One fundamental challenge in graph machine learning is generalizing to new graphs. Many existing methods following the inductive setup can generalize to test graphs with new structures, but assuming the feature and label spaces remain the same as the training ones. This paper introduces a fully-inductive setup, where models should perform inference on arbitrary test graphs with new structures, feature and label spaces. We propose GraphAny as the first attempt at this challenging setup. GraphAny models inference on a new graph as an analytical solution to a LinearGNN, which can be naturally applied to graphs with any feature and label spaces. To further build a stronger model with learning capacity, we fuse multiple LinearGNN predictions with learned inductive attention scores. Specifically, the attention module is carefully parameterized as a function of the entropy-normalized distance features between pairs of LinearGNN predictions to ensure generalization to new graphs. Empirically, GraphAny trained on a single Wisconsin dataset with only 120 labeled nodes can generalize to 30 new graphs with an average accuracy of 67.26%, surpassing not only all inductive baselines, but also strong transductive methods trained separately on each of the 30 test graphs.

The dominant paradigm for learning on graphs is message passing. Despite being a strong inductive bias, the local message passing mechanism faces challenges such as over-smoothing, over-squashing, and limited expressivity. To address these issues, we introduce Bundle Neural Networks (BuNNs), a novel graph neural network architecture that operates via *message diffusion* on *flat vector bundles* — geometrically inspired structures that assign to each node a vector space and an orthogonal map. A BuNN layer evolves node features through a diffusion-type partial differential equation, where its discrete form acts as a special case of the recently introduced Sheaf Neural Network (SNN), effectively alleviating over-smoothing. The continuous nature of message diffusion enables BuNNs to operate at larger scales, reducing over-squashing. We establish the universality of BuNNs in approximating feature transformations on infinite families of graphs with injective positional encodings, marking the first positive expressivity result of its kind. We support our claims with formal analysis and synthetic experiments. Empirically, BuNNs perform strongly on heterophilic and long-range tasks, which demonstrates their robustness on a diverse range of challenging real-world tasks.

Graph Transformers are popular neural networks that extend the well-known Transformer architecture to the graph domain. These architectures operate by applying self-attention on graph nodes and incorporating graph structure through the use of positional encodings (e.g., Laplacian positional encoding) or structural encodings (e.g., random-walk structural encoding). The quality of such encodings is critical, since they provide the necessary \emph{graph inductive biases} to condition the model on graph structure. In this work, we propose \emph{motif structural encoding} (MoSE) as a flexible and powerful structural encoding framework based on counting graph homomorphisms. Theoretically, we compare the expressive power of MoSE to random-walk structural encoding and relate both encodings to the expressive power of standard message passing neural networks. Empirically, we observe that MoSE outperforms other well-known positional and structural encodings across a range of architectures, and it achieves state-of-the-art performance on a widely studied molecular property prediction dataset.

We propose a class of trainable deep learning-based geometries called Neural SpaceTimes (NSTs), which can universally represent nodes in weighted Directed Acyclic Graphs (DAGs) as events in a spacetime manifold. While most works in the literature focus on undirected graph representation learning or causality embedding separately, our differentiable geometry can encode both graph edge weights in its spatial dimensions and causality in the form of edge directionality in its temporal dimensions. We use a product manifold that combines a quasi-metric (for space) and a partial order (for time). NSTs are implemented as three neural networks trained in an end-to-end manner: an embedding network, which learns to optimize the location of nodes as events in the spacetime manifold, and two other networks that optimize the space and time geometries in parallel, which we call a neural (quasi-)metric and a neural partial order, respectively. The latter two networks leverage recent ideas at the intersection of fractal geometry and deep learning to shape the geometry of the representation space in a data-driven fashion, unlike other works in the literature that use fixed spacetime manifolds such as Minkowski space or De Sitter space to embed DAGs. Our main theoretical guarantee is a universal embedding theorem, showing that any $k$-point DAG can be embedded into an NST with $1+\mathcal{O}(\log(k))$ distortion while exactly preserving its causal structure. The total number of parameters defining the NST is sub-cubic in $k$ and linear in the width of the DAG. If the DAG has a planar Hasse diagram, this is improved to $\mathcal{O}(\log(k) + 2)$ spatial and 2 temporal dimensions. We validate our framework computationally with synthetic weighted DAGs and real-world network embeddings; in both cases, the NSTs achieve lower embedding distortions than their counterparts using fixed spacetime geometries.

Topological deep learning (TDL) is a rapidly growing field that seeks to leverage topological structure in data and facilitate learning from data supported on topological objects, ranging from molecules to 3D shapes. Most TDL architectures can be unified under the framework of higher-order message-passing (HOMP), which generalizes graph message-passing to higher-order domains. In the first part of the paper, we explore HOMP's expressive power from a topological perspective, demonstrating the framework's inability to capture fundamental topological and metric invariants such as diameter, orientability, planarity, and homology. In addition, we demonstrate HOMP's limitations in fully leveraging lifting and pooling methods on graphs. To the best of our knowledge, this is the first work to study the expressivity of TDL from a topological perspective. In the second part of the paper, we develop two new classes of architectures -- multi-cellular networks (MCN) and scalable MCN (SMCN) -- which draw inspiration from expressive GNNs. MCN can reach full expressivity, but scaling it to large data objects can be computationally expansive. Designed as a more scalable alternative, SMCN still mitigates many of HOMP's expressivity limitations. Finally, we design new benchmarks for evaluating models based on their ability to learn topological properties of complexes. We then evaluate SMCN on these benchmarks as well as on real-world graph datasets, demonstrating improvements over both HOMP baselines and expressive graph methods, highlighting the value of expressively leveraging topological information.

Generative modeling of discrete data underlies important applications spanning text-based agents like ChatGPT to the design of the very building blocks of life in protein sequences. However, application domains need to exert control over the generated data by steering the generative process—typically via RLHF—to satisfy a specified property, reward, or affinity metric. In this paper, we study the problem of steering Masked Diffusion Models (MDMs), a recent class of discrete diffusion models that offer a compelling alternative to traditional autoregressive models. We introduce Discrete Denoising Posterior Prediction (DDPP), a novel framework that casts the task of steering pretrained MDMs as a problem of probabilistic inference by learning to sample from a target Bayesian posterior. Our DDPP framework leads to a family of three novel objectives that are all simulation-free, and thus scalable while applying to general non-differentiable reward functions. Empirically, we instantiate DDPP by steering MDMs to perform class-conditional pixel-level image modeling, RLHF-based alignment of MDMs using text based rewards, and finetuning protein language models to generate more diverse secondary structures and shorter proteins. We substantiate our designs via wet-lab validation, where we observe transient expression of reward-optimized protein sequences.

We introduce DrugFlow, a generative model for structure-based drug design that integrates continuous flow matching with discrete Markov bridges, demonstrating state-of-the-art performance in learning chemical, geometric, and physical aspects of three-dimensional protein-ligand data. We endow DrugFlow with an uncertainty estimate that is able to detect out-of-distribution samples. To further enhance the sampling process towards distribution regions with desirable metric values, we propose a joint preference alignment scheme applicable to both flow matching and Markov bridge frameworks. Furthermore, we extend our model to also explore the conformational landscape of the protein by jointly sampling side chain angles and molecules.

While message passing neural networks (MPNNs) have convincing success in a range of applications, they exhibit limitations such as the oversquashing problem and their inability to capture long-range interactions. Augmenting MPNNs with a virtual node (VN) removes the locality constraint of the layer aggregation and has been found to improve performance on a range of benchmarks. We provide a comprehensive theoretical analysis of the role of VNs and benefits thereof, through the lenses of oversquashing and sensitivity analysis. First, we characterize, precisely, how the improvement afforded by VNs on the mixing abilities of the network and hence in mitigating oversquashing, depends on the underlying topology. We then highlight that, unlike Graph-Transformers (GTs), classical instantiations of the VN are often constrained to assign uniform importance to different nodes. Consequently, we propose a variant of VN with the same computational complexity, which can have different sensitivity to nodes based on the graph structure. We show that this is an extremely effective and computationally efficient baseline for graph-level tasks.

Spectral graph convolution, an important tool of data filtering on graphs, relies on two essential decisions: selecting spectral bases for signal transformation and parameterizing the kernel for frequency analysis. While recent techniques mainly focus on standard Fourier transform and vector-valued spectral functions, they fall short in flexibility to model signal distributions over large spatial ranges, and capacity of spectral function. In this paper, we present a novel wavelet-based graph convolution network, namely WaveGC, which integrates multi-resolution spectral bases and a matrix-valued filter kernel. Theoretically, we establish that WaveGC can effectively capture and decouple short-range and long-range information, providing superior filtering flexibility, surpassing existing graph wavelet neural networks. To instantiate WaveGC, we introduce a novel technique for learning general graph wavelets by separately combining odd and even terms of Chebyshev polynomials. This approach strictly satisfies wavelet admissibility criteria. Our numerical experiments showcase the consistent improvements in both short-range and long-range tasks. This underscores the effectiveness of the proposed model in handling different scenarios.

Long-range graph tasks — those dependent on interactions between ‘distant’ nodes — are an open problem in graph neural network research. Real-world benchmark tasks, especially the Long Range Graph Benchmark, have become popular for validating the long-range capability of proposed architectures. However, this is an empirical approach that lacks both robustness and theoretical underpinning; a more principled characterization of the long-range problem is required. To bridge this gap, we formalize long-range interactions in graph tasks, introduce a range measure for operators on graphs, and validate it with synthetic experiments. We then leverage our measure to examine commonly used tasks and architectures, and discuss to what extent they are, in fact, long-range. We believe our work advances efforts to define and address the long-range problem on graphs, and that our range measure will aid evaluation of new datasets and architectures.

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the *motifs* that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are *binary*, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

Subgraph GNNs have emerged as promising architectures that overcome the expressiveness limitations of Graph Neural Networks (GNNs) by processing bags of subgraphs. Despite their compelling empirical performance, these methods are afflicted by a high computational complexity: they process bags whose size grows linearly in the number of nodes, hindering their applicability to larger graphs. In this work, we propose an effective and easy-to-implement approach to dramatically alleviate the computational cost of Subgraph GNNs and unleash broader applications thereof. Our method, dubbed HyMN, leverages walk-based centrality measures to sample a small number of relevant subgraphs and drastically reduce the bag size. By drawing a connection to perturbation analysis, we highlight the strength of the proposed centrality-based subgraph sampling, and further prove that these walk-based centralities can be additionally used as Structural Encodings for improved discriminative power. A comprehensive set of experimental results demonstrates that HyMN provides an effective synthesis of expressiveness, efficiency, and downstream performance, unlocking the application of Subgraph GNNs to dramatically larger graphs. Not only does our method outperform more sophisticated subgraph sampling approaches, it is also competitive, and sometimes better, than other state-of-the-art approaches for a fraction of their runtime.

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated samples under the target distribution. In this paper, we extend the Boltzmann generator framework with two key contributions, denoting our framework Sequential Boltzmann Generators (SBG). The first is a highly efficient Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to the equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient during both sample generation and likelihood evaluation. This efficiency unlocks more sophisticated inference strategies beyond standard importance sampling. In particular, we perform inference-time scaling of flow samples using a continuous-time variant of sequential Monte Carlo, in which flow samples are transported towards the target distribution with annealed Langevin dynamics. SBG achieves state-of-the-art performance w.r.t. all metrics on peptide systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri-, tetra- and hexa-peptides that were thus far intractable for prior Boltzmann generators.

The capability of generalization is a cornerstone for the success of modern learning systems. For non-Euclidean data, e.g., graphs, that particularly involves topological structures, one important aspect neglected by prior studies is how machine learning models generalize under topological shifts. This paper proposes AdvDIFFormer, a physics-inspired graph Transformer model designed to address this challenge. The model is derived from advective diffusion equations which describe a class of continuous message passing process with observed and latent topological structures. We show that AdvDIFFormer has provable capability for controlling generalization error with topological shifts, which in contrast cannot be guaranteed by graph diffusion models, i.e., the generalization of common graph neural networks in continuous space. Empirically, the model demonstrates superiority in various predictive tasks across information networks, molecular screening and protein interactions

The Temporal Graph Learning (TGL) workshop, now in its third edition at KDD 2025, offers an interdisciplinary platform for researchers to explore the evolving applications of temporal networks in various domains, including recommender systems, social network analysis, traffic analytics, and epidemiological data analysis.The workshop aims to facilitate the exchange of ideas across disciplines, highlight successes and challenges in TGL, and outline future research directions.The workshop welcomes diverse contributions, offers keynote talks from academic and industry experts, and is complemented by a panel discussion on emerging aspects of TGL.

Sampling efficiently from a target unnormalized probability density remains a core challenge, with relevance across countless high-impact scientific applications. A promising approach towards this challenge is the design of amortized samplers that borrow key ideas, such as probability path design, from state-of-the-art generative diffusion models. However, all existing diffusion-based samplers remain unable to draw samples from distributions at the scale of even simple molecular systems. In this paper, we propose Progressive Inference-Time Annealing (PITA) a novel framework to learn diffusion-based samplers that combines two complementary interpolation techniques: I.) Annealing of the Boltzmann distribution and II.) Diffusion smoothing. PITA trains a sequence of diffusion models from high to low temperatures by sequentially training each model at progressively higher temperatures, leveraging engineered easy access to samples of the temperature-annealed target density. In the subsequent step, PITA enables simulating the trained diffusion model to *procure training samples at a lower temperature* for the next diffusion model through inference-time annealing using a novel Feynman-Kac PDE combined with Sequential Monte Carlo. Empirically, PITA enables, for the first time, equilibrium sampling of $N$-body particle systems, Alanine Dipeptide, and tripeptides in Cartesian coordinates with dramatically lower energy function evaluations.

Graph Neural Networks (GNNs) are models that leverage the graph structure to transmit information between nodes, typically through the message-passing operation. While widely successful, this approach is well-known to suffer from representational collapse as the number of layers increases and insensitivity to the information contained at distant and poorly connected nodes. In this paper, we present a unified view of on the appearance of these issues through the lens of vanishing gradients, using ideas from linear control theory for our analysis. We propose an interpretation of GNNs as recurrent models and empirically demonstrate that a simple state-space formulation of an GNN effectively alleviates these issues at no extra trainable parameter cost. Further, we show theoretically and empirically that (i) Traditional GNNs are by design prone to extreme gradient vanishing even after few layers; (ii) Feature collapse is directly related to the mechanism causing vanishing gradients; (iii) Long-range modeling is most easily achieved by a combination of graph rewiring and vanishing gradient mitigation. We believe our work will help bridge the gap between the recurrent and graph neural network literature and will unlock the design of new deep and performant GNNs.

Graph machine learning architectures are typically tailored to specific tasks on specific datasets, which hinders their broader applicability. This has led to a new quest in graph machine learning: \emph{how to build graph foundation models (GFMs)} capable of generalizing across arbitrary graphs and features? In this work, we present a recipe for designing GFMs for node-level tasks from first principles. The key ingredient underpinning our study is a systematic investigation of the symmetries that a graph foundation model must respect. In a nutshell, we argue that label permutation-equivariance alongside feature permutation-invariance are necessary in addition to the common node permutation-equivariance on each local neighborhood of the graph. To this end, we first characterize the space of linear transformations that are equivariant to permutations of nodes and labels, and invariant to permutations of features. We then prove that the resulting network is a universal approximator on multisets that respect the aforementioned symmetries. Our recipe uses such layers on the multiset of features induced by the local neighborhood of the graph to obtain a class of graph foundation models for node property prediction. We validate our approach through extensive experiments on 29 real-world node classification datasets, demonstrating both strong zero-shot empirical performance and consistent improvement as the number of training graphs increases.

Gradients of neural networks encode valuable information for optimization, editing, and analysis of models. Therefore, practitioners often treat gradients as inputs to task-specific algorithms, e.g., using gradient statistics for pruning or optimization. Recent works explore *learning* algorithms that operate directly on gradients but use architectures that are not specifically designed for gradient processing, hindering their applicability. In this paper, we present a principled approach for designing architectures that process gradients. Our approach is guided by three principles: (1) equivariant design that preserves neuron permutation symmetries, (2) processing sets of gradients across multiple data points to capture curvature information, and (3) efficient gradient representation through rank-1 decomposition. Based on these principles, we introduce GradMetaNet, a novel architecture for learning on gradients, constructed from simple equivariant blocks. We prove universality results for GradMetaNet, and show that previous approaches cannot approximate natural gradient-based functions that GradMetaNet can. We then demonstrate GradMetaNet's effectiveness on a diverse set of gradient-based tasks for *MLPs* and *transformers*, such as learned optimization, INR editing, and loss landscape curvature estimation.

Modern Parameter-Efficient Fine-Tuning (PEFT) methods such as low-rank adaptation (LoRA) reduce the cost of customizing large language models (LLMs), yet still require a separate optimization run for every downstream dataset. We introduce \textbf{Drag-and-Drop LLMs (\textit{DnD})}, a prompt-conditioned parameter generator that eliminates per-task training by mapping a handful of unlabeled task prompts directly to LoRA weight updates. A lightweight text encoder distills each prompt batch into condition embeddings, which are then transformed by a cascaded hyper-convolutional decoder into the full set of LoRA matrices. Once trained in a diverse collection of prompt-checkpoint pairs, DnD produces task-specific parameters in seconds, yielding i) up to \textbf{12,000$\times$} lower overhead than full fine-tuning, ii) average gains up to \textbf{30\%} in performance over the strongest training LoRAs on unseen common-sense reasoning, math, coding, and multimodal benchmarks, and iii) robust cross-domain generalization improving \textbf{40\%} performance without access to the target data or labels. Our results demonstrate that prompt-conditioned parameter generation is a viable alternative to gradient-based adaptation for rapidly specializing LLMs. We open source \href{https://jerryliang24.github.io/DnD}{our project} in support of future research.

Graph Neural Networks (GNNs) have achieved remarkable success across various domains. However, recent theoretical advances have identified fundamental limitations in their information propagation capabilities, such as over-squashing, where distant nodes fail to effectively exchange information. While extensively studied in static contexts, this issue remains unexplored in Spatiotemporal GNNs (STGNNs), which process sequences associated with graph nodes. Nonetheless, the temporal dimension amplifies this challenge by increasing the information that must be propagated. In this work, we formalize the spatiotemporal over-squashing problem and demonstrate its distinct characteristics compared to the static case. Our analysis reveals that, counterintuitively, convolutional STGNNs favor information propagation from points temporally distant rather than close in time. Moreover, we prove that architectures that follow either time-and-space or time-then-space processing paradigms are equally affected by this phenomenon, providing theoretical justification for computationally efficient implementations. We validate our findings on synthetic and real-world datasets, providing deeper insights into their operational dynamics and principled guidance for more effective designs.

Modeling the transport dynamics of natural processes from population-level observations is a ubiquitous problem in the natural sciences. Such models rely on key assumptions about the underlying process in order to enable faithful learning of governing dynamics that mimic the actual system behavior. The de facto assumption in current approaches relies on the principle of least action that results in gradient field dynamics and leads to trajectories minimizing an energy functional between two probability measures. However, many real-world systems, such as cell cycles in single-cell RNA, are known to exhibit non-gradient, periodic behavior, which fundamentally cannot be captured by current state-of-the-art methods such as flow and bridge matching. In this paper, we introduce Curly Flow Matching (Curly-FM), a novel approach that is capable of learning non-gradient field dynamics by designing and solving a Schrödinger bridge problem with a non-zero drift reference process---in stark contrast to typical zero-drift reference processes---which is constructed using inferred velocities in addition to population snapshot data. We showcase Curly-FM by solving the trajectory inference problems for single cells, computational fluid dynamics, and ocean currents with approximate velocities. We demonstrate that Curly-FM can learn trajectories that better match both the reference process and population marginals. Curly-FM expands flow matching models beyond the modeling of populations and towards the modeling of known periodic behavior in physical systems. Our code repository is accessible at: https://github.com/kpetrovicc/curly-flow-matching.git

Rectified Flows learn ODE vector fields whose trajectories are straight between source and target distributions, enabling near one-step inference. We show that this straight-path objective reveals fundamental failure modes: under deterministic training, low gradient variance drives memorization of arbitrary training pairings, even when interpolant lines between training pairs intersect. To analyze this mechanism, we study Gaussian-to-Gaussian transport and use the loss gradient variance across stochastic and deterministic regimes to characterize which vector fields optimization favors in each setting. We then show that, in a setting where all interpolating lines intersect, applying Rectified Flow yields the same specific pairings at inference as during training. More generally, we prove that a memorizing vector field exists even when training interpolants intersect, and that optimizing the straight-path objective converges to this ill-defined field. At inference, deterministic integration reproduces the exact training pairings. We validate our findings empirically on the CelebA dataset, confirming that deterministic interpolants induce memorization, while the injection of small noise restores generalization.

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in full for each system of interest. The widespread success of generative models has inspired interest towards overcoming this limitation through learning sampling algorithms. Despite performing competitively with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We demonstrate that deep learning enables the design of scalable and transferable samplers by introducing Prose, a 285 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Prose draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Prose as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve competitive performance to established methods such as sequential Monte Carlo. We open-source the Prose codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.

The convolution operator at the core of many modern neural architectures can effectively be seen as performing a dot product between an input matrix and a filter. While this is readily applicable to data such as images, which can be represented as regular grids in the Euclidean space, extending the convolution operator to work on graphs proves more challenging, due to their irregular structure. In this article, we propose to use graph kernels, i.e., kernel functions that compute an inner product on graphs, to extend the standard convolution operator to the graph domain. This allows us to define an entirely structural model that does not require computing the embedding of the input graph. Our architecture allows to plug-in any type of graph kernels and has the added benefit of providing some interpretability in terms of the structural masks that are learned during the training process, similar to what happens for convolutional masks in traditional convolutional neural networks (CNNs). We perform an extensive ablation study to investigate the model hyperparameters' impact and show that our model achieves competitive performance on standard graph classification and regression datasets.

Graph Neural Networks (GNNs) are popular models for machine learning on graphs that typically follow the message-passing paradigm, whereby the feature of a node is updated recursively upon aggregating information over its neighbors. While exchanging messages over the input graph endows GNNs with a strong inductive bias, it can also make GNNs susceptible to over-squashing, thereby preventing them from capturing long-range interactions in the given graph. To rectify this issue, graph rewiring techniques have been proposed as a means of improving information flow by altering the graph connectivity. In this work, we identify three desiderata for graph-rewiring: (i) reduce over-squashing, (ii) respect the locality of the graph, and (iii) preserve the sparsity of the graph. We highlight fundamental trade-offs that occur between spatial and spectral rewiring techniques; while the former often satisfy (i) and (ii) but not (iii), the latter generally satisfy (i) and (iii) at the expense of (ii). We propose a novel rewiring framework that satisfies all of (i)--(iii) through a locality-aware sequence of rewiring operations. We then discuss a specific instance of such rewiring framework and validate its effectiveness on several real-world benchmarks, showing that it either matches or significantly outperforms existing rewiring approaches.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message-passing networks layers and train it in an end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce \foldflow, a series of novel generative models of increasing modeling power based on the flow-matching paradigm over $3\mathrm{D}$ rigid motions---i.e. the group $\mathrm{SE(3)}$---enabling accurate modeling of protein backbones. We first introduce $\text{FoldFlow-Base}$, a simulation-free approach to learning deterministic continuous-time dynamics and matching invariant target distributions on $\mathrm{SE(3)}$. We next accelerate training by incorporating Riemannian optimal transport to create $\text{FoldFlow-OT}$, leading to the construction of both more simple and stable flows. Finally, we design \foldflowsfm, coupling both Riemannian OT and simulation-free training to learn stochastic continuous-time dynamics over $\mathrm{SE(3)}$. Our family of $\text{FoldFlow}$, generative models offers several key advantages over previous approaches to the generative modeling of proteins: they are more stable and faster to train than diffusion-based approaches, and our models enjoy the ability to map any invariant source distribution to any invariant target distribution over $\mathrm{SE(3)}$. Empirically, we validate $\text{FoldFlow}$, on protein backbone generation of up to $300$ amino acids leading to high-quality designable, diverse, and novel samples.

Retrosynthesis planning is a fundamental challenge in chemistry which aims at designing multi-step reaction pathways from commercially available starting materials to a target molecule. Each step in multi-step retrosynthesis planning requires accurate prediction of possible precursor molecules given the target molecule and confidence estimates to guide heuristic search algorithms. We model single-step retrosynthesis as a distribution learning problem in a discrete state space. First, we introduce the Markov Bridge Model, a generative framework aimed to approximate the dependency between two intractable discrete distributions accessible via a finite sample of coupled data points. Our framework is based on the concept of a Markov bridge, a Markov process pinned at its endpoints. Unlike diffusion-based methods, our Markov Bridge Model does not need a tractable noise distribution as a sampling proxy and directly operates on the input product molecules as samples from the intractable prior distribution. We then address the retrosynthesis planning problem with our novel framework and introduce RetroBridge, a template-free retrosynthesis modeling approach that achieves state-of-the-art results on standard evaluation benchmarks.

Machine learning on graphs, especially using graph neural networks (GNNs), has seen a surge in interest due to the wide availability of graph data across a broad spectrum of disciplines, from life to social and engineering sciences. Despite their practical success, our theoretical understanding of the properties of GNNs remains highly incomplete. Recent theoretical advancements primarily focus on elucidating the coarse-grained expressive power of GNNs, predominantly employing combinatorial techniques. However, these studies do not perfectly align with practice, particularly in understanding the generalization behavior of GNNs when trained with stochastic first-order optimization techniques. In this position paper, we argue that the graph machine learning community needs to shift its attention to developing a balanced theory of graph machine learning, focusing on a more thorough understanding of the interplay of expressive power, generalization, and optimization.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either listen, broadcast, listen and broadcast, or to isolate. The standard message propagation scheme can then be viewed as a special case of this framework where every node listens and broadcasts to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic and real-world datasets.

A large body of work has investigated the properties of graph neural networks and identified several limitations, particularly pertaining to their expressive power. Their inability to count certain patterns (e.g., cycles) in a graph lies at the heart of such limitations, since many functions to be learned rely on the ability of counting such patterns. Two prominent paradigms aim to address this limitation by enriching the graph features with subgraph or homomorphism pattern counts. In this work, we show that both of these approaches are sub-optimal in a certain sense and argue for a more fine-grained approach, which incorporates the homomorphism counts of all structures in the “basis” of the target pattern. This yields strictly more expressive architectures without incurring any additional overhead in terms of computational complexity compared to existing approaches. We prove a series of theoretical results on node-level and graph-level motif parameters and empirically validate them on standard benchmark datasets.

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent alternatives based on diffusion or flow-matching falling short of their impressive performance in continuous data settings, such as image or video generation. In this work, we introduce Fisher-Flow, a novel flow-matching model for discrete data. Fisher-Flow takes a manifestly geometric perspective by considering categorical distributions over discrete data as points residing on a statistical manifold equipped with its natural Riemannian metric: the \emph{Fisher-Rao metric}. As a result, we demonstrate discrete data itself can be continuously reparameterised to points on the positive orthant of the $d$-hypersphere $\mathbb{S}^d_+$, which allows us to define flows that map any source distribution to target in a principled manner by transporting mass along (closed-form) geodesics of $\mathbb{S}^d_+$. Furthermore, the learned flows in Fisher-Flow can be further bootstrapped by leveraging Riemannian optimal transport leading to improved training dynamics. We prove that the gradient flow induced by Fisher-FLow is optimal in reducing the forward KL divergence. We evaluate Fisher-Flow on an array of synthetic and diverse real-world benchmarks, including designing DNA Promoter, and DNA Enhancer sequences. Empirically, we find that Fisher-Flow improves over prior diffusion and flow-matching models on these benchmarks.

Message Passing Neural Networks (MPNNs) are a staple of graph machine learning. MPNNs iteratively update each node’s representation in an input graph by aggregating messages from the node’s neighbors, which necessitates a memory complexity of the order of the __number of graph edges__. This complexity might quickly become prohibitive for large graphs provided they are not very sparse. In this paper, we propose a novel approach to alleviate this problem by approximating the input graph as an intersecting community graph (ICG) -- a combination of intersecting cliques. The key insight is that the number of communities required to approximate a graph __does not depend on the graph size__. We develop a new constructive version of the Weak Graph Regularity Lemma to efficiently construct an approximating ICG for any input graph. We then devise an efficient graph learning algorithm operating directly on ICG in linear memory and time with respect to the __number of nodes__ (rather than edges). This offers a new and fundamentally different pipeline for learning on very large non-sparse graphs, whose applicability is demonstrated empirically on node classification tasks and spatio-temporal data processing.

Proteins are essential for almost all biological processes and derive their diverse functions from complex $3 \rm D$ structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive bias of amino acid sequences and introduce FoldFlow++, a novel sequence-conditioned $\text{SE}(3)$-equivariant flow matching model for protein structure generation. FoldFlow++ presents substantial new architectural features over the previous FoldFlow family of models including a protein large language model to encode sequence, a new multi-modal fusion trunk that combines structure and sequence representations, and a geometric transformer based decoder. To increase diversity and novelty of generated samples -- crucial for de-novo drug design -- we train FoldFlow++ at scale on a new dataset that is an order of magnitude larger than PDB datasets of prior works, containing both known proteins in PDB and high-quality synthetic structures achieved through filtering. We further demonstrate the ability to align FoldFlow++ to arbitrary rewards, e.g. increasing secondary structures diversity, by introducing a Reinforced Finetuning (ReFT) objective. We empirically observe that FoldFlow++ outperforms previous state-of-the-art protein structure-based generative models, improving over RFDiffusion in terms of unconditional generation across all metrics including designability, diversity, and novelty across all protein lengths, as well as exhibiting generalization on the task of equilibrium conformation sampling. Finally, we demonstrate that a fine-tuned FoldFlow++ makes progress on challenging conditional design tasks such as designing scaffolds for the VHH nanobody.

Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source distribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of $\textit{Euclidean geometry}$, resulting in straight interpolations. However, this can be particularly restrictive for tasks such as trajectory inference, where straight paths might lie outside the data manifold, thus failing to capture the underlying dynamics giving rise to the observed marginals. In this paper, we propose Metric Flow Matching (MFM), a novel simulation-free framework for conditional flow matching where interpolants are approximate geodesics learned by minimizing the kinetic energy of a data-induced Riemannian metric. This way, the generative model matches vector fields on the data manifold, which corresponds to lower uncertainty and more meaningful interpolations. We prescribe general metrics to instantiate MFM, independent of the task, and test it on a suite of challenging problems including LiDAR navigation, unpaired image translation, and modeling cellular dynamics. We observe that MFM outperforms the Euclidean baselines, particularly achieving SOTA on single-cell trajectory prediction.

Bounding and predicting the generalization gap of overparameterized neural networks remains a central open problem in theoretical machine learning. There is a recent and growing body of literature that proposes the framework of fractals to model optimization trajectories of neural networks, motivating generalization bounds and measures based on the fractal dimension of the trajectory. Notably, the persistent homology dimension has been proposed to correlate with the generalization gap. This paper performs an empirical evaluation of these persistent homology-based generalization measures, with an in-depth statistical analysis. Our study reveals confounding effects in the observed correlation between generalization and topological measures due to the variation of hyperparameters. We also observe that fractal dimension fails to predict generalization of models trained from poor initializations. We lastly reveal the intriguing manifestation of model-wise double descent in these topological generalization measures. Our work forms a basis for a deeper investigation of the causal relationships between fractal geometry, topological data analysis, and neural network optimization.

Denoising diffusion models are a class of generative models that have recently achieved state-of-the-art results across many domains. Gradual noise is added to the data using a diffusion process, which transforms the data distribution into a Gaussian. Samples from the generative model are then obtained by simulating an approximation of the time reversal of this diffusion initialized by Gaussian samples. Recent research has explored the sampling error achieved by diffusion models under the assumption of an absolute error $\epsilon$ achieved via a neural approximation of the score. To the best of our knowledge, no work formally quantifies the error of such neural approximation to the score. In this paper, we close the gap and present quantitative error bounds for approximating the score of denoising diffusion models using neural networks leveraging ideas from stochastic control. Finally, through simulation, we explore some of the insights that arise from our results confirming that diffusion models based on the Ornstein-Uhlenbeck (OU) process require fewer parameters to better approximate the score than those based on the Fölmer drift / Pinned Brownian Motion.

In the sequential decision making setting, an agent aims to achieve systematic generalization over a large, possibly infinite, set of environments. Such environments are modeled as discrete Markov decision processes with both states and actions represented through a feature vector. The underlying structure of the environments allows the transition dynamics to be factored into two components: one that is environment-specific and another that is shared. Consider a set of environments that share the laws of motion as an example. In this setting, the agent can take a finite amount of reward-free interactions from a subset of these environments. The agent then must be able to approximately solve any planning task defined over any environment in the original set, relying on the above interactions only. Can we design a provably efficient algorithm that achieves this ambitious goal of systematic generalization? In this paper, we give a partially positive answer to this question. First, we provide a tractable formulation of systematic generalization by employing a causal viewpoint. Then, under specific structural assumptions, we provide a simple learning algorithm that guarantees any desired planning error up to an unavoidable sub-optimality term, while showcasing a polynomial sample complexity.

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive to information contained at distant nodes. Despite recent methods introduced to mitigate this issue, an understanding of the causes for over-squashing and of possible solutions are lacking. In this theoretical work, we prove that: (i) Neural network width can mitigate over-squashing, but at the cost of making the whole network more sensitive; (ii) Conversely, depth cannot help mitigate over-squashing: increasing the number of layers leads to over-squashing being dominated by vanishing gradients; (iii) The graph topology plays the greatest role, since over-squashing occurs between nodes at high commute time. Our analysis provides a unified framework to study different recent methods introduced to cope with over-squashing and serves as a justification for a class of methods that fall under graph rewiring.

Message passing neural networks (MPNNs) have been shown to suffer from the phenomenon of over-squashing that causes poor performance for tasks relying on long-range interactions. This can be largely attributed to message passing only occurring locally, over a node’s immediate neighbours. Rewiring approaches attempting to make graphs ’more connected’, and supposedly better suited to long-range tasks, often lose the inductive bias provided by distance on the graph since they make distant nodes communicate instantly at every layer. In this paper we propose a framework, applicable to any MPNN architecture, that performs a layer-dependent rewiring to ensure gradual densification of the graph. We also propose a delay mechanism that permits skip connections between nodes depending on the layer and their mutual distance. We validate our approach on several long-range tasks and show that it outperforms graph Transformers and multi-hop MPNNs.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Graph generative model evaluation necessitates understanding differences between graphs on the distributional level. This entails being able to harness salient attributes of graphs in an efficient manner. Curvature constitutes one such property of graphs, and has recently started to prove useful in characterising graphs. Its expressive properties, stability, and practical utility in model evaluation remain largely unexplored, however. We combine graph curvature descriptors with emerging methods from topological data analysis to obtain robust, expressive descriptors for evaluating graph generative models.

While Graph Neural Networks (GNNs) have achieved remarkable results in a variety of applications, recent studies exposed important shortcomings in their ability to capture the structure of the underlying graph. It has been shown that the expressive power of standard GNNs is bounded by the Weisfeiler-Leman (WL) graph isomorphism test, from which they inherit proven limitations such as the inability to detect and count graph substructures. On the other hand, there is significant empirical evidence, e.g. in network science and bioinformatics, that substructures are often intimately related to downstream tasks. To this end, we propose "Graph Substructure Networks" (GSN), a topologically-aware message passing scheme based on substructure encoding. We theoretically analyse the expressive power of our architecture, showing that it is strictly more expressive than the WL test, and provide sufficient conditions for universality. Importantly, we do not attempt to adhere to the WL hierarchy; this allows us to retain multiple attractive properties of standard GNNs such as locality and linear network complexity, while being able to disambiguate even hard instances of graph isomorphism. We perform an extensive experimental evaluation on graph classification and regression tasks and obtain state-of-the-art results in diverse real-world settings including molecular graphs and social networks.

Graph deep learning has recently emerged as a powerful ML concept allowing to generalize successful deep neural architectures to non-euclidean structured data. Such methods have shown promising results on a broad spectrum of applications ranging from social science, biomedicine, and particle physics to computer vision, graphics, and chemistry. One of the limitations of the majority of current graph neural network architectures is that they are often restricted to the transductive setting and rely on the assumption that the underlying graph is known and fixed. Often, this assumption is not true since the graph may be noisy, or partially and even completely unknown. In such cases, it would be helpful to infer the graph directly from the data, especially in inductive settings where some nodes were not present in the graph at training time. Furthermore, learning a graph may become an end in itself, as the inferred structure may provide complementary insights next to the downstream task. In this paper, we introduce Differentiable Graph Module (DGM), a learnable function that predicts edge probabilities in the graph which are optimal for the downstream task. DGM can be combined with convolutional graph neural network layers and trained in an end-to-end fashion. We provide an extensive evaluation of applications from the domains of healthcare (disease prediction), brain imaging (age prediction), computer graphics (3D point cloud segmentation), and computer vision (zero-shot learning). We show that our model provides a significant improvement over baselines both in transductive and inductive settings and achieves state-of-the-art results.

Strategic interactions between a group of individuals or organisations can be modelled as games played on networks, where a player’s payoff depends not only on their actions but also on those of their neighbours. Inferring the network structure from observed game outcomes (equilibrium actions) is an important problem with numerous potential applications in economics and social sciences. Existing methods mostly require the knowledge of the utility function associated with the game, which is often unrealistic to obtain in real-world scenarios. We adopt a transformer-like architecture which correctly accounts for the symmetries of the problem and learns a mapping from the equilibrium actions to the network structure of the game without explicit knowledge of the utility function. We test our method on three different types of network games using both synthetic and real-world data, and demonstrate its effectiveness in network structure inference and superior performance over existing methods.

We propose Graph-Coupled Oscillator Networks (GraphCON), a novel framework for deep learning on graphs. It is based on discretizations of a second-order system of ordinary differential equations (ODEs), which model a network of nonlinear controlled and damped oscillators, coupled via the adjacency structure of the underlying graph. The flexibility of our framework permits any basic GNN layer (e.g. convolutional or attentional) as the coupling function, from which a multi-layer deep neural network is built up via the dynamics of the proposed ODEs. We relate the oversmoothing problem, commonly encountered in GNNs, to the stability of steady states of the underlying ODE and show that zero-Dirichlet energy steady states are not stable for our proposed ODEs. This demonstrates that the proposed framework mitigates the oversmoothing problem. Moreover, we prove that GraphCON mitigates the exploding and vanishing gradients problem to facilitate training of deep multi-layer GNNs. Finally, we show that our approach offers competitive performance with respect to the state-of-the-art on a variety of graph-based learning tasks.

Recommender systems are fundamental building blocks of modern consumer web applications that seek to predict user preferences to better serve relevant items. As such, high-quality user and item representations as inputs to recommender systems are crucial for personalized recommendation. To construct these user and item representations, self-supervised graph embedding has emerged as a principled approach to embed relational data such as user social graphs, user membership graphs, user-item engagements, and other heterogeneous graphs. In this tutorial we discuss different families of approaches to self-supervised graph embedding. Within each family, we outline a variety of techniques, their merits and disadvantages, and expound on latest works. Finally, we demonstrate how to effectively utilize the resultant large embedding tables to improve candidate retrieval and ranking in modern industry-scale deep-learning recommender systems.

Cellular sheaves equip graphs with a ``geometrical'' structure by assigning vector spaces and linear maps to nodes and edges. Graph Neural Networks (GNNs) implicitly assume a graph with a trivial underlying sheaf. This choice is reflected in the structure of the graph Laplacian operator, the properties of the associated diffusion equation, and the characteristics of the convolutional models that discretise this equation. In this paper, we use cellular sheaf theory to show that the underlying geometry of the graph is deeply linked with the performance of GNNs in heterophilic settings and their oversmoothing behaviour. By considering a hierarchy of increasingly general sheaves, we study how the ability of the sheaf diffusion process to achieve linear separation of the classes in the infinite time limit expands. At the same time, we prove that when the sheaf is non-trivial, discretised parametric diffusion processes have greater control than GNNs over their asymptotic behaviour. On the practical side, we study how sheaves can be learned from data. The resulting sheaf diffusion models have many desirable properties that address the limitations of classical graph diffusion equations (and corresponding GNN models) and obtain competitive results in heterophilic settings. Overall, our work provides new connections between GNNs and algebraic topology and would be of interest to both fields.

Subgraph GNNs are a recent class of expressive Graph Neural Networks (GNNs) which model graphs as collections of subgraphs. So far, the design space of possible Subgraph GNN architectures as well as their basic theoretical properties are still largely unexplored. In this paper, we study the most prominent form of subgraph methods, which employs node-based subgraph selection policies such as ego-networks or node marking and deletion. We address two central questions: (1) What is the upper-bound of the expressive power of these methods? and (2) What is the family of equivariant message passing layers on these sets of subgraphs?. Our first step in answering these questions is a novel symmetry analysis which shows that modelling the symmetries of node-based subgraph collections requires a significantly smaller symmetry group than the one adopted in previous works. This analysis is then used to establish a link between Subgraph GNNs and Invariant Graph Networks (IGNs). We answer the questions above by first bounding the expressive power of subgraph methods by 3-WL, and then proposing a general family of message-passing layers for subgraph methods that generalises all previous node-based Subgraph GNNs. Finally, we design a novel Subgraph GNN dubbed SUN, which theoretically unifies previous architectures while providing better empirical performance on multiple benchmarks.

Abstract The Average Mixing Kernel Signature is a novel spectral signature for points on non-rigid three-dimensional shapes. It is based on a quantum exploration process of the shape surface, where the average transition probabilities between the points of the shape are summarised in the finite-time average mixing kernel. A band-filtered spectral analysis of this kernel then yields the AMKS. Crucially, we show that opting for a finite time-evolution allows the signature to account for a mixing of the Laplacian eigenspaces, similar to what is observed in the presence of noise, explaining the increased noise robustness of this signature when compared to alternative signatures. We perform an extensive experimental analysis of the AMKS under a wide range of problem scenarios, evaluating the performance of our descriptor under different sources of noise (vertex jitter and topological), shape representations (mesh and point clouds), as well as when only a partial view of the shape is available. Our experiments show that the AMKS consistently outperforms two of the most widely used spectral signatures, the Heat Kernel Signature and the Wave Kernel Signature, and suggest that the AMKS should be the signature of choice for various compute vision problems, including as input of deep convolutional architectures for shape analysis.

Over the past decade, deep learning has had a revolutionary impact on a broad range of fields such as computer vision and image processing, computational photography, medical imaging and speech and language analysis and synthesis etc. Deep learning technologies are estimated to have added billions in business value, created new markets, and transformed entire industrial segments. Most of today’s successful deep learning methods such as Convolutional Neural Networks (CNNs) rely on classical signal processing models that limit their applicability to data with underlying Euclidean grid-like structure, e.g., images or acoustic signals. Yet, many applications deal with non-Euclidean (graph- or manifold-structured) data. For example, in social network analysis the users and their attributes are generally modeled as signals on the vertices of graphs. In biology protein-to-protein interactions are modeled as graphs. In computer vision & graphics 3D objects are modeled as meshes or point clouds. Furthermore, a graph representation is a very natural way to describe interactions between objects or signals. The classical deep learning paradigm on Euclidean domains falls short in providing appropriate tools for such kind of data. Until recently, the lack of deep learning models capable of correctly dealing with non-Euclidean data has been a major obstacle in these fields. This special section addresses the need to bring together leading efforts in non-Euclidean deep learning across all communities. From the papers that the special received twelve were selected for publication. The selected papers can naturally fall in three distinct categories: (a) methodologies that advance machine learning on data that are represented as graphs, (b) methodologies that advance machine learning on manifold-valued data, and (c) applications of machine learning methodologies on non-Euclidean spaces in computer vision and medical imaging. We briefly review the accepted papers in each of the groups.

Proteins’ biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional sites, such as binding targets for potential drugs. Unfortunately though, the use of meshes as the underlying representation for protein structure has multiple drawbacks including the need to pre-compute the input features and mesh connectivities. This becomes a bottleneck for many important tasks in protein science.In this paper, we present a new framework for deep learning on protein structures that addresses these limitations. Among the key advantages of our method are the computation and sampling of the molecular surface on-the-fly from the underlying atomic point cloud and a novel efficient geometric convolutional layer. As a result, we are able to process large collections of proteins in an end-to-end fashion, taking as the sole input the raw 3D coordinates and chemical types of their atoms, eliminating the need for any hand-crafted pre-computed features.To showcase the performance of our approach, we test it on two tasks in the field of protein structural bioinformatics: the identification of interaction sites and the prediction of protein-protein interactions. On both tasks, we achieve state-of-the-art performance with much faster run times and fewer parameters than previous models. These results will considerably ease the deployment of deep learning methods in protein science and open the door for end-to-end differentiable approaches in protein modeling tasks such as function prediction and design.

We present Graph Neural Diffusion (GRAND) that approaches deep learning on graphs as a continuous diffusion process and treats Graph Neural Networks (GNNs) as discretisations of an underlying PDE. In our model, the layer structure and topology correspond to the discretisation choices of temporal and spatial operators. Our approach allows a principled development of a broad new class of GNNs that are able to address the common plights of graph learning models such as depth, oversmoothing, and bottlenecks. Key to the success of our models are stability with respect to perturbations in the data and this is addressed for both implicit and explicit discretisation schemes. We develop linear and nonlinear versions of GRAND, which achieve competitive results on many standard graph benchmarks.

The pairwise interaction paradigm of graph machine learning has predominantly governed the modelling of relational systems. However, graphs alone cannot capture the multi-level interactions present in many complex systems and the expressive power of such schemes was proven to be limited. To overcome these limitations, we propose Message Passing Simplicial Networks (MPSNs), a class of models that perform message passing on simplicial complexes (SCs). To theoretically analyse the expressivity of our model we introduce a Simplicial Weisfeiler-Lehman (SWL) colouring procedure for distinguishing non-isomorphic SCs. We relate the power of SWL to the problem of distinguishing non-isomorphic graphs and show that SWL and MPSNs are strictly more powerful than the WL test and not less powerful than the 3-WL test. We deepen the analysis by comparing our model with traditional graph neural networks (GNNs) with ReLU activations in terms of the number of linear regions of the functions they can represent. We empirically support our theoretical claims by showing that MPSNs can distinguish challenging strongly regular graphs for which GNNs fail and, when equipped with orientation equivariant layers, they can improve classification accuracy in oriented SCs compared to a GNN baseline.

Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the computational graph and the input graph structure. The recently proposed Message Passing Simplicial Networks naturally decouple these elements by performing message passing on the clique complex of the graph. Nevertheless, these models can be severely constrained by the rigid combinatorial structure of Simplicial Complexes (SCs). In this work, we extend recent theoretical results on SCs to regular Cell Complexes, topological objects that flexibly subsume SCs and graphs. We show that this generalisation provides a powerful set of graph "lifting" transformations, each leading to a unique hierarchical message passing procedure. The resulting methods, which we collectively call CW Networks (CWNs), are strictly more powerful than the WL test and not less powerful than the 3-WL test. In particular, we demonstrate the effectiveness of one such scheme, based on rings, when applied to molecular graph problems. The proposed architecture benefits from provably larger expressivity than commonly used GNNs, principled modelling of higher-order signals and from compressing the distances between nodes. We demonstrate that our model achieves state-of-the-art results on a variety of molecular datasets.

Can we use machine learning to compress graph data? The absence of ordering in graphs poses a significant challenge to conventional compression algorithms, limiting their attainable gains as well as their ability to discover relevant patterns. On the other hand, most graph compression approaches rely on domain-dependent handcrafted representations and cannot adapt to different underlying graph distributions. This work aims to establish the necessary principles a lossless graph compression method should follow to approach the entropy storage lower bound. Instead of making rigid assumptions about the graph distribution, we formulate the compressor as a probabilistic model that can be learned from data and generalise to unseen instances. Our “Partition and Code” framework entails three steps: first, a partitioning algorithm decomposes the graph into subgraphs, then these are mapped to the elements of a small dictionary on which we learn a probability distribution, and finally, an entropy encoder translates the representation into bits. All the components (partitioning, dictionary and distribution) are parametric and can be trained with gradient descent. We theoretically compare the compression quality of several graph encodings and prove, under mild conditions, that PnC achieves compression gains that grow either linearly or quadratically with the number of vertices. Empirically, PnC yields significant compression improvements on diverse real-world networks.

We propose a novel class of graph neural networks based on the discretized Beltrami flow, a non-Euclidean diffusion PDE. In our model, node features are supplemented with positional encodings derived from the graph topology and jointly evolved by the Beltrami flow, producing simultaneously continuous feature learning, topology evolution. The resulting model generalizes many popular graph neural networks and achieves state-of-the-art results on several benchmarks.

The workshop features presentations of accepted contributions to the RecSys Challenge 2021, organized by Politecnico di Bari, ETH Zürich, Jönköping University, and the data set is provided by Twitter. The challenge focuses on a real-world task of tweet engagement prediction in a dynamic environment. For 2021, the challenge considers four different engagement types: Likes, Retweet, Quote, and replies. This year’s challenge brings the problem even closer to Twitter’s real recommender systems by introducing latency constraints. We also increases the data size to encourage novel methods. Also, the data density is increased in terms of the graph where users are considered to be nodes and interactions as edges. The goal is twofold: to predict the probability of different engagement types of a target user for a set of Tweets based on heterogeneous input data while providing fair recommendations. In fact, multi-goal optimization considering accuracy and fairness is particularly challenging. However, we believed that the recommendation community was nowadays mature enough to face the challenge of providing accurate and, at the same time, fair recommendations. To this end, Twitter has released a public dataset of close to 1 billion data points, > 40 million each day over 28 days. Week 1 − 3 will be used for training and week 4 for evaluation and testing. Each datapoint contains the tweet along with engagement features, user features, and tweet features. A peculiarity of this challenge is related to keeping the dataset updated with the platform: if a user deletes a Tweet, or their data from Twitter, the dataset is promptly updated. Moreover, each change in the dataset implied new evaluations of all submissions and the update of the leaderboard metrics. The challenge was well received with 578 registered users, and 386 submissions.

Graph neural networks (GNNs) have recently gained significant momentum in the recommendation community, demonstrating state-of-the-art performance in top-k recommendation and next-item recommendation. Despite promising results on GNN-based recommendation and search, most of the current GNN research remains essentially concentrated on more traditional tasks such as classification or regression. The GReS workshop on Graph Neural Networks for Recommendation and Search is then a first endeavor to bridge the gap between the RecSys and GNN communities, and promote recommendation and search problems amongst GNN practitioners.

Graph machine learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets - amongst other data types. Herein, we present a multidisciplinary academic-industrial review of the topic within the context of drug discovery and development. After introducing key terms and modelling approaches, we move chronologically through the drug development pipeline to identify and summarize work incorporating: target identification, design of small molecules and biologics, and drug repurposing. Whilst the field is still emerging, key milestones including repurposed drugs entering in vivo studies, suggest GML will become a modelling framework of choice within biomedical machine learning.

Abstract We propose a novel approach for the approximation and transfer of signals across 3D shapes. The proposed solution is based on taking pointwise polynomials of the Fourier‐like Laplacian eigenbasis, which provides a compact and expressive representation for general signals defined on the surface. Key to our approach is the construction of a new orthonormal basis upon the set of these linearly dependent polynomials. We analyze the properties of this representation, and further provide a complete analysis of the involved parameters. Our technique results in accurate approximation and transfer of various families of signals between near‐isometric and non‐isometric shapes, even under poor initialization. Our experiments, showcased on a selection of downstream tasks such as filtering and detail transfer, show that our method is more robust to discretization artifacts, deformation and noise as compared to alternative approaches.

Abstract Standard registration algorithms need to be independently applied to each surface to register, following careful pre-processing and hand-tuning. Recently, learning-based approaches have emerged that reduce the registration of new scans to running inference with a previously-trained model. The potential benefits are multifold: inference is typically orders of magnitude faster than solving a new instance of a difficult optimization problem, deep learning models can be made robust to noise and corruption, and the trained model may be re-used for other tasks, e.g. through transfer learning. In this paper, we cast the registration task as a surface-to-surface translation problem, and design a model to reliably capture the latent geometric information directly from raw 3D face scans. We introduce Shape-My-Face (SMF), a powerful encoder-decoder architecture based on an improved point cloud encoder, a novel visual attention mechanism, graph convolutional decoders with skip connections, and a specialized mouth model that we smoothly integrate with the mesh convolutions. Compared to the previous state-of-the-art learning algorithms for non-rigid registration of face scans, SMF only requires the raw data to be rigidly aligned (with scaling) with a pre-defined face template. Additionally, our model provides topologically-sound meshes with minimal supervision, offers faster training time, has orders of magnitude fewer trainable parameters, is more robust to noise, and can generalize to previously unseen datasets. We extensively evaluate the quality of our registrations on diverse data. We demonstrate the robustness and generalizability of our model with in-the-wild face scans across different modalities, sensor types, and resolutions. Finally, we show that, by learning to register scans, SMF produces a hybrid linear and non-linear morphable model. Manipulation of the latent space of SMF allows for shape generation, and morphing applications such as expression transfer in-the-wild. We train SMF on a dataset of human faces comprising 9 large-scale databases on commodity hardware.

This paper focuses on spectral graph convolutional neural networks (ConvNets), where filters are defined as elementwise multiplication in the frequency domain of a graph. In machine learning settings where the data set consists of signals defined on many different graphs, the trained ConvNet should generalize to signals on graphs unseen in the training set. It is thus important to transfer ConvNets between graphs. Transferability, which is a certain type of generalization capability, can be loosely defined as follows: if two graphs describe the same phenomenon, then a single filter or ConvNet should have similar repercussions on both graphs. This paper aims at debunking the common misconception that spectral filters are not transferable. We show that if two graphs discretize the same “continuous” space, then a spectral filter or ConvNet has approximately the same repercussion on both graphs. Our analysis is more permissive than the standard analysis. Transferability is typically described as the robustness of the filter to small graph perturbations and re-indexing of the vertices. Our analysis accounts also for large graph perturbations. We prove transferability between graphs that can have completely different dimensions and topologies, only requiring that both graphs discretize the same underlying space in some generic sense.

Graph convolution operators bring the advantages of deep learning to a variety of graph and mesh processing tasks previously deemed out of reach. With their continued success comes the desire to design more powerful architectures, often by adapting existing deep learning techniques to non-Euclidean data. In this paper, we argue geometry should remain the primary driving force behind innovation in the emerging field of geometric deep learning. We relate graph neural networks to widely successful computer graphics and data approximation models: radial basis functions (RBFs). We conjecture that, like RBFs, graph convolution layers would benefit from the addition of simple functions to the powerful convolution kernels. We introduce affine skip connections, a novel building block formed by combining a fully connected layer with any graph convolution operator. We experimentally demonstrate the effectiveness of our technique, and show the improved performance is the consequence of more than the increased number of parameters. Operators equipped with the affine skip connection markedly outperform their base performance on every task we evaluated, i.e., shape reconstruction, dense shape correspondence, and graph classification. We hope our simple and effective approach will serve as a solid baseline and help ease future research in graph neural networks.

We introduce a simple and effective network architecture for monocular 3D hand pose estimation consisting of an image encoder followed by a mesh convolutional decoder that is trained through a direct 3D hand mesh reconstruction loss. We train our network by gathering a large-scale dataset of hand action in YouTube videos and use it as a source of weak supervision. Our weakly-supervised mesh convolutions-based system largely outperforms state-of-the-art methods, even halving the errors on the in the wild benchmark. The dataset and additional resources are available at https://arielai.com/mesh_hands.

The research in biometric recognition using hand shape has been somewhat stagnating in the last decade. Meanwhile, computer vision and machine learning have experienced a paradigm shift with the renaissance of deep learning, which has set the new state-of-the-art in many related fields. Inspired by successful applications of deep learning for other biometric modalities, we propose a novel approach to 3D hand shape recognition from RGB-D data based on geometric deep learning techniques. We show how to train our model on synthetic data and retain the performance on real samples during test time. To evaluate our method, we provide a new dataset NNHand RGB- D of short video sequences and show encouraging performance compared to diverse baselines on the new data, as well as current benchmark dataset HKPolyU. Moreover, the new dataset opens door to many new research directions in hand shape recognition.

Face recognition is a widely accepted biometric verification tool, as the face contains a lot of information about the identity of a person. In this study, a 2-step neural-based pipeline is presented for matching 3D facial shape to multiple DNA-related properties (sex, age, BMI and genomic background). The first step consists of a triplet loss-based metric learner that compresses facial shape into a lower dimensional embedding while preserving information about the property of interest. Most studies in the field of metric learning have only focused on 2D Euclidean data. In this work, geometric deep learning is employed to learn directly from 3D facial meshes. To this end, spiral convolutions are used along with a novel mesh-sampling scheme that retains uniformly sampled 3D points at different levels of resolution. The second step is a multi-biometric fusion by a fully connected neural network. The network takes an ensemble of embeddings and property labels as input and returns genuine and imposter scores. Since embeddings are accepted as an input, there is no need to train classifiers for the different properties and available data can be used more efficiently. Results obtained by a to-fold cross-validation for biometric verification show that combining multiple properties leads to stronger biometric systems. Furthermore, the proposed neural-based pipeline outperforms a linear baseline, which consists of principal component analysis, followed by classification with linear support vector machines and a Naïve Bayes-based score-fuser.

Geometric methods rely on tensors that can be encoded using a symbolic formula and data arrays, such as kernel and distance matrices. We present an extension for standard machine learning frameworks that provides comprehensive support for this abstraction on CPUs and GPUs: our toolbox combines a versatile, transparent user interface with fast runtimes and low memory usage. Unlike general purpose acceleration frameworks such as XLA, our library turns generic Python code into binaries whose performances are competitive with state-of-the-art geometric libraries - such as FAISS for nearest neighbor search - with the added benefit of flexibility. We perform an extensive evaluation on a broad class of problems: Gaussian modelling, K-nearest neighbors search, geometric deep learning, non-Euclidean embeddings and optimal transport theory. In practice, for geometric problems that involve 1k to 1M samples in dimension 1 to 100, our library speeds up baseline GPU implementations by up to two orders of magnitude.

The workshop features presentations of accepted contributions to the RecSys Challenge 2020, organized by Politecnico di Bari, Free University of Bozen-Bolzano, TU Wien, University of Colorado, Boulder, and Universidade Federal de Campina Grande, and sponsored by Twitter. The challenge focuses on a real-world task of Tweet engagement prediction in a dynamic environment. The goal is to predict the probability for different types of engagement (Like, Reply, Retweet, and Retweet with comment) of a target user for a set of Tweets, based on heterogeneous input data. To this end, Twitter has released a large public dataset of ~160M public Tweets, obtained by subsampling within ~2 weeks, that contains engagement features, user features, and Tweet features. A peculiarity of this challenge is related to the recent regulations on data protection and privacy. The challenge data set was compliant: if a user deleted a Tweet, or their data from Twitter, the dataset was promptly updated. Moreover, each change in the dataset implied new evaluations of all submissions and the update of the leaderboard metrics.

Word2vec is a powerful machine learning tool that emerged from Natural Language Processing (NLP) and is now applied in multiple domains, including recommender systems, forecasting, and network analysis. As Word2vec is often used off the shelf, we address the question of whether the default hyperparameters are suitable for recommender systems. The answer is emphatically no. In this paper, we first elucidate the importance of hyperparameter optimization and show that unconstrained optimization yields an average 221% improvement in hit rate over the default parameters. However, unconstrained optimization leads to hyperparameter settings that are very expensive and not feasible for large scale recommendation tasks. To this end, we demonstrate 138% average improvement in hit rate with a runtime budget-constrained hyperparameter optimization. Furthermore, to make hyperparameter optimization applicable for large scale recommendation problems where the target dataset is too large to search over, we investigate generalizing hyperparameters settings from samples. We show that applying constrained hyperparameter optimization using only a 10% sample of the data still yields a 91% average improvement in hit rate over the default parameters when applied to the full datasets. Finally, we apply hyperparameters learned using our method of constrained optimization on a sample to the Who To Follow recommendation service at Twitter and are able to increase follow rates by 15%.

Intel® RealSense™ SR300 is a depth camera capable of providing a VGA-size depth map at 60 fps and 0.125mm depth resolution. In addition, it outputs an infrared VGA-resolution image and a 1080p color texture image at 30 fps. SR300 form-factor enables it to be integrated into small consumer products and as a front facing camera in laptops and Ultrabooks™. The SR300 depth camera is based on a coded-light technology where triangulation between projected patterns and images captured by a dedicated sensor is used to produce the depth map. Each projected line is coded by a special temporal optical code, that enables a dense depth map reconstruction from its reflection. The solid mechanical assembly of the camera allows it to stay calibrated throughout temperature and pressure changes, drops, and hits. In addition, active dynamic control maintains a calibrated depth output. An extended API LibRS released with the camera allows developers to integrate the camera in various applications. Algorithms for 3D scanning, facial analysis, hand gesture recognition, and tracking are within reach for applications using the SR300. In this paper, we describe the underlying technology, hardware, and algorithms of the SR300, as well as its calibration procedure, and outline some use cases. We believe that this paper will provide a full case study of a mass-produced depth sensing product and technology.

The question whether one can recover the shape of a geometric object from its Laplacian spectrum (`hear the shape of the drum') is a classical problem in spectral geometry with a broad range of implications and applications. While theoretically the answer to this question is negative (there exist examples of iso-spectral but non-isometric manifolds), little is known about the practical possibility of using the spectrum for shape reconstruction and optimization. In this paper, we introduce a numerical procedure called isospectralization, consisting of deforming one shape to make its Laplacian spectrum match that of another. We implement the isospectralization procedure using modern differentiable programming techniques and exemplify its applications in some of the classical and notoriously hard problems in geometry processing, computer vision, and graphics such as shape reconstruction, pose and style transfer, and dense deformable correspondence.

We introduce GFrames, a novel local reference frame (LRF) construction for 3D meshes and point clouds. GFrames are based on the computation of the intrinsic gradient of a scalar field defined on top of the input shape. The resulting tangent vector field defines a repeatable tangent direction of the local frame at each point; importantly, it directly inherits the properties and invariance classes of the underlying scalar function, making it remarkably robust under strong sampling artifacts, vertex noise, as well as non-rigid deformations. Existing local descriptors can directly benefit from our repeatable frames, as we showcase in a selection of 3D vision and shape analysis applications where we demonstrate state-of-the-art performance in a variety of challenging settings.

Generative models for 3D geometric data arise in many important applications in 3D computer vision and graphics. In this paper, we focus on 3D deformable shapes that share a common topological structure, such as human faces and bodies. Morphable Models and their variants, despite their linear formulation, have been widely used for shape representation, while most of the recently proposed nonlinear approaches resort to intermediate representations, such as 3D voxel grids or 2D views. In this work, we introduce a novel graph convolutional operator, acting directly on the 3D mesh, that explicitly models the inductive bias of the fixed underlying graph. This is achieved by enforcing consistent local orderings of the vertices of the graph, through the spiral operator, thus breaking the permutation invariance property that is adopted by all the prior work on Graph Neural Networks. Our operator comes by construction with desirable properties (anisotropic, topology-aware, lightweight, easy-to-optimise), and by using it as a building block for traditional deep generative architectures, we demonstrate state-of-the-art results on a variety of 3D shape datasets compared to the linear Morphable Model and other graph convolutional operators.

Abstract We consider the tasks of representing, analysing and manipulating maps between shapes. We model maps as densities over the product manifold of the input shapes; these densities can be treated as scalar functions and therefore are manipulable using the language of signal processing on manifolds. Being a manifold itself, the product space endows the set of maps with a geometry of its own, which we exploit to define map operations in the spectral domain; we also derive relationships with other existing representations (soft maps and functional maps). To apply these ideas in practice, we discretize product manifolds and their Laplace–Beltrami operators, and we introduce localized spectral analysis of the product manifold as a novel tool for map processing. Our framework applies to maps defined between and across 2D and 3D shapes without requiring special adjustment, and it can be implemented efficiently with simple operations on sparse matrices.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information, so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds, including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks, including ModelNet40, ShapeNetPart, and S3DIS.

The availability of affordable and portable depth sensors has made scanning objects and people simpler than ever. However, dealing with occlusions and missing parts is still a significant challenge. The problem of reconstructing a (possibly non-rigidly moving) 3D object from a single or multiple partial scans has received increasing attention in recent years. In this work, we propose a novel learning-based method for the completion of partial shapes. Unlike the majority of existing approaches, our method focuses on objects that can undergo non-rigid deformations. The core of our method is a variational autoencoder with graph convolutional operations that learns a latent space for complete realistic shapes. At inference, we optimize to find the representation in this latent space that best fits the generated shape to the known partial input. The completed shape exhibits a realistic appearance on the unknown part. We show promising results towards the completion of synthetic and real scans of human body and face meshes exhibiting different styles of articulation and partiality.

In the last years, Graph Convolutional Neural Networks gained popularity in the Machine Learning community for their capability of extracting local compositional features on signals defined on non-Euclidean domains. Shape correspondence, document classification, molecular properties predictions are just few of the many different problems where these techniques have been successfully applied. In this paper we will present Deep Geometric Matrix Completion, a recent application of Graph Convolutional Neural Networks to the matrix completion problem. We will illustrate MGCNN (a multi-graph CNN able to deal with signals defined over multiple domains) and we will show how coupling such technique with a RNN, a learnable diffusion process can be realized for reconstructing the desired information. Extensive experimental evaluation shows how Geometric Deep Learning techniques allow to outperform previous state of the art solutions on the matrix completion problem.

Tasks involving the analysis of geometric (graph-and manifold-structured) data have recently gained prominence in the machine learning community, giving birth to a rapidly developing field of geometric deep learning. In this work, we leverage graph neural networks to improve signal detection in the IceCube neutrino observatory. The IceCube detector array is modeled as a graph, where vertices are sensors and edges are a learned function of the sensors spatial coordinates. As only a subset of IceCubes sensors is active during a given observation, we note the adaptive nature of our GNN, wherein computation is restricted to the input signal support. We demonstrate the effectiveness of our GNN architecture on a task classifying IceCube events, where it outperforms both a traditional physics-based method as well as classical 3D convolution neural networks.

Abstract Functional maps have gained popularity as a versatile framework for representing intrinsic correspondence between 3D shapes using algebraic machinery. A key ingredient for this framework is the ability to find pairs of corresponding functions (typically, feature descriptors) across the shapes. This is a challenging problem on its own, and when the shapes are strongly non‐isometric, nearly impossible to solve automatically. In this paper, we use feature curve correspondences to provide flexible abstractions of semantically similar parts of non‐isometric shapes. We design a user interface implementing an interactive process for constructing shape correspondence, allowing the user to update the functional map at interactive rates by introducing feature curve correspondences. We add feature curve preservation constraints to the functional map framework and propose an efficient numerical method to optimize the map with immediate feedback. Experimental results show that our approach establishes correspondences between geometrically diverse shapes with just a few clicks.

Abstract The use of Laplacian eigenfunctions is ubiquitous in a wide range of computer graphics and geometry processing applications. In particular, Laplacian eigenbases allow generalizing the classical Fourier analysis to manifolds. A key drawback of such bases is their inherently global nature, as the Laplacian eigenfunctions carry geometric and topological structure of the entire manifold. In this paper, we introduce a new framework for local spectral shape analysis. We show how to efficiently construct localized orthogonal bases by solving an optimization problem that in turn can be posed as the eigendecomposition of a new operator obtained by a modification of the standard Laplacian. We study the theoretical and computational aspects of the proposed framework and showcase our new construction on the classical problems of shape approximation and correspondence. We obtain significant improvement compared to classical Laplacian eigenbases as well as other alternatives for constructing localized bases.

Abstract In this paper, we consider the problem of information transfer across shapes and propose an extension to the widely used functional map representation. Our main observation is that in addition to the vector space structure of the functional spaces, which has been heavily exploited in the functional map framework, the functional algebra (i.e., the ability to take pointwise products of functions) can significantly extend the power of this framework. Equipped with this observation, we show how to improve one of the key applications of functional maps, namely transferring real‐valued functions without conversion to point‐to‐point correspondences. We demonstrate through extensive experiments that by decomposing a given function into a linear combination consisting not only of basis functions but also of their pointwise products, both the representation power and the quality of the function transfer can be improved significantly. Our modification, while computationally simple, allows us to achieve higher transfer accuracy while keeping the size of the basis and the functional map fixed. We also analyze the computational complexity of optimally representing functions through linear combinations of products in a given basis and prove NP‐completeness in some general cases. Finally, we argue that the use of function products can have a wide‐reaching effect in extending the power of functional maps in a variety of applications, in particular by enabling the transfer of high‐frequency functions without changing the representation size or complexity.

Abstract Functional maps provide a means of extracting correspondences between surfaces using linear‐algebraic machinery. While the functional framework suggests efficient algorithms for map computation, the basic technique does not incorporate the intuition that pointwise modifications of a descriptor function (e.g. composition of a descriptor and a nonlinearity) should be preserved under the mapping; the end result is that the basic functional maps problem can be underdetermined without regularization or additional assumptions on the map. In this paper, we show how this problem can be addressed through kernelization, in which descriptors are lifted to higher‐dimensional vectors or even infinite‐length sequences of values. The key observation is that optimization problems for functional maps only depend on inner products between descriptors rather than descriptor values themselves. These inner products can be evaluated efficiently through use of kernel functions. In addition to deriving a kernelized version of functional maps including a recent extension in terms of pointwise multiplication operators, we provide an efficient conjugate gradient algorithm for optimizing our generalized problem as well as a strategy for low‐rank estimation of kernel matrices through the Nyström approximation.

Functional representation is a well-established approach to represent dense correspondences between deformable shapes. The approach provides an efficient low rank representation of a continuous mapping between two shapes, however under that framework the correspondences are only intrinsically captured, which implies that the induced map is not guaranteed to map the whole surface, much less to form a continuous mapping. In this work, we define a novel approach to the computation of a continuous bijective map between two surfaces moving from the low rank spectral representation to a sparse spatial representation. Key to this is the observation that continuity and smoothness of the optimal map induces structure both on the spectral and the spatial domain, the former providing effective low rank approximations, while the latter exhibiting strong sparsity and locality that can be used in the solution of large-scale problems. We cast our approach in terms of the functional transfer through a fuzzy map between shapes satisfying infinitesimal mass transportation at each point. The result is that, not only the spatial map induces a sub-vertex correspondence between the surfaces, but also the transportation of the whole surface, and thus the bijectivity of the induced map is assured. The performance of the proposed method is assessed on several popular benchmarks.

We present a method to match three dimensional shapes under non-isometric deformations, topology changes and partiality. We formulate the problem as matching between a set of pair-wise and point-wise descriptors, imposing a continuity prior on the mapping, and propose a projected descent optimization procedure inspired by difference of convex functions (DC) programming.

Deep learning has achieved a remarkable performance breakthrough in several fields, most notably in speech recognition, natural language processing, and computer vision. In particular, convolutional neural network (CNN) architectures currently produce state-of-the-art performance on a variety of image analysis tasks such as object detection and recognition. Most of deep learning research has so far focused on dealing with 1D, 2D, or 3D Euclidean-structured data such as acoustic signals, images, or videos. Recently, there has been an increasing interest in geometric deep learning, attempting to generalize deep learning methods to non-Euclidean structured data such as graphs and manifolds, with a variety of applications from the domains of network analysis, computational social science, or computer graphics. In this paper, we propose a unified framework allowing to generalize CNN architectures to non-Euclidean domains (graphs and manifolds) and learn local, stationary, and compositional task-specific features. We show that various non-Euclidean CNN methods previously proposed in the literature can be considered as particular instances of our framework. We test the proposed method on standard tasks from the realms of image-, graph-and 3D shape analysis and show that it consistently outperforms previous approaches.

Performance of fingerprint recognition depends heavily on the extraction of minutiae points. Enhancement of the fingerprint ridge pattern is thus an essential pre-processing step that noticeably reduces false positive and negative detection rates. A particularly challenging setting is when the fingerprint images are corrupted or partially missing. In this work, we apply generative convolutional networks to denoise visible minutiae and predict the missing parts of the ridge pattern. The proposed enhancement approach is tested as a pre-processing step in combination with several standard feature extraction methods such as MINDTCT, followed by biometric comparison using MCC and BO-ZORTH3. We evaluate our method on several publicly available latent fingerprint datasets captured using different sensors.

We introduce a new framework for learning dense correspondence between deformable 3D shapes. Existing learning based approaches model shape correspondence as a labelling problem, where each point of a query shape receives a label identifying a point on some reference domain; the correspondence is then constructed a posteriori by composing the label predictions of two input shapes. We propose a paradigm shift and design a structured prediction model in the space of functional maps, linear operators that provide a compact representation of the correspondence. We model the learning process via a deep residual network which takes dense descriptor fields defined on two shapes as input, and outputs a soft map between the two given objects. The resulting correspondence is shown to be accurate on several challenging benchmarks comprising multiple categories, synthetic models, real scans with acquisition artifacts, topological noise, and partiality.

Matrix completion models are among the most common formulations of recommender systems. Recent works have showed a boost of performance of these techniques when introducing the pairwise relationships between users/items in the form of graphs, and imposing smoothness priors on these graphs. However, such techniques do not fully exploit the local stationary structures on user/item graphs, and the number of parameters to learn is linear w.r.t. the number of users and items. We propose a novel approach to overcome these limitations by using geometric deep learning on graphs. Our matrix completion architecture combines a novel multi-graph convolutional neural network that can learn meaningful statistical graph-structured patterns from users and items, and a recurrent neural network that applies a learnable diffusion on the score matrix. Our neural network system is computationally attractive as it requires a constant number of parameters independent of the matrix size. We apply our method on several standard datasets, showing that it outperforms state-of-the-art matrix completion techniques.

We propose an efficient procedure for calculating partial dense intrinsic correspondence between deformable shapes performed entirely in the spectral domain. Our technique relies on the recently introduced partial functional maps formalism and on the joint approximate diagonalization (JAD) of the Laplace-Beltrami operators previously introduced for matching non-isometric shapes. We show that a variant of the JAD problem with an appropriately modified coupling term (surprisingly) allows to construct quasi-harmonic bases localized on the latent corresponding parts. This circumvents the need to explicitly compute the unknown parts by means of the cumbersome alternating minimization used in the previous approaches, and allows performing all the calculations in the spectral domain with constant complexity independent of the number of shape vertices. We provide an extensive evaluation of the proposed technique on standard non-rigid correspondence benchmarks and show state-of-the-art performance in various settings, including partiality and the presence of topological noise.

Abstract In this paper, we propose a method for computing partial functional correspondence between non‐rigid shapes. We use perturbation analysis to show how removal of shape parts changes the Laplace–Beltrami eigenfunctions, and exploit it as a prior on the spectral representation of the correspondence. Corresponding parts are optimization variables in our problem and are used to weight the functional correspondence; we are looking for the largest and most regular (in the Mumford–Shah sense) parts that minimize correspondence distortion. We show that our approach can cope with very challenging correspondence settings.

We consider the problem of deformable object detection and dense correspondence in cluttered 3D scenes. Key ingredient to our method is the choice of representation: we formulate the problem in the spectral domain using the functional maps framework, where we seek for the most regular nearly-isometric parts in the model and the scene that minimize correspondence error. The problem is initialized by solving a sparse relaxation of a quadratic assignment problem on features obtained via data-driven metric learning. The resulting matching pipeline is solved efficiently, and yields accurate results in challenging settings that were previously left unexplored in the literature.

Classical formulations of the shape matching problem involve the definition of a matching cost that directly depends on the action of the desired map when applied to some input data. Such formulations are typically one-sided - they seek for a mapping from one shape to the other, but not vice versa. In this paper we consider an unbiased formulation of this problem, in which we solve simultaneously for a low-distortion map relating the two given shapes and its inverse. We phrase the problem in the spectral domain using the language of functional maps, resulting in an especially compact and efficient optimization problem. The benefits of our proposed regularization are especially evident in the scarce data setting, where we demonstrate highly competitive results with respect to the state of the art.

We propose Anisotropic Windowed Fourier Transform (AWFT), a framework for localized space-frequency analysis of deformable 3D shapes. With AWFT, we are able to extract meaningful intrinsic localized orientation-sensitive structures on surfaces, and use them in applications such as shape segmentation, salient point detection, feature point description, and matching. Our method outperforms previous approaches in the considered applications.

We propose the first algorithm for non-rigid 2D-to-3D shape matching, where the input is a 2D query shape as well as a 3D target shape and the output is a continuous matching curve represented as a closed contour on the 3D shape. We cast the problem as finding the shortest circular path on the product 3-manifold of the two shapes. We prove that the optimal matching can be computed in polynomial time with a (worst-case) complexity of O(mn2 log(n)), wherem and n denote the number of vertices on the 2D and the 3D shape respectively. Quantitative evaluation confirms that the method provides excellent results for sketch-based deformable 3D shape retrieval.

In the past years, deep convolutional neural networks (CNNs) have become extremely popular in the computer vision and pattern recognition community. The computational power of modern processors, efficient stochastic optimization algorithms, and large amounts of training data allowed training complex tasks-specific features directly from the data in an end-to-end fashion, as opposed to the traditional way of using hand-crafted feature descriptors. CNNs are currently state-of-the-art methods in many computer vision problems, and have been successfully used in biometric applications such as face, fingerpring, and voice recognition. In palmprint recognition applications, CNNs have not yet been explored, and the majority of methods still rely on hand-crafted representations which do not scale well to large datasets and that usually require a complex manual parameter tuning. In this work, we show that CNNs can be successfully used for palmprint recognition. The training of our network uses a novel loss function related to the d-prime index, which allows to achieve a better genuine/impostor score distribution separation than previous approaches with only little training data required. Our approach does not require cumbersome parameter tuning and achieves state-of-the-art results on the standard IIT Delhi and CASIA palmprint datasets.

Convolutional neural networks have achieved extraordinary results in many computer vision and pattern recognition applications; however, their adoption in the computer graphics and geometry processing communities is limited due to the non-Euclidean structure of their data. In this paper, we propose Anisotropic Convolutional Neural Network (ACNN), a generalization of classical CNNs to non-Euclidean domains, where classical convolutions are replaced by projections over a set of oriented anisotropic diffusion kernels. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes, a fundamental problem in geometry processing, arising in a wide variety of applications. We tested ACNNs performance in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks.

Abstract The recent introduction of 3D shape analysis frameworks able to quantify the deformation of a shape into another in terms of the variation of real functions yields a new interpretation of the 3D shape similarity assessment and opens new perspectives. Indeed, while the classical approaches to similarity mainly quantify it as a numerical score, map‐based methods also define (dense) shape correspondences. After presenting in detail the theoretical foundations underlying these approaches, we classify them by looking at their most salient features, including the kind of structure and invariance properties they capture, as well as the distances and the output modalities according to which the similarity between shapes is assessed and returned. We also review the usage of these methods in a number of 3D shape application domains, ranging from matching and retrieval to annotation and segmentation. Finally, the most promising directions for future research developments are discussed.

Abstract Spectral methods have recently gained popularity in many domains of computer graphics and geometry processing, especially shape processing, computation of shape descriptors, distances, and correspondence. Spectral geometric structures are intrinsic and thus invariant to isometric deformations, are efficiently computed, and can be constructed on shapes in different representations. A notable drawback of these constructions, however, is that they areisotropic, i.e., insensitive to direction. In this paper, we show how to construct direction‐sensitive spectral feature descriptors usinganisotropic diffusionon meshes and point clouds. The core of our construction are directed local kernels acting similarly to steerable filters, which are learned in a task‐specific manner. Remarkably, while being intrinsic, our descriptors allow to disambiguate reflection symmetries. We show the application of anisotropic descriptors for problems of shape correspondence on meshes and point clouds, achieving results significantly better than state‐of‐the‐art methods.

Abstract Shape correspondence is a fundamental problem in computer graphics and vision, with applications in various problems including animation, texture mapping, robotic vision, medical imaging, archaeology and many more. In settings where the shapes are allowed to undergo non‐rigid deformations and only partial views are available, the problem becomes very challenging. To this end, we present a non‐rigid multi‐part shape matching algorithm. We assume to be given a reference shape and its multiple parts undergoing a non‐rigid deformation. Each of these query parts can be additionally contaminated by clutter, may overlap with other parts, and there might be missing parts or redundant ones. Our method simultaneously solves for the segmentation of the reference model, and for a dense correspondence to (subsets of) the parts. Experimental results on synthetic as well as real scans demonstrate the effectiveness of our method in dealing with this challenging matching scenario.

3D models of humans are commonly used within computer graphics and vision, and so the ability to distinguish between body shapes is an important shape retrieval problem. We extend our recent paper which provided a benchmark for testing non-rigid 3D shape retrieval algorithms on 3D human models. This benchmark provided a far stricter challenge than previous shape benchmarks. We have added 145 new models for use as a separate training set, in order to standardise the training data used and provide a fairer comparison. We have also included experiments with the FAUST dataset of human scans. All participants of the previous benchmark study have taken part in the new tests reported here, many providing updated results using the new data. In addition, further participants have also taken part, and we provide extra analysis of the retrieval results. A total of 25 different shape retrieval methods are compared.

In this paper, we consider the problem of finding dense intrinsic correspondence between manifolds using the recently introduced functional framework. We pose the functional correspondence problem as matrix completion with manifold geometric structure and inducing functional localization with the L1norm. We discuss efficient numerical procedures for the solution of our problem. Our method compares favorably to the accuracy of state-of-the-art correspondence algorithms on non-rigid shape matching benchmarks, and is especially advantageous in settings when only scarce data is available.

Principal Component Analysis (PCA) is the most widely used tool for linear dimensionality reduction and clustering. Still it is highly sensitive to outliers and does not scale well with respect to the number of data samples. Robust PCA solves the first issue with a sparse penalty term. The second issue can be handled with the matrix factorization model, which is however non-convex. Besides, PCA based clustering can also be enhanced by using a graph of data similarity. In this article, we introduce a new model called 'Robust PCA on Graphs' which incorporates spectral graph regularization into the Robust PCA framework. Our proposed model benefits from 1) the robustness of principal components to occlusions and missing values, 2) enhanced low-rank recovery, 3) improved clustering property due to the graph smoothness assumption on the low-rank matrix, and 4) convexity of the resulting optimization problem. Extensive experiments on 8 benchmark, 3 video and 2 artificial datasets with corruptions clearly reveal that our model outperforms 10 other state-of-the-art models in its clustering and low-rank recovery tasks.

Abstract We formulate the problem of shape‐from‐operator (SfO), recovering an embedding of a mesh from intrinsic operators defined through the discrete metric (edge lengths). Particularly interesting instances of our SfO problem include: shape‐from‐Laplacian, allowing to transfer style between shapes; shape‐from‐difference operator, used to synthesize shape analogies; and shape‐from‐eigenvectors, allowing to generate ‘intrinsic averages’ of shape collections. Numerically, we approach the SfO problem by splitting it into two optimization sub‐problems: metric‐from‐operator (reconstruction of the discrete metric from the intrinsic operator) and embedding‐from‐metric (finding a shape embedding that would realize a given metric, a setting of the multidimensional scaling problem). We study numerical properties of our problem, exemplify it on several applications, and discuss its imitations.

Abstract In this paper, we propose a generalization of convolutional neural networks (CNN) to non‐Euclidean domains for the analysis of deformable shapes. Our construction is based on localized frequency analysis (a generalization of the windowed Fourier transform to manifolds) that is used to extract the local behavior of some dense intrinsic descriptor, roughly acting as an analogy to patches in images. The resulting local frequency representations are then passed through a bank of filters whose coefficient are determined by a learning procedure minimizing a task‐specific cost. Our approach generalizes several previous methods such as HKS, WKS, spectral CNN, and GPS embeddings. Experimental results show that the proposed approach allows learning class‐specific shape descriptors significantly outperforming recent state‐of‐the‐art methods on standard benchmarks.

We construct an extension of spectral and diffusion geometry to multiple modalities through simultaneous diagonalization of Laplacian matrices. This naturally extends classical data analysis tools based on spectral geometry, such as diffusion maps and spectral clustering. We provide several synthetic and real examples of manifold learning, object classification, and clustering, showing that the joint spectral geometry better captures the inherent structure of multi-modal data. We also show the relation of many previous approaches for multimodal manifold analysis to our framework.

In this paper, we present a gamut mapping algorithm that is based on spectral properties of image Laplacians as image structure descriptors. Using the fact that structurally similar images have similar Laplacian eigenvectors and employing the relation between joint diagonalizability and commutativity of matrices, we minimize the Laplacians commutator w.r.t. the parameters of a color transformation to achieve optimal structure preservation while complying with the target gamut. Our method is computationally efficient, favorably compares to state-of-the-art approaches in terms of quality, allows mapping to devices with any number of primaries, and supports gamma correction, accounting for brightness response of computer displays.

Abstract Mappings between color spaces are ubiquitous in image processing problems such as gamut mapping, decolorization, and image optimization for color‐blind people. Simple color transformations often result in information loss and ambiguities, and one wishes to find an image‐specific transformation that would preserve as much as possible the structure of the original image in the target color space. In this paper, we propose Laplacian colormaps, a generic framework for structure‐preserving color transformations between images. We use the image Laplacian to capture the structural information, and show that if the color transformation between two images preserves the structure, the respective Laplacians have similar eigenvectors, or in other words, are approximately jointly diagonalizable. Employing the relation between joint diagonalizability and commutativity of matrices, we use Laplacians commutativity as a criterion of color mapping quality and minimize it w.r.t. the parameters of a color transformation to achieve optimal structure preservation. We show numerous applications of our approach, including color‐to‐gray conversion, gamut mapping, multispectral image fusion, and image optimization for color deficient viewers.

Abstract We present a method for supervised learning of shape descriptors for shape retrieval applications. Many content‐based shape retrieval approaches follow the bag‐of‐features (BoF) paradigm commonly used in text and image retrieval by first computing local shape descriptors, and then representing them in a ‘geometric dictionary’ using vector quantization. A major drawback of such approaches is that the dictionary is constructed in an unsupervised manner using clustering, unaware of the last stage of the process (pooling of the local descriptors into a BoF, and comparison of the latter using some metric). In this paper, we replace the clustering with dictionary learning, where every atom acts as a feature, followed by sparse coding and pooling to get the final BoF descriptor. Both the dictionary and the sparse codes can be learned in the supervised regime via bi‐level optimization using a task‐specific objective that promotes invariance desired in the specific application. We show significant performance improvement on several standard shape retrieval benchmarks.

We introduce an efficient computational framework for hashing data belonging to multiple modalities into a single representation space where they become mutually comparable. The proposed approach is based on a novel coupled siamese neural network architecture and allows unified treatment of intra- and inter-modality similarity learning. Unlike existing cross-modality similarity learning approaches, our hashing functions are not limited to binarized linear projections and can assume arbitrarily complex forms. We show experimentally that our method significantly outperforms state-of-the-art hashing approaches on multimedia retrieval tasks.

In this paper we present a framework for real time enhancement of speech signals. Our method leverages a new process-centric approach for sparse and parsimonious models, where the representation pursuit is obtained applying a deterministic function or process rather than solving an optimization problem. We first propose a rank-regularized robust version of non-negative matrix factorization (NMF) for modeling time-frequency representations of speech signals in which the spectral frames are decomposed as sparse linear combinations of atoms of a low-rank dictionary. Then, a parametric family of pursuit processes is derived from the iteration of the proximal descent method for solving this model. We present several experiments showing successful results and the potential of the proposed framework. Incorporating discriminative learning makes the proposed method significantly outperform exact NMF algorithms, with fixed latency and at a fraction of it's computational complexity.

Abstract The use of Laplacian eigenbases has been shown to be fruitful in many computer graphics applications. Today, state‐of‐the‐art approaches to shape analysis, synthesis, and correspondence rely on these natural harmonic bases that allow using classical tools from harmonic analysis on manifolds. However, many applications involving multiple shapes are obstacled by the fact that Laplacian eigenbases computed independently on different shapes are often incompatible with each other. In this paper, we propose the construction of common approximate eigenbases for multiple shapes using approximate joint diagonalization algorithms, taking as input a set of corresponding functions (e.g. indicator functions of stable regions) on the two shapes. We illustrate the benefits of the proposed approach on tasks from shape editing, pose transfer, correspondence, and similarity.

Abstract We present a novel sparse modeling approach to non‐rigid shape matching using only the ability to detect repeatable regions. As the input to our algorithm, we are given only two sets of regions in two shapes; no descriptors are provided so the correspondence between the regions is not know, nor we know how many regions correspond in the two shapes. We show that even with such scarce information, it is possible to establish very accurate correspondence between the shapes by using methods from the field of sparse modeling, being this, the first non‐trivial use of sparse models in shape correspondence. We formulate the problem ofpermuted sparse coding, in which we solve simultaneously for an unknown permutation ordering the regions on two shapes and for an unknown correspondence in functional representation. We also propose a robust variant capable of handling incomplete matches. Numerically, the problem is solved efficiently by alternating the solution of a linear assignment and a sparse coding problem. The proposed methods are evaluated qualitatively and quantitatively on standard benchmarks containing both synthetic and scanned objects.

In this work, we present intrinsic shape context (ISC) descriptors for 3D shapes. We generalize to surfaces the polar sampling of the image domain used in shape contexts: for this purpose, we chart the surface by shooting geodesic outwards from the point being analyzed; `angle' is treated as tantamount to geodesic shooting direction, and radius as geodesic distance. To deal with orientation ambiguity, we exploit properties of the Fourier transform. Our charting method is intrinsic, i.e., invariant to isometric shape transformations. The resulting descriptor is a meta-descriptor that can be applied to any photometric or geometric property field defined on the shape, in particular, we can leverage recent developments in intrinsic shape analysis and construct ISC based on state-of-the-art dense shape descriptors such as heat kernel signatures. Our experiments demonstrate a notable improvement in shape matching on standard benchmarks.

SIFT-like local feature descriptors are ubiquitously employed in computer vision applications such as content-based retrieval, video analysis, copy detection, object recognition, photo tourism, and 3D reconstruction. Feature descriptors can be designed to be invariant to certain classes of photometric and geometric transformations, in particular, affine and intensity scale transformations. However, real transformations that an image can undergo can only be approximately modeled in this way, and thus most descriptors are only approximately invariant in practice. Second, descriptors are usually high dimensional (e.g., SIFT is represented as a 128-dimensional vector). In large-scale retrieval and matching problems, this can pose challenges in storing and retrieving descriptor data. We map the descriptor vectors into the Hamming space in which the Hamming metric is used to compare the resulting representations. This way, we reduce the size of the descriptors by representing them as short binary strings and learn descriptor invariance from examples. We show extensive experimental validation, demonstrating the advantage of the proposed approach.

We introduce an (equi-)affine invariant diffusion geometry by which surfaces that go through squeeze and shear transformations can still be properly analyzed. The definition of an affine invariant metric enables us to construct an invariant Laplacian from which local and global geometric structures are extracted. Applications of the proposed framework demonstrate its power in generalizing and enriching the existing set of tools for shape analysis.

Recent works have shown the use of diffusion geometry for various pattern recognition applications, including nonrigid shape analysis. In this paper, we introduce spectral shape distance as a general framework for distribution-based shape similarity and show that two recent methods for shape similarity due to Rustamov and Mahmoudi and Sapiro are particular cases thereof.

Detection and description of affine-invariant features is a cornerstone component in numerous computer vision applications. In this note, we analyze the notion of maximally stable extremal regions (MSERs) through the prism of the curvature scale space, and conclude that in its original definition, MSER prefers regular (round) regions. Arguing that interesting features in natural images usually have irregular shapes, we propose alternative definitions of MSER which are free of this bias, yet maintain their invariance properties.

Bilateral filter is one of the state-of-the-art methods for noise reduction in images. The plausible visual result the filter produces makes it a common choice for image and video processing applications, yet, its high computational complexity makes a real-time implementation a challenging task. Presented here is a parallel version of the bilateral filter using a lazy sliding window, suitable for SIMD-type architectures.

The computer vision and pattern recognition communities have recently witnessed a surge of feature-based methods in object recognition and image retrieval applications. These methods allow representing images as collections of “visual words” and treat them using text search approaches following the “bag of features” paradigm. In this article, we explore analogous approaches in the 3D world applied to the problem of nonrigid shape retrieval in large databases. Using multiscale diffusion heat kernels as “geometric words,” we construct compact and informative shape descriptors by means of the “bag of features” approach. We also show that considering pairs of “geometric words” (“geometric expressions”) allows creating spatially sensitive bags of features with better discriminative power. Finally, adopting metric learning approaches, we show that shapes can be efficiently represented as binary codes. Our approach achieves state-of-the-art results on the SHREC 2010 large-scale shape retrieval benchmark.

International audience

One of the biggest challenges in non-rigid shape retrieval and comparison is the design of a shape descriptor that would maintain invariance under a wide class of transformations the shape can undergo. Recently, heat kernel signature was introduced as an intrinsic local shape descriptor based on diffusion scale-space analysis. In this paper, we develop a scale-invariant version of the heat kernel descriptor. Our construction is based on a logarithmically sampled scale-space in which shape scaling corresponds, up to a multiplicative constant, to a translation. This translation is undone using the magnitude of the Fourier transform. The proposed scale-invariant local descriptors can be used in the bag-of-features framework for shape retrieval in the presence of transformations such as isometric deformations, missing data, topological noise, and global and local scaling. We get significant performance improvement over state-of-the-art algorithms on recently established non-rigid shape retrieval benchmarks.

We present an efficient O( n ) numerical algorithm for first-order approximation of geodesic distances on geometry images, where n is the number of points on the surface. The structure of our algorithm allows efficient implementation on parallel architectures. Two implementations on a SIMD processor and on a GPU are discussed. Numerical results demonstrate up to four orders of magnitude improvement in execution time compared to the state-of-the-art algorithms.

This paper explores similarity criteria between non-rigid shapes. Broadly speaking, such criteria are divided into intrinsic and extrinsic, the first referring to the metric structure of the objects and the latter to the geometry of the shapes in the Euclidean space. Both criteria have their advantages and disadvantages; extrinsic similarity is sensitive to non-rigid deformations of the shapes, while intrinsic similarity is sensitive to topological noise. Here, we present an approach unifying both criteria in a single distance. Numerical results demonstrate the robustness of our approach in cases where using only extrinsic or intrinsic criteria fail.

Symmetry and self-similarity is the cornerstone of Nature, exhibiting itself through the shapes of natural creations and ubiquitous laws of physics. Since many natural objects are symmetric, the absence of symmetry can often be an indication of some anomaly or abnormal behavior. Therefore, detection of asymmetries is important in numerous practical applications, including crystallography, medical imaging, and face recognition, to mention a few. Conversely, the assumption of underlying shape symmetry can facilitate solutions to many problems in shape reconstruction and analysis. Traditionally, symmetries are described as extrinsic geometric properties of the shape. While being adequate for rigid shapes, such a description is inappropriate for non-rigid ones. Extrinsic symmetry can be broken as a result of shape deformations, while its intrinsic symmetry is preserved. In this paper, we pose the problem of finding intrinsic symmetries of non-rigid shapes and propose an efficient method for their computation.

Addressed here is the problem of constructing and analyzing expression-invariant representations of human faces. We demonstrate and justify experimentally a simple geometric model that allows to describe facial expressions as isometric deformations of the facial surface. The main step in the construction of expression-invariant representation of a face involves embedding of the facial intrinsic geometric structure into some low-dimensional space. We study the influence of the embedding space geometry and dimensionality choice on the representation accuracy and argue that compared to its Euclidean counterpart, spherical embedding leads to notably smaller metric distortions. We experimentally support our claim showing that a smaller embedding error leads to better recognition.

The experience of motion sickness in a virtual environment may be measured through pre and postexperiment self-reported questionnaires such as the Simulator Sickness Questionnaire (SSQ). Although research provides converging evidence that users of virtual environments can experience motion sickness, there have been no controlled studies to determine to what extent the user's subjective response is a demand characteristic resulting from pre and posttest measures. In this study, subjects were given either SSQ's both pre and postvirtual environment immersion, or only postimmersion. This technique tested for contrast effects due to demand characteristics in which administration of the questionnaire itself suggested to the participant that the virtual environment may produce motion sickness. Results indicate that reports of motion sickness after immersion in a virtual environment are much greater when both pre and postquestionnaires are given than when only a posttest questionnaire is used. The implications for assessments of motion sickness in virtual environments are discussed.

Recently, it was proven empirically that facial expressions can be modelled as isometries, that is, geodesic distances on the facial surface were shown to be significantly less sensitive to facial expressions compared to Euclidean ones. Based on this assumption, the 3DFACE face recognition system was built. The system efficiently computes expression invariant signatures based on isometry-invariant representation of the facial surface. One of the crucial steps in the recognition system was embedding of the face geometric structure into a Euclidean (flat) space. Here, we propose to replace the flat embedding by a spherical one to construct isometric invariant representations of the facial image. We refer to these new invariants as spherical canonical images. Compared to its Euclidean counterpart, spherical embedding leads to notably smaller metric distortion. We demonstrate experimentally that representations with lower embedding error lead to better recognition. In order to efficiently compute the invariants we introduce a dissimilarity measure between the spherical canonical images based on the spherical harmonic transform.

We pose the problem of tissue classification in MRI as a blind source separation (BSS) problem and solve it by means of sparse component analysis (SCA). Assuming that most MR images can be sparsely represented, we consider their optimal sparse representation. Sparse components define a physically-meaningful feature space for classification. We demonstrate our approach on simulated and real multi-contrast MRI data. The proposed framework is general in that it is applicable to other modalities of medical imaging as well, whenever the linear mixing model is applicable.

The relative Newton algorithm, previously proposed for quasi-maximum likelihood blind source separation and blind deconvolution of one-dimensional signals is generalized for blind deconvolution of images. Smooth approximation of the absolute value is used as the nonlinear term for sparse sources. In addition, we propose a method of sparsification, which allows blind deconvolution of arbitrary sources, and show how to find optimal sparsifying transformations by supervised learning.

We discuss the synthesis between the 3D and the 2D data in three-dimensional face recognition. We show how to compensate for the illumination and racial expressions using the 3D facial geometry and present the approach of canonical images, which allows us to incorporate geometric information into standard face recognition approaches.

We present an efficient Newton-like algorithm for quasimaximum likelihood (QML) blind deconvolution of images. This algorithm exploits the sparse structure of the Hessian. An optimal distribution-shaping approach by means of sparsification allows one to use simple and convenient sparsity prior for processing of a wide range of natural images. Simulation results demonstrate the efficiency of the proposed method.

We address the problem of blind source separation (BSS) of superimposed images and, in particular, consider the recovery of a scene recorded through a semireflective medium (e.g. glass windshield) from its mixture with a virtual reflected image. We extend the sparse ICA (SPICA) approach to BSS and apply it to the separation of the desired image from the superimposed images, without having any a priori knowledge about its structure and/or statistics. Advances in the SPICA approach are discussed. Simulations and experimental results illustrate the efficiency of the proposed approach, and of its specific implementation in a simple algorithm of a low computational cost. The approach and the algorithm are generic in that they can be adapted and applied to a wide range of BSS problems involving one-dimensional signals or images.

In this paper, we consider the problem of recovery of a scene recorded through a semireflective medium from its mixture with a virtual reflected image using the blind source separation (BSS) framework. We extend the sparse ICA (SPICA) approach and apply it to the separation of the desired image from the superimposed images, without having any a priory knowledge about its structure and/or statistics. Advances in the SPICA approach are discussed. Simulations and experimental results illustrate the efficiency of the proposed approach, and of its specific implementation in a simple algorithm of a low computational cost. The approach and the algorithm are generic and can be adapted and applied to a wide range of BSS problems involving one-dimensional signals or images.

We show an iterative reconstruction framework for diffraction ultrasound tomography. The use of broad-band illumination allows significant reduction of the number of projections compared to straight ray tomography. The proposed algorithm makes use of forward nonuniform fast Fourier transform (NUFFT) for iterative Fourier inversion. Incorporation of total variation regularization allows the reduction of noise and Gibbs phenomena while preserving the edges. The complexity of the NUFFT-based reconstruction is comparable to the frequency-domain interpolation (gridding) algorithm, whereas the reconstruction accuracy (in sense of the L2 and the L(infinity) norm) is better.