Daily Papers

Differentiable architecture search (DARTS) is an effective method for data-driven neural network design based on solving a bilevel optimization problem. Despite its success in many architecture search tasks, there are still some concerns about the accuracy of first-order DARTS and the efficiency of the second-order DARTS. In this paper, we formulate a single level alternative and a relaxed architecture search (RARTS) method that utilizes the whole dataset in architecture learning via both data and network splitting, without involving mixed second derivatives of the corresponding loss functions like DARTS. In our formulation of network splitting, two networks with different but related weights cooperate in search of a shared architecture. The advantage of RARTS over DARTS is justified by a convergence theorem and an analytically solvable model. Moreover, RARTS outperforms DARTS and its variants in accuracy and search efficiency, as shown in adequate experimental results. For the task of searching topological architecture, i.e., the edges and the operations, RARTS obtains a higher accuracy and 60\% reduction of computational cost than second-order DARTS on CIFAR-10. RARTS continues to out-perform DARTS upon transfer to ImageNet and is on par with recent variants of DARTS even though our innovation is purely on the training algorithm without modifying search space. For the task of searching width, i.e., the number of channels in convolutional layers, RARTS also outperforms the traditional network pruning benchmarks. Further experiments on the public architecture search benchmark like NATS-Bench also support the preeminence of RARTS.

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive accuracy, interpretability, and computational efficiency remains a major challenge. In this work, we introduce a novel Graph Neural Network (GNN) architecture that combines compressed higher-order topological signals with standard molecular features. Our approach captures global geometric information while preserving computational tractability and human-interpretable structure. We evaluate our model across a range of benchmarks, from small-molecule datasets to complex material datasets, and demonstrate superior performance using a parameter-efficient architecture. We achieve the best performing results in both accuracy and robustness across almost all benchmarks. We open source all code All code and results can be found on Github https://github.com/rahulkhorana/TFC-PACT-Net.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

We introduce LeapfrogLayers, an invertible neural network architecture that can be trained to efficiently sample the topology of a 2D U(1) lattice gauge theory. We show an improvement in the integrated autocorrelation time of the topological charge when compared with traditional HMC, and look at how different quantities transform under our model. Our implementation is open source, and is publicly available on github at https://github.com/saforem2/l2hmc-qcd.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

Manipulation of elastoplastic objects like dough often involves topological changes such as splitting and merging. The ability to accurately predict these topological changes that a specific action might incur is critical for planning interactions with elastoplastic objects. We present DoughNet, a Transformer-based architecture for handling these challenges, consisting of two components. First, a denoising autoencoder represents deformable objects of varying topology as sets of latent codes. Second, a visual predictive model performs autoregressive set prediction to determine long-horizon geometrical deformation and topological changes purely in latent space. Given a partial initial state and desired manipulation trajectories, it infers all resulting object geometries and topologies at each step. DoughNet thereby allows to plan robotic manipulation; selecting a suited tool, its pose and opening width to recreate robot- or human-made goals. Our experiments in simulated and real environments show that DoughNet is able to significantly outperform related approaches that consider deformation only as geometrical change.

Predicting neural architecture performance is a challenging task and is crucial to neural architecture design and search. Existing approaches either rely on neural performance predictors which are limited to modeling architectures in a predefined design space involving specific sets of operators and connection rules, and cannot generalize to unseen architectures, or resort to zero-cost proxies which are not always accurate. In this paper, we propose GENNAPE, a Generalized Neural Architecture Performance Estimator, which is pretrained on open neural architecture benchmarks, and aims to generalize to completely unseen architectures through combined innovations in network representation, contrastive pretraining, and fuzzy clustering-based predictor ensemble. Specifically, GENNAPE represents a given neural network as a Computation Graph (CG) of atomic operations which can model an arbitrary architecture. It first learns a graph encoder via Contrastive Learning to encourage network separation by topological features, and then trains multiple predictor heads, which are soft-aggregated according to the fuzzy membership of a neural network. Experiments show that GENNAPE pretrained on NAS-Bench-101 can achieve superior transferability to 5 different public neural network benchmarks, including NAS-Bench-201, NAS-Bench-301, MobileNet and ResNet families under no or minimum fine-tuning. We further introduce 3 challenging newly labelled neural network benchmarks: HiAML, Inception and Two-Path, which can concentrate in narrow accuracy ranges. Extensive experiments show that GENNAPE can correctly discern high-performance architectures in these families. Finally, when paired with a search algorithm, GENNAPE can find architectures that improve accuracy while reducing FLOPs on three families.

Current neural architecture search (NAS) strategies focus only on finding a single, good, architecture. They offer little insight into why a specific network is performing well, or how we should modify the architecture if we want further improvements. We propose a Bayesian optimisation (BO) approach for NAS that combines the Weisfeiler-Lehman graph kernel with a Gaussian process surrogate. Our method optimises the architecture in a highly data-efficient manner: it is capable of capturing the topological structures of the architectures and is scalable to large graphs, thus making the high-dimensional and graph-like search spaces amenable to BO. More importantly, our method affords interpretability by discovering useful network features and their corresponding impact on the network performance. Indeed, we demonstrate empirically that our surrogate model is capable of identifying useful motifs which can guide the generation of new architectures. We finally show that our method outperforms existing NAS approaches to achieve the state of the art on both closed- and open-domain search spaces.

This work introduces TopoBenchmarkX, a modular open-source library designed to standardize benchmarking and accelerate research in Topological Deep Learning (TDL). TopoBenchmarkX maps the TDL pipeline into a sequence of independent and modular components for data loading and processing, as well as model training, optimization, and evaluation. This modular organization provides flexibility for modifications and facilitates the adaptation and optimization of various TDL pipelines. A key feature of TopoBenchmarkX is that it allows for the transformation and lifting between topological domains. This enables, for example, to obtain richer data representations and more fine-grained analyses by mapping the topology and features of a graph to higher-order topological domains such as simplicial and cell complexes. The range of applicability of TopoBenchmarkX is demonstrated by benchmarking several TDL architectures for various tasks and datasets.

In the literature, it has been shown that the evolution of the known explicit 3D surface to the target one can be learned from 2D images using the instantaneous flow field, where the known and target 3D surfaces may largely differ in topology. We are interested in capturing 4D shapes whose topology changes largely over time. We encounter that the straightforward extension of the existing 3D-based method to the desired 4D case performs poorly. In this work, we address the challenges in extending 3D neural evolution to 4D under large topological changes by proposing two novel modifications. More precisely, we introduce (i) a new architecture to discretize and encode the deformation and learn the SDF and (ii) a technique to impose the temporal consistency. (iii) Also, we propose a rendering scheme for color prediction based on Gaussian splatting. Furthermore, to facilitate learning directly from 2D images, we propose a learning framework that can disentangle the geometry and appearance from RGB images. This method of disentanglement, while also useful for the 4D evolution problem that we are concentrating on, is also novel and valid for static scenes. Our extensive experiments on various data provide awesome results and, most importantly, open a new approach toward reconstructing challenging scenes with significant topological changes and deformations. Our source code and the dataset are publicly available at https://github.com/insait-institute/N4DE.

The learnability of different neural architectures can be characterized directly by computable measures of data complexity. In this paper, we reframe the problem of architecture selection as understanding how data determines the most expressive and generalizable architectures suited to that data, beyond inductive bias. After suggesting algebraic topology as a measure for data complexity, we show that the power of a network to express the topological complexity of a dataset in its decision region is a strictly limiting factor in its ability to generalize. We then provide the first empirical characterization of the topological capacity of neural networks. Our empirical analysis shows that at every level of dataset complexity, neural networks exhibit topological phase transitions. This observation allowed us to connect existing theory to empirically driven conjectures on the choice of architectures for fully-connected neural networks.

We present SkexGen, a novel autoregressive generative model for computer-aided design (CAD) construction sequences containing sketch-and-extrude modeling operations. Our model utilizes distinct Transformer architectures to encode topological, geometric, and extrusion variations of construction sequences into disentangled codebooks. Autoregressive Transformer decoders generate CAD construction sequences sharing certain properties specified by the codebook vectors. Extensive experiments demonstrate that our disentangled codebook representation generates diverse and high-quality CAD models, enhances user control, and enables efficient exploration of the design space. The code is available at https://samxuxiang.github.io/skexgen.

Recent advances in 4D content generation have attracted increasing attention, yet creating high-quality animated 3D models remains challenging due to the complexity of modeling spatio-temporal distributions and the scarcity of 4D training data. In this paper, we present AnimateAnyMesh, the first feed-forward framework that enables efficient text-driven animation of arbitrary 3D meshes. Our approach leverages a novel DyMeshVAE architecture that effectively compresses and reconstructs dynamic mesh sequences by disentangling spatial and temporal features while preserving local topological structures. To enable high-quality text-conditional generation, we employ a Rectified Flow-based training strategy in the compressed latent space. Additionally, we contribute the DyMesh Dataset, containing over 4M diverse dynamic mesh sequences with text annotations. Experimental results demonstrate that our method generates semantically accurate and temporally coherent mesh animations in a few seconds, significantly outperforming existing approaches in both quality and efficiency. Our work marks a substantial step forward in making 4D content creation more accessible and practical. All the data, code, and models will be open-released.

We present VecFusion, a new neural architecture that can generate vector fonts with varying topological structures and precise control point positions. Our approach is a cascaded diffusion model which consists of a raster diffusion model followed by a vector diffusion model. The raster model generates low-resolution, rasterized fonts with auxiliary control point information, capturing the global style and shape of the font, while the vector model synthesizes vector fonts conditioned on the low-resolution raster fonts from the first stage. To synthesize long and complex curves, our vector diffusion model uses a transformer architecture and a novel vector representation that enables the modeling of diverse vector geometry and the precise prediction of control points. Our experiments show that, in contrast to previous generative models for vector graphics, our new cascaded vector diffusion model generates higher quality vector fonts, with complex structures and diverse styles.

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

We present Neural Autoregressive Distribution Estimation (NADE) models, which are neural network architectures applied to the problem of unsupervised distribution and density estimation. They leverage the probability product rule and a weight sharing scheme inspired from restricted Boltzmann machines, to yield an estimator that is both tractable and has good generalization performance. We discuss how they achieve competitive performance in modeling both binary and real-valued observations. We also present how deep NADE models can be trained to be agnostic to the ordering of input dimensions used by the autoregressive product rule decomposition. Finally, we also show how to exploit the topological structure of pixels in images using a deep convolutional architecture for NADE.

The Transformer architecture has become a cornerstone of modern artificial intelligence, but its core self-attention mechanism suffers from a complexity bottleneck that scales quadratically with sequence length, severely limiting its application in long-sequence tasks. To address this challenge, existing linear attention methods typically sacrifice model performance by relying on data-agnostic kernel approximations or restrictive context selection. This paper returns to the first principles of connectionism, starting from the topological structure of information flow, to introduce a novel linear attention architecture-TLinFormer. By reconfiguring neuron connection patterns, TLinFormer achieves strict linear complexity while computing exact attention scores and ensuring information flow remains aware of the full historical context. This design aims to bridge the performance gap prevalent between existing efficient attention methods and standard attention. Through a series of experiments, we systematically evaluate the performance of TLinFormer against a standard Transformer baseline on long-sequence inference tasks. The results demonstrate that TLinFormer exhibits overwhelming advantages in key metrics such as inference latency, KV cache efficiency, memory footprint, and overall speedup.

Accurate reconstruction of both the geometric and topological details of a 3D object from a single 2D image embodies a fundamental challenge in computer vision. Existing explicit/implicit solutions to this problem struggle to recover self-occluded geometry and/or faithfully reconstruct topological shape structures. To resolve this dilemma, we introduce LIST, a novel neural architecture that leverages local and global image features to accurately reconstruct the geometric and topological structure of a 3D object from a single image. We utilize global 2D features to predict a coarse shape of the target object and then use it as a base for higher-resolution reconstruction. By leveraging both local 2D features from the image and 3D features from the coarse prediction, we can predict the signed distance between an arbitrary point and the target surface via an implicit predictor with great accuracy. Furthermore, our model does not require camera estimation or pixel alignment. It provides an uninfluenced reconstruction from the input-view direction. Through qualitative and quantitative analysis, we show the superiority of our model in reconstructing 3D objects from both synthetic and real-world images against the state of the art.

Characteristic classes, which are abstract topological invariants associated with vector bundles, have become an important notion in modern physics with surprising real-world consequences. As a representative example, the incredible properties of topological insulators, which are insulators in their bulk but conductors on their surface, can be completely characterized by a specific characteristic class associated with their electronic band structure, the first Chern class. Given their importance to next generation computing and the computational challenge of calculating them using first-principles approaches, there is a need to develop machine learning approaches to predict the characteristic classes associated with a material system. To aid in this program we introduce the {Haldane bundle dataset}, which consists of synthetically generated complex line bundles on the 2-torus. We envision this dataset, which is not as challenging as noisy and sparsely measured real-world datasets but (as we show) still difficult for off-the-shelf architectures, to be a testing ground for architectures that incorporate the rich topological and geometric priors underlying characteristic classes.

While many approaches to make neural networks more fathomable have been proposed, they are restricted to interrogating the network with input data. Measures for characterizing and monitoring structural properties, however, have not been developed. In this work, we propose neural persistence, a complexity measure for neural network architectures based on topological data analysis on weighted stratified graphs. To demonstrate the usefulness of our approach, we show that neural persistence reflects best practices developed in the deep learning community such as dropout and batch normalization. Moreover, we derive a neural persistence-based stopping criterion that shortens the training process while achieving comparable accuracies as early stopping based on validation loss.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

Massively multilingual models for neural machine translation (NMT) are theoretically attractive, but often underperform bilingual models and deliver poor zero-shot translations. In this paper, we explore ways to improve them. We argue that multilingual NMT requires stronger modeling capacity to support language pairs with varying typological characteristics, and overcome this bottleneck via language-specific components and deepening NMT architectures. We identify the off-target translation issue (i.e. translating into a wrong target language) as the major source of the inferior zero-shot performance, and propose random online backtranslation to enforce the translation of unseen training language pairs. Experiments on OPUS-100 (a novel multilingual dataset with 100 languages) show that our approach substantially narrows the performance gap with bilingual models in both one-to-many and many-to-many settings, and improves zero-shot performance by ~10 BLEU, approaching conventional pivot-based methods.

We introduce DivEMT, the first publicly available post-editing study of Neural Machine Translation (NMT) over a typologically diverse set of target languages. Using a strictly controlled setup, 18 professional translators were instructed to translate or post-edit the same set of English documents into Arabic, Dutch, Italian, Turkish, Ukrainian, and Vietnamese. During the process, their edits, keystrokes, editing times and pauses were recorded, enabling an in-depth, cross-lingual evaluation of NMT quality and post-editing effectiveness. Using this new dataset, we assess the impact of two state-of-the-art NMT systems, Google Translate and the multilingual mBART-50 model, on translation productivity. We find that post-editing is consistently faster than translation from scratch. However, the magnitude of productivity gains varies widely across systems and languages, highlighting major disparities in post-editing effectiveness for languages at different degrees of typological relatedness to English, even when controlling for system architecture and training data size. We publicly release the complete dataset including all collected behavioral data, to foster new research on the translation capabilities of NMT systems for typologically diverse languages.

Chomsky and others have very directly claimed that large language models (LLMs) are equally capable of learning languages that are possible and impossible for humans to learn. However, there is very little published experimental evidence to support such a claim. Here, we develop a set of synthetic impossible languages of differing complexity, each designed by systematically altering English data with unnatural word orders and grammar rules. These languages lie on an impossibility continuum: at one end are languages that are inherently impossible, such as random and irreversible shuffles of English words, and on the other, languages that may not be intuitively impossible but are often considered so in linguistics, particularly those with rules based on counting word positions. We report on a wide range of evaluations to assess the capacity of GPT-2 small models to learn these uncontroversially impossible languages, and crucially, we perform these assessments at various stages throughout training to compare the learning process for each language. Our core finding is that GPT-2 struggles to learn impossible languages when compared to English as a control, challenging the core claim. More importantly, we hope our approach opens up a productive line of inquiry in which different LLM architectures are tested on a variety of impossible languages in an effort to learn more about how LLMs can be used as tools for these cognitive and typological investigations.