF combines generative replay and the Instant Neural Graphics Primitives (NGP) architecture to effectively prevent catastrophic forgetting and efficiently update the model when new data arrives. We also add trainable appearance and geometry embeddings to NGP, allowing a single compact model to handle complex scene changes. Without the need to store historical images, CLNeRF trained sequentially over multiple scans of a changing scene performs on-par with the upper bound model trained on all scans at once. Compared to other CL baselines CLNeRF performs much better across standard benchmarks and WAT. The source code, a demo, and the WAT dataset are available at https://github.com/IntelLabs/CLNeRF.

Numair Khan, Lei Xiao, Douglas Lanman

The task of synthesizing novel views from a single image has useful applications in virtual reality and mobile computing, and a number of approaches to the problem have been proposed in recent years. A Multiplane Image (MPI) estimates the scene as a stack of RGBA layers, and can model complex appearance effects, anti-alias depth errors and synthesize soft edges better than methods that use textured meshes or layered depth images. And unlike neural radiance fields, an MPI can be efficiently rendered on graphics hardware. However, MPIs are highly redundant and require a large number of depth layers to achieve plausible results. Based on the observation that the depth complexity in local image regions is lower than that over the entire image, we split an MPI into many small, tiled regions, each with only a few depth planes. We call this representation a Tiled Multiplane Image (TMPI). We propose a method for generating a TMPI with adaptive depth planes for single-view 3D photography in the wild. Our synthesized results are comparable to state-of-the-art single-view MPI methods while having lower computational overhead. each with only a few depth planes. We call this representation a Tiled Multiplane Image (TMPI). We propose a method for generating a TMPI with adaptive depth planes for single-view 3D photography in the wild. Our synthesized results are comparable to state-of-the-art single-view MPI methods while having lower computational overhead.