Graham W. Taylor

Joakim Bruslund Haurum, Sergio Escalera, Graham W. Taylor et al.

Since the introduction of the Vision Transformer (ViT), researchers have sought to make ViTs more efficient by removing redundant information in the processed tokens. While different methods have been explored to achieve this goal, we still lack understanding of the resulting reduction patterns and how those patterns differ across token reduction methods and datasets. To close this gap, we set out to understand the reduction patterns of 10 different token reduction methods using four image classification datasets. By systematically comparing these methods on the different classification tasks, we find that the Top-K pruning method is a surprisingly strong baseline. Through in-depth analysis of the different methods, we determine that: the reduction patterns are generally not consistent when varying the capacity of the backbone model, the reduction patterns of pruning-based methods significantly differ from fixed radial patterns, and the reduction patterns of pruning-based methods are correlated across classification datasets. Finally we report that the similarity of reduction patterns is a moderate-to-strong proxy for model performance. Project page at https://vap.aau.dk/tokens.

Neelu Madan, Àlex Pujol, Andreas Møgelmose et al.

Slot attention has emerged as a powerful framework for unsupervised object-centric learning, decomposing visual scenes into a small set of compact vector representations called \emph{slots}, each capturing a distinct region or object. However, these slots are learned in Euclidean space, which provides no geometric inductive bias for the hierarchical relationships that naturally structure visual scenes. In this work, we propose a simple post-hoc pipeline to project Euclidean slot embeddings onto the Lorentz hyperboloid of hyperbolic space, without modifying the underlying training pipeline. We construct five-level visual hierarchies directly from slot attention masks and analyse whether hyperbolic geometry reveals latent hierarchical structure that remains invisible in Euclidean space. Integrating our pipeline with SPOT (images), VideoSAUR (video), and SlotContrast (video), We find that hyperbolic projection exposes a consistent scene-level to object-level organisation, where coarse slots occupy greater manifold depth than fine slots, which is absent in Euclidean space. We further identify a "curvature--task tradeoff": low curvature ($c{=}0.2$) matches or outperforms Euclidean on parent slot retrieval, while moderate curvature ($c{=}0.5$) achieves better inter-level separation. Together, these findings suggest that slot representations already encode latent hierarchy that hyperbolic geometry reveals, motivating end-to-end hyperbolic training as a natural next step. Code and models are available at \href{https://github.com/NeeluMadan/HHS}{github.com/NeeluMadan/HHS}.

Shaina Raza, Iuliia Zarubiieva, Ahmed Y. Radwan et al.

Open-source AI is scaling rapidly, and model hubs now host millions of artifacts. Each foundation model can spawn large numbers of fine-tunes, adapters, quantizations, merges, and forks. We take the position that compute efficiency alone is insufficient for sustainability in open-source AI: lower per-run costs can accelerate experimentation and deployment, increasing aggregate environmental footprint unless impacts are measurable and comparable across derivative lineages. However, the energy use, water consumption, and emissions of these derivative lineages are rarely measured or disclosed in a consistent, comparable manner, leaving ecosystem-level impact largely invisible. We argue that sustainable open-source AI requires coordination infrastructure that tracks impacts across model lineages, not only base models. We propose Data and Impact Accounting (DIA), a lightweight, non-restrictive transparency layer that (i) standardizes carbon and water reporting metadata, (ii) integrates low-friction measurement into common training and inference pipelines, and (iii) aggregates reports through public dashboards to summarize cumulative impacts across releases and derivatives. DIA makes derivative costs visible and supports ecosystem-level accountability while preserving openness. https://vectorinstitute.github.io/ai-impact-accounting/

Pablo Millan Arias, Niousha Sadjadi, Monireh Safari et al.

In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of life. Although machine learning algorithms specifically designed for the analysis of DNA barcodes are becoming more popular, most existing methodologies rely on generic supervised training algorithms. We introduce BarcodeBERT, a family of models tailored to biodiversity analysis and trained exclusively on data from a reference library of 1.5M invertebrate DNA barcodes. We compared the performance of BarcodeBERT on taxonomic identification tasks against a spectrum of machine learning approaches including supervised training of classical neural architectures and fine-tuning of general DNA foundation models. Our self-supervised pretraining strategies on domain-specific data outperform fine-tuned foundation models, especially in identification tasks involving lower taxa such as genera and species. We also compared BarcodeBERT with BLAST, one of the most widely used bioinformatics tools for sequence searching, and found that our method matched BLAST's performance in species-level classification while being 55 times faster. Our analysis of masking and tokenization strategies also provides practical guidance for building customized DNA language models, emphasizing the importance of aligning model training strategies with dataset characteristics and domain knowledge. The code repository is available at https://github.com/bioscan-ml/BarcodeBERT.

Zahra Gharaee, ZeMing Gong, Nicholas Pellegrino et al.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Cong Wei, Brendan Duke, Ruowei Jiang et al.

Vision Transformers (ViT) have shown their competitive advantages performance-wise compared to convolutional neural networks (CNNs) though they often come with high computational costs. To this end, previous methods explore different attention patterns by limiting a fixed number of spatially nearby tokens to accelerate the ViT's multi-head self-attention (MHSA) operations. However, such structured attention patterns limit the token-to-token connections to their spatial relevance, which disregards learned semantic connections from a full attention mask. In this work, we propose a novel approach to learn instance-dependent attention patterns, by devising a lightweight connectivity predictor module to estimate the connectivity score of each pair of tokens. Intuitively, two tokens have high connectivity scores if the features are considered relevant either spatially or semantically. As each token only attends to a small number of other tokens, the binarized connectivity masks are often very sparse by nature and therefore provide the opportunity to accelerate the network via sparse computations. Equipped with the learned unstructured attention pattern, sparse attention ViT (Sparsifiner) produces a superior Pareto-optimal trade-off between FLOPs and top-1 accuracy on ImageNet compared to token sparsity. Our method reduces 48% to 69% FLOPs of MHSA while the accuracy drop is within 0.4%. We also show that combining attention and token sparsity reduces ViT FLOPs by over 60%.

Mingjie Wang, Yande Li, Jun Zhou et al.

The class-agnostic counting (CAC) problem has caught increasing attention recently due to its wide societal applications and arduous challenges. To count objects of different categories, existing approaches rely on user-provided exemplars, which is hard-to-obtain and limits their generality. In this paper, we aim to empower the framework to recognize adaptive exemplars within the whole images. A zero-shot Generalized Counting Network (GCNet) is developed, which uses a pseudo-Siamese structure to automatically and effectively learn pseudo exemplar clues from inherent repetition patterns. In addition, a weakly-supervised scheme is presented to reduce the burden of laborious density maps required by all contemporary CAC models, allowing GCNet to be trained using count-level supervisory signals in an end-to-end manner. Without providing any spatial location hints, GCNet is capable of adaptively capturing them through a carefully-designed self-similarity learning strategy. Extensive experiments and ablation studies on the prevailing benchmark FSC147 for zero-shot CAC demonstrate the superiority of our GCNet. It performs on par with existing exemplar-dependent methods and shows stunning cross-dataset generality on crowd-specific datasets, e.g., ShanghaiTech Part A, Part B and UCF_QNRF.

Kevin Kasa, Graham W. Taylor

Conformal prediction has emerged as a rigorous means of providing deep learning models with reliable uncertainty estimates and safety guarantees. Yet, its performance is known to degrade under distribution shift and long-tailed class distributions, which are often present in real world applications. Here, we characterize the performance of several post-hoc and training-based conformal prediction methods under these settings, providing the first empirical evaluation on large-scale datasets and models. We show that across numerous conformal methods and neural network families, performance greatly degrades under distribution shifts violating safety guarantees. Similarly, we show that in long-tailed settings the guarantees are frequently violated on many classes. Understanding the limitations of these methods is necessary for deployment in real world and safety-critical applications.

Mohammed Adnan, Yani Ioannou, Chuan-Yung Tsai et al.

The failure of deep neural networks to generalize to out-of-distribution data is a well-known problem and raises concerns about the deployment of trained networks in safety-critical domains such as healthcare, finance and autonomous vehicles. We study a particular kind of distribution shift $\unicode{x2013}$ shortcuts or spurious correlations in the training data. Shortcut learning is often only exposed when models are evaluated on real-world data that does not contain the same spurious correlations, posing a serious dilemma for AI practitioners to properly assess the effectiveness of a trained model for real-world applications. In this work, we propose to use the mutual information (MI) between the learned representation and the input as a metric to find where in training, the network latches onto shortcuts. Experiments demonstrate that MI can be used as a domain-agnostic metric for monitoring shortcut learning.

Joakim Bruslund Haurum, Sergio Escalera, Graham W. Taylor et al.

We present Agglomerative Token Clustering (ATC), a novel token merging method that consistently outperforms previous token merging and pruning methods across image classification, image synthesis, and object detection & segmentation tasks. ATC merges clusters through bottom-up hierarchical clustering, without the introduction of extra learnable parameters. We find that ATC achieves state-of-the-art performance across all tasks, and can even perform on par with prior state-of-the-art when applied off-the-shelf, i.e. without fine-tuning. ATC is particularly effective when applied with low keep rates, where only a small fraction of tokens are kept and retaining task performance is especially difficult.

Angus Galloway, Anna Golubeva, Mahmoud Salem et al.

Estimating the Generalization Error (GE) of Deep Neural Networks (DNNs) is an important task that often relies on availability of held-out data. The ability to better predict GE based on a single training set may yield overarching DNN design principles to reduce a reliance on trial-and-error, along with other performance assessment advantages. In search of a quantity relevant to GE, we investigate the Mutual Information (MI) between the input and final layer representations, using the infinite-width DNN limit to bound MI. An existing input compression-based GE bound is used to link MI and GE. To the best of our knowledge, this represents the first empirical study of this bound. In our attempt to empirically falsify the theoretical bound, we find that it is often tight for best-performing models. Furthermore, it detects randomization of training labels in many cases, reflects test-time perturbation robustness, and works well given only few training samples. These results are promising given that input compression is broadly applicable where MI can be estimated with confidence.

Rishika Bhagwatkar, Kevin Kasa, Abhay Puri et al.

AI agents are vulnerable to indirect prompt injection attacks, where malicious instructions embedded in external content or tool outputs cause unintended or harmful behavior. Inspired by the well-established concept of firewalls, we show that a simple, modular, and model-agnostic defense operating at the agent--tool interface achieves perfect security with high utility across all four public benchmarks: AgentDojo, Agent Security Bench, InjecAgent and tau-Bench, while achieving a state-of-the-art security--utility tradeoff compared to prior results. Specifically, we employ two firewalls: a Tool-Input Firewall (Minimizer) and a Tool-Output Firewall (Sanitizer). Unlike prior complex approaches, this defense makes minimal assumptions about the agent and can be deployed out of the box. This makes it highly generalizable while maintaining strong performance without compromising utility. Our analysis also reveals critical limitations in these existing benchmarks, including flawed success metrics, implementation bugs, and most importantly, weak attacks, hindering progress. To address this, we present targeted fixes to these issues for AgentDojo and Agent Security Bench, and propose best practices for more robust benchmark design. Moreover, we introduce a three-stage attack strategy that cascades standard prompt injection attacks, second-order attacks, and adaptive attacks to evaluate the robustness beyond existing attacks. Overall, our work shows that existing agentic security benchmarks are easily saturated by a simple approach and highlights the need for stronger benchmarks with carefully chosen evaluation metrics and strong adaptive attacks.

Eu Wern Teh, Graham W. Taylor

We consider annotation efficient learning in Digital Pathology (DP), where expert annotations are expensive and thus scarce. We explore the impact of image and input resolution on DP patch classification performance. We use two cancer patch classification datasets PCam and CRC, to validate the results of our study. Our experiments show that patch classification performance can be improved by manipulating both the image and input resolution in annotation-scarce and annotation-rich environments. We show a positive correlation between the image and input resolution and the patch classification accuracy on both datasets. By exploiting the image and input resolution, our final model trained on < 1% of data performs equally well compared to the model trained on 100% of data in the original image resolution on the PCam dataset.

Juan Carrasquilla, Mohamed Hibat-Allah, Estelle Inack et al.

Binary neural networks, i.e., neural networks whose parameters and activations are constrained to only two possible values, offer a compelling avenue for the deployment of deep learning models on energy- and memory-limited devices. However, their training, architectural design, and hyperparameter tuning remain challenging as these involve multiple computationally expensive combinatorial optimization problems. Here we introduce quantum hypernetworks as a mechanism to train binary neural networks on quantum computers, which unify the search over parameters, hyperparameters, and architectures in a single optimization loop. Through classical simulations, we demonstrate that our approach effectively finds optimal parameters, hyperparameters and architectural choices with high probability on classification problems including a two-dimensional Gaussian dataset and a scaled-down version of the MNIST handwritten digits. We represent our quantum hypernetworks as variational quantum circuits, and find that an optimal circuit depth maximizes the probability of finding performant binary neural networks. Our unified approach provides an immense scope for other applications in the field of machine learning.

Tiancheng Gao, Scott C. Lowe, Brendan Furneaux et al.

Accurate taxonomic classification from DNA barcodes is a cornerstone of global biodiversity monitoring, yet fungi present extreme challenges due to sparse labelling and long-tailed taxa distributions. Conventional supervised learning methods often falter in this domain, struggling to generalize to unseen species and to capture the hierarchical nature of the data. To address these limitations, we introduce BarcodeMamba+, a foundation model for fungal barcode classification built on a powerful and efficient state-space model architecture. We employ a pretrain and fine-tune paradigm, which utilizes partially labelled data and we demonstrate this is substantially more effective than traditional fully-supervised methods in this data-sparse environment. During fine-tuning, we systematically integrate and evaluate a suite of enhancements--including hierarchical label smoothing, a weighted loss function, and a multi-head output layer from MycoAI--to specifically tackle the challenges of fungal taxonomy. Our experiments show that each of these components yields significant performance gains. On a challenging fungal classification benchmark with distinct taxonomic distribution shifts from the broad training set, our final model outperforms a range of existing methods across all taxonomic levels. Our work provides a powerful new tool for genomics-based biodiversity research and establishes an effective and scalable training paradigm for this challenging domain. Our code is publicly available at https://github.com/bioscan-ml/BarcodeMamba.

Tiancheng Gao, Graham W. Taylor

DNA barcodes are crucial in biodiversity analysis for building automatic identification systems that recognize known species and discover unseen species. Unlike human genome modeling, barcode-based invertebrate identification poses challenges in the vast diversity of species and taxonomic complexity. Among Transformer-based foundation models, BarcodeBERT excelled in species-level identification of invertebrates, highlighting the effectiveness of self-supervised pretraining on barcode-specific datasets. Recently, structured state space models (SSMs) have emerged, with a time complexity that scales sub-quadratically with the context length. SSMs provide an efficient parameterization of sequence modeling relative to attention-based architectures. Given the success of Mamba and Mamba-2 in natural language, we designed BarcodeMamba, a performant and efficient foundation model for DNA barcodes in biodiversity analysis. We conducted a comprehensive ablation study on the impacts of self-supervised training and tokenization methods, and compared both versions of Mamba layers in terms of expressiveness and their capacity to identify "unseen" species held back from training. Our study shows that BarcodeMamba has better performance than BarcodeBERT even when using only 8.3% as many parameters, and improves accuracy to 99.2% on species-level accuracy in linear probing without fine-tuning for "seen" species. In our scaling study, BarcodeMamba with 63.6% of BarcodeBERT's parameters achieved 70.2% genus-level accuracy in 1-nearest neighbor (1-NN) probing for unseen species. The code repository to reproduce our experiments is available at https://github.com/bioscan-ml/BarcodeMamba.

Scott C. Lowe, Anthony Fuller, Sageev Oore et al.

The landscape of self-supervised learning (SSL) is currently dominated by generative approaches (e.g., MAE) that reconstruct raw low-level data, and predictive approaches (e.g., I-JEPA) that predict high-level abstract embeddings. While generative methods provide strong grounding, they are computationally inefficient for high-redundancy modalities like imagery, and their training objective does not prioritize learning high-level, conceptual features. Conversely, predictive methods often suffer from training instability due to their reliance on the non-stationary targets of final-layer self-distillation. We introduce Bootleg, a method that bridges this divide by tasking the model with predicting latent representations from multiple hidden layers of a teacher network. This hierarchical objective forces the model to capture features at varying levels of abstraction simultaneously. We demonstrate that Bootleg significantly outperforms comparable baselines (+10% over I-JEPA) on classification of ImageNet-1K and iNaturalist-21, and semantic segmentation of ADE20K and Cityscapes.

Michal Lisicki, Mihai Nica, Graham W. Taylor

We introduce a novel approach for batch selection in Stochastic Gradient Descent (SGD) training, leveraging combinatorial bandit algorithms. Our methodology focuses on optimizing the learning process in the presence of label noise, a prevalent issue in real-world datasets. Experimental evaluations on the CIFAR-10 dataset reveal that our approach consistently outperforms existing methods across various levels of label corruption. Importantly, we achieve this superior performance without incurring the computational overhead commonly associated with auxiliary neural network models. This work presents a balanced trade-off between computational efficiency and model efficacy, offering a scalable solution for complex machine learning applications.

Zahra Gharaee, Scott C. Lowe, ZeMing Gong et al.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, geographical, and size information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at https://github.com/bioscan-ml/BIOSCAN-5M.

Scott C. Lowe, Joakim Bruslund Haurum, Sageev Oore et al.

Can pretrained models generalize to new datasets without any retraining? We deploy pretrained image models on datasets they were not trained for, and investigate whether their embeddings form meaningful clusters. Our suite of benchmarking experiments use encoders pretrained solely on ImageNet-1k with either supervised or self-supervised training techniques, deployed on image datasets that were not seen during training, and clustered with conventional clustering algorithms. This evaluation provides new insights into the embeddings of self-supervised models, which prioritize different features to supervised models. Supervised encoders typically offer more utility than SSL encoders within the training domain, and vice-versa far outside of it, however, fine-tuned encoders demonstrate the opposite trend. Clustering provides a way to evaluate the utility of self-supervised learned representations orthogonal to existing methods such as kNN. Additionally, we find the silhouette score when measured in a UMAP-reduced space is highly correlated with clustering performance, and can therefore be used as a proxy for clustering performance on data with no ground truth labels. Our code implementation is available at \url{https://github.com/scottclowe/zs-ssl-clustering/}.

Rylee Thompson, Boris Knyazev, Elahe Ghalebi et al.

In image generation, generative models can be evaluated naturally by visually inspecting model outputs. However, this is not always the case for graph generative models (GGMs), making their evaluation challenging. Currently, the standard process for evaluating GGMs suffers from three critical limitations: i) it does not produce a single score which makes model selection challenging, ii) in many cases it fails to consider underlying edge and node features, and iii) it is prohibitively slow to perform. In this work, we mitigate these issues by searching for scalar, domain-agnostic, and scalable metrics for evaluating and ranking GGMs. To this end, we study existing GGM metrics and neural-network-based metrics emerging from generative models of images that use embeddings extracted from a task-specific network. Motivated by the power of certain Graph Neural Networks (GNNs) to extract meaningful graph representations without any training, we introduce several metrics based on the features extracted by an untrained random GNN. We design experiments to thoroughly test metrics on their ability to measure the diversity and fidelity of generated graphs, as well as their sample and computational efficiency. Depending on the quantity of samples, we recommend one of two random-GNN-based metrics that we show to be more expressive than pre-existing metrics. While we focus on applying these metrics to GGM evaluation, in practice this enables the ability to easily compute the dissimilarity between any two sets of graphs regardless of domain. Our code is released at: https://github.com/uoguelph-mlrg/GGM-metrics.

Rohit Saha, Brendan Duke, Florian Shkurti et al.

Hairstyle transfer is challenging due to hair structure differences in the source and target hair. Therefore, we propose Latent Optimization of Hairstyles via Orthogonalization (LOHO), an optimization-based approach using GAN inversion to infill missing hair structure details in latent space during hairstyle transfer. Our approach decomposes hair into three attributes: perceptual structure, appearance, and style, and includes tailored losses to model each of these attributes independently. Furthermore, we propose two-stage optimization and gradient orthogonalization to enable disentangled latent space optimization of our hair attributes. Using LOHO for latent space manipulation, users can synthesize novel photorealistic images by manipulating hair attributes either individually or jointly, transferring the desired attributes from reference hairstyles. LOHO achieves a superior FID compared with the current state-of-the-art (SOTA) for hairstyle transfer. Additionally, LOHO preserves the subject's identity comparably well according to PSNR and SSIM when compared to SOTA image embedding pipelines. Code is available at https://github.com/dukebw/LOHO.

Brendan Duke, Abdalla Ahmed, Christian Wolf et al.

In this paper we introduce a Transformer-based approach to video object segmentation (VOS). To address compounding error and scalability issues of prior work, we propose a scalable, end-to-end method for VOS called Sparse Spatiotemporal Transformers (SST). SST extracts per-pixel representations for each object in a video using sparse attention over spatiotemporal features. Our attention-based formulation for VOS allows a model to learn to attend over a history of multiple frames and provides suitable inductive bias for performing correspondence-like computations necessary for solving motion segmentation. We demonstrate the effectiveness of attention-based over recurrent networks in the spatiotemporal domain. Our method achieves competitive results on YouTube-VOS and DAVIS 2017 with improved scalability and robustness to occlusions compared with the state of the art. Code is available at https://github.com/dukebw/SSTVOS.

Rylee Thompson, Elahe Ghalebi, Terrance DeVries et al.

Generative models are now used to create a variety of high-quality digital artifacts. Yet their use in designing physical objects has received far less attention. In this paper, we advocate for the construction toy, LEGO, as a platform for developing generative models of sequential assembly. We develop a generative model based on graph-structured neural networks that can learn from human-built structures and produce visually compelling designs. Our code is released at: https://github.com/uoguelph-mlrg/GenerativeLEGO.

Nolan Dey, Eric Taylor, Alexander Wong et al.

High quality explanations of neural networks (NNs) should exhibit two key properties. Completeness ensures that they accurately reflect a network's function and interpretability makes them understandable to humans. Many existing methods provide explanations of individual neurons within a network. In this work we provide evidence that for AlexNet pretrained on ImageNet, neuron-based explanation methods sacrifice both completeness and interpretability compared to activation principal components. Neurons are a poor basis for AlexNet embeddings because they don't account for the distributed nature of these representations. By examining two quantitative measures of completeness and conducting a user study to measure interpretability, we show the most important principal components provide more complete and interpretable explanations than the most important neurons. Much of the activation variance may be explained by examining relatively few high-variance PCs, as opposed to studying every neuron. These principal components also strongly affect network function, and are significantly more interpretable than neurons. Our findings suggest that explanation methods for networks like AlexNet should avoid using neurons as a basis for embeddings and instead choose a basis, such as principal components, which accounts for the high dimensional and distributed nature of a network's internal representations. Interactive demo and code available at https://ndey96.github.io/neuron-explanations-sacrifice.

Terrance DeVries, Michal Drozdzal, Graham W. Taylor

Recent advances in Generative Adversarial Networks (GANs) have led to their widespread adoption for the purposes of generating high quality synthetic imagery. While capable of generating photo-realistic images, these models often produce unrealistic samples which fall outside of the data manifold. Several recently proposed techniques attempt to avoid spurious samples, either by rejecting them after generation, or by truncating the model's latent space. While effective, these methods are inefficient, as a large fraction of training time and model capacity are dedicated towards samples that will ultimately go unused. In this work we propose a novel approach to improve sample quality: altering the training dataset via instance selection before model training has taken place. By refining the empirical data distribution before training, we redirect model capacity towards high-density regions, which ultimately improves sample fidelity, lowers model capacity requirements, and significantly reduces training time. Code is available at https://github.com/uoguelph-mlrg/instance_selection_for_gans.

Terrance DeVries, Adriana Romero, Luis Pineda et al.

Conditional Generative Adversarial Networks (cGANs) are finding increasingly widespread use in many application domains. Despite outstanding progress, quantitative evaluation of such models often involves multiple distinct metrics to assess different desirable properties, such as image quality, conditional consistency, and intra-conditioning diversity. In this setting, model benchmarking becomes a challenge, as each metric may indicate a different "best" model. In this paper, we propose the Frechet Joint Distance (FJD), which is defined as the Frechet distance between joint distributions of images and conditioning, allowing it to implicitly capture the aforementioned properties in a single metric. We conduct proof-of-concept experiments on a controllable synthetic dataset, which consistently highlight the benefits of FJD when compared to currently established metrics. Moreover, we use the newly introduced metric to compare existing cGAN-based models for a variety of conditioning modalities (e.g. class labels, object masks, bounding boxes, images, and text captions). We show that FJD can be used as a promising single metric for cGAN benchmarking and model selection. Code can be found at https://github.com/facebookresearch/fjd.

Boris Knyazev, Graham W. Taylor, Mohamed R. Amer

We aim to better understand attention over nodes in graph neural networks (GNNs) and identify factors influencing its effectiveness. We particularly focus on the ability of attention GNNs to generalize to larger, more complex or noisy graphs. Motivated by insights from the work on Graph Isomorphism Networks, we design simple graph reasoning tasks that allow us to study attention in a controlled environment. We find that under typical conditions the effect of attention is negligible or even harmful, but under certain conditions it provides an exceptional gain in performance of more than 60% in some of our classification tasks. Satisfying these conditions in practice is challenging and often requires optimal initialization or supervised training of attention. We propose an alternative recipe and train attention in a weakly-supervised fashion that approaches the performance of supervised models, and, compared to unsupervised models, improves results on several synthetic as well as real datasets. Source code and datasets are available at https://github.com/bknyaz/graph_attention_pool.

Fabien Baradel, Christian Wolf, Julien Mille et al.

We propose a method for human activity recognition from RGB data that does not rely on any pose information during test time and does not explicitly calculate pose information internally. Instead, a visual attention module learns to predict glimpse sequences in each frame. These glimpses correspond to interest points in the scene that are relevant to the classified activities. No spatial coherence is forced on the glimpse locations, which gives the module liberty to explore different points at each frame and better optimize the process of scrutinizing visual information. Tracking and sequentially integrating this kind of unstructured data is a challenge, which we address by separating the set of glimpses from a set of recurrent tracking/recognition workers. These workers receive glimpses, jointly performing subsequent motion tracking and activity prediction. The glimpses are soft-assigned to the workers, optimizing coherence of the assignments in space, time and feature space using an external memory module. No hard decisions are taken, i.e. each glimpse point is assigned to all existing workers, albeit with different importance. Our methods outperform state-of-the-art methods on the largest human activity recognition dataset available to-date; NTU RGB+D Dataset, and on a smaller human action recognition dataset Northwestern-UCLA Multiview Action 3D Dataset. Our code is publicly available at https://github.com/fabienbaradel/glimpse_clouds.

Terrance DeVries, Graham W. Taylor

Convolutional neural networks are capable of learning powerful representational spaces, which are necessary for tackling complex learning tasks. However, due to the model capacity required to capture such representations, they are often susceptible to overfitting and therefore require proper regularization in order to generalize well. In this paper, we show that the simple regularization technique of randomly masking out square regions of input during training, which we call cutout, can be used to improve the robustness and overall performance of convolutional neural networks. Not only is this method extremely easy to implement, but we also demonstrate that it can be used in conjunction with existing forms of data augmentation and other regularizers to further improve model performance. We evaluate this method by applying it to current state-of-the-art architectures on the CIFAR-10, CIFAR-100, and SVHN datasets, yielding new state-of-the-art results of 2.56%, 15.20%, and 1.30% test error respectively. Code is available at https://github.com/uoguelph-mlrg/Cutout

He Ma, Fei Mao, Graham W. Taylor

We develop a scalable and extendable training framework that can utilize GPUs across nodes in a cluster and accelerate the training of deep learning models based on data parallelism. Both synchronous and asynchronous training are implemented in our framework, where parameter exchange among GPUs is based on CUDA-aware MPI. In this report, we analyze the convergence and capability of the framework to reduce training time when scaling the synchronous training of AlexNet and GoogLeNet from 2 GPUs to 8 GPUs. In addition, we explore novel ways to reduce the communication overhead caused by exchanging parameters. Finally, we release the framework as open-source for further research on distributed deep learning

Akshita Gupta, Gaurav Mittal, Ahmed Magooda et al.

Temporal Action Localization (TAL) involves localizing and classifying action snippets in an untrimmed video. The emergence of large video foundation models has led RGB-only video backbones to outperform previous methods needing both RGB and optical flow modalities. Leveraging these large models is often limited to training only the TAL head due to the prohibitively large GPU memory required to adapt the video backbone for TAL. To overcome this limitation, we introduce LoSA, the first memory-and-parameter-efficient backbone adapter designed specifically for TAL to handle untrimmed videos. LoSA specializes for TAL by introducing Long-Short-range Adapters that adapt the intermediate layers of the video backbone over different temporal ranges. These adapters run parallel to the video backbone to significantly reduce memory footprint. LoSA also includes Long-Short-range Gated Fusion that strategically combines the output of these adapters from the video backbone layers to enhance the video features provided to the TAL head. Experiments show that LoSA significantly outperforms all existing methods on standard TAL benchmarks, THUMOS-14 and ActivityNet-v1.3, by scaling end-to-end backbone adaptation to billion-parameter-plus models like VideoMAEv2~(ViT-g) and leveraging them beyond head-only transfer learning.

Johanna Orsholm, John Quinto, Hannu Autto et al.

Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding and high-resolution imaging showing strong potential for automatic taxonomic classification. However, most image-based approaches rely on individual specimen data, unlike the unsorted bulk samples collected in large-scale ecological surveys. We present the Mixed Arthropod Sample Segmentation and Identification (MassID45) dataset for training automatic classifiers of bulk insect samples. It uniquely combines molecular and imaging data at both the unsorted sample level and the full set of individual specimens. Human annotators, supported by an AI-assisted tool, performed two tasks on bulk images: creating segmentation masks around each individual arthropod and assigning taxonomic labels to over 17 000 specimens. Combining the taxonomic resolution of DNA barcodes with precise abundance estimates of bulk images holds great potential for rapid, large-scale characterization of insect communities. This dataset pushes the boundaries of tiny object detection and instance segmentation, fostering innovation in both ecological and machine learning research.

Monireh Safari, Pablo Millan Arias, Scott C. Lowe et al.

Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for various downstream tasks, the distribution shift between pretraining and inference detrimentally impacts performance, as the pretraining task is to map [MASK] tokens to predictions, yet the [MASK] is absent during downstream applications. This means the encoder does not prioritize its encodings of non-[MASK] tokens, and expends parameters and compute on work only relevant to the MLM task, despite this being irrelevant at deployment time. In this work, we propose a modified encoder-decoder architecture based on the masked autoencoder framework, designed to address this inefficiency within a BERT-based transformer. We empirically show that the resulting mismatch is particularly detrimental in genomic pipelines where models are often used for feature extraction without fine-tuning. We evaluate our approach on the BIOSCAN-5M dataset, comprising over 2 million unique DNA barcodes. We achieve substantial performance gains in both closed-world and open-world classification tasks when compared against causal models and bidirectional architectures pretrained with MLM tasks.

S M Rayeed, Mridul Khurana, Alyson East et al.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.

ZeMing Gong, Chuanqi Tang, Xiaoliang Huo et al.

Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities such as images and genetic information. We investigate whether hyperbolic networks can provide a better embedding space for such hierarchical models. Our method embeds multimodal inputs into a shared hyperbolic space using contrastive and a novel stacked entailment-based objective. Experiments on the BIOSCAN-1M dataset show that hyperbolic embedding achieves competitive performance with Euclidean baselines, and outperforms all other models on unseen species classification using DNA barcodes. However, fine-grained classification and open-world generalization remain challenging. Our framework offers a structure-aware foundation for biodiversity modelling, with potential applications to species discovery, ecological monitoring, and conservation efforts.

Nathaniel Lesperance, Sujeevan Ratnasingham, Graham W. Taylor

In the context of pressing climate change challenges and the significant biodiversity loss among arthropods, automated taxonomic classification from organismal images is a subject of intense research. However, traditional AI pipelines based on deep neural visual architectures such as CNNs or ViTs face limitations such as degraded performance on the long-tail of classes and the inability to reason about their predictions. We integrate image captioning and retrieval-augmented generation (RAG) with large language models (LLMs) to enhance biodiversity monitoring, showing particular promise for characterizing rare and unknown arthropod species. While a naive Vision-Language Model (VLM) excels in classifying images of common species, the RAG model enables classification of rarer taxa by matching explicit textual descriptions of taxonomic features to contextual biodiversity text data from external sources. The RAG model shows promise in reducing overconfidence and enhancing accuracy relative to naive LLMs, suggesting its viability in capturing the nuances of taxonomic hierarchy, particularly at the challenging family and genus levels. Our findings highlight the potential for modern vision-language AI pipelines to support biodiversity conservation initiatives, emphasizing the role of comprehensive data curation and collaboration with citizen science platforms to improve species identification, unknown species characterization and ultimately inform conservation strategies.

Kristina L. Kupferschmidt, James Requiema, Mya Simpson et al.

In this work, we address a lack of systematic understanding of fluctuations in food affordability in Canada. Canada's Food Price Report (CPFR) is an annual publication that predicts food inflation over the next calendar year. The published predictions are a collaborative effort between forecasting teams that each employ their own approach at Canadian Universities: Dalhousie University, the University of British Columbia, the University of Saskatchewan, and the University of Guelph/Vector Institute. While the University of Guelph/Vector Institute forecasting team has leveraged machine learning (ML) in previous reports, the most recent editions (2024--2025) have also included a human-in-the-loop approach. For the 2025 report, this focus was expanded to evaluate several different data-centric approaches to improve forecast accuracy. In this study, we evaluate how different types of forecasting models perform when estimating food price fluctuations. We also examine the sensitivity of models that curate time series data representing key factors in food pricing.

Akshita Gupta, Aditya Arora, Sanath Narayan et al.

Open-Vocabulary Temporal Action Localization (OVTAL) enables a model to recognize any desired action category in videos without the need to explicitly curate training data for all categories. However, this flexibility poses significant challenges, as the model must recognize not only the action categories seen during training but also novel categories specified at inference. Unlike standard temporal action localization, where training and test categories are predetermined, OVTAL requires understanding contextual cues that reveal the semantics of novel categories. To address these challenges, we introduce OVFormer, a novel open-vocabulary framework extending ActionFormer with three key contributions. First, we employ task-specific prompts as input to a large language model to obtain rich class-specific descriptions for action categories. Second, we introduce a cross-attention mechanism to learn the alignment between class representations and frame-level video features, facilitating the multimodal guided features. Third, we propose a two-stage training strategy which includes training with a larger vocabulary dataset and finetuning to downstream data to generalize to novel categories. OVFormer extends existing TAL methods to open-vocabulary settings. Comprehensive evaluations on the THUMOS14 and ActivityNet-1.3 benchmarks demonstrate the effectiveness of our method. Code and pretrained models will be publicly released.

Kevin Kasa, Zhiyu Zhang, Heng Yang et al.

Recently there has been a surge of interest to deploy confidence set predictions rather than point predictions in machine learning. Unfortunately, the effectiveness of such prediction sets is frequently impaired by distribution shifts in practice, and the challenge is often compounded by the lack of ground truth labels at test time. Focusing on a standard set-valued prediction framework called conformal prediction (CP), this paper studies how to improve its practical performance using only unlabeled data from the shifted test domain. This is achieved by two new methods called ECP and EACP, whose main idea is to adjust the score function in CP according to its base model's own uncertainty evaluation. Through extensive experiments on a number of large-scale datasets and neural network architectures, we show that our methods provide consistent improvement over existing baselines and nearly match the performance of fully supervised methods.

Chuan-Yung Tsai, Graham W. Taylor

Although machine learning (ML) has been successful in automating various software engineering needs, software testing still remains a highly challenging topic. In this paper, we aim to improve the generative testing of software by directly augmenting the random number generator (RNG) with a deep reinforcement learning (RL) agent using an efficient, automatically extractable state representation of the software under test. Using the Cosmos SDK as the testbed, we show that the proposed DeepRNG framework provides a statistically significant improvement to the testing of the highly complex software library with over 350,000 lines of code. The source code of the DeepRNG framework is publicly available online.

Eu Wern Teh, Graham W. Taylor

A critical challenge of training deep learning models in the Digital Pathology (DP) domain is the high annotation cost by medical experts. One way to tackle this issue is via transfer learning from the natural image domain (NI), where the annotation cost is considerably cheaper. Cross-domain transfer learning from NI to DP is shown to be successful via class labels. One potential weakness of relying on class labels is the lack of spatial information, which can be obtained from spatial labels such as full pixel-wise segmentation labels and scribble labels. We demonstrate that scribble labels from NI domain can boost the performance of DP models on two cancer classification datasets (Patch Camelyon Breast Cancer and Colorectal Cancer dataset). Furthermore, we show that models trained with scribble labels yield the same performance boost as full pixel-wise segmentation labels despite being significantly easier and faster to collect.

Mohammed Adnan, Yani A. Ioannou, Chuan-Yung Tsai et al.

Recent advancements in self-supervised learning have reduced the gap between supervised and unsupervised representation learning. However, most self-supervised and deep clustering techniques rely heavily on data augmentation, rendering them ineffective for many learning tasks where insufficient domain knowledge exists for performing augmentation. We propose a new self-distillation based algorithm for domain-agnostic clustering. Our method builds upon the existing deep clustering frameworks and requires no separate student model. The proposed method outperforms existing domain agnostic (augmentation-free) algorithms on CIFAR-10. We empirically demonstrate that knowledge distillation can improve unsupervised representation learning by extracting richer `dark knowledge' from the model than using predicted labels alone. Preliminary experiments also suggest that self-distillation improves the convergence of DeepCluster-v2.

Michal Lisicki, Arash Afkanpour, Graham W. Taylor

Neural bandits have been shown to provide an efficient solution to practical sequential decision tasks that have nonlinear reward functions. The main contributor to that success is approximate Bayesian inference, which enables neural network (NN) training with uncertainty estimates. However, Bayesian NNs often suffer from a prohibitive computational overhead or operate on a subset of parameters. Alternatively, certain classes of infinite neural networks were shown to directly correspond to Gaussian processes (GP) with neural kernels (NK). NK-GPs provide accurate uncertainty estimates and can be trained faster than most Bayesian NNs. We propose to guide common bandit policies with NK distributions and show that NK bandits achieve state-of-the-art performance on nonlinear structured data. Moreover, we propose a framework for measuring independently the ability of a bandit algorithm to learn representations and explore, and use it to analyze the impact of NK distributions w.r.t.~those two aspects. We consider policies based on a GP and a Student's t-process (TP). Furthermore, we study practical considerations, such as training frequency and model partitioning. We believe our work will help better understand the impact of utilizing NKs in applied settings.

Hyunsoo Chung, Jungtaek Kim, Boris Knyazev et al.

Discovering a solution in a combinatorial space is prevalent in many real-world problems but it is also challenging due to diverse complex constraints and the vast number of possible combinations. To address such a problem, we introduce a novel formulation, combinatorial construction, which requires a building agent to assemble unit primitives (i.e., LEGO bricks) sequentially -- every connection between two bricks must follow a fixed rule, while no bricks mutually overlap. To construct a target object, we provide incomplete knowledge about the desired target (i.e., 2D images) instead of exact and explicit volumetric information to the agent. This problem requires a comprehensive understanding of partial information and long-term planning to append a brick sequentially, which leads us to employ reinforcement learning. The approach has to consider a variable-sized action space where a large number of invalid actions, which would cause overlap between bricks, exist. To resolve these issues, our model, dubbed Brick-by-Brick, adopts an action validity prediction network that efficiently filters invalid actions for an actor-critic network. We demonstrate that the proposed method successfully learns to construct an unseen object conditioned on a single image or multiple views of a target object.

Boris Knyazev, Michal Drozdzal, Graham W. Taylor et al.

Deep learning has been successful in automating the design of features in machine learning pipelines. However, the algorithms optimizing neural network parameters remain largely hand-designed and computationally inefficient. We study if we can use deep learning to directly predict these parameters by exploiting the past knowledge of training other networks. We introduce a large-scale dataset of diverse computational graphs of neural architectures - DeepNets-1M - and use it to explore parameter prediction on CIFAR-10 and ImageNet. By leveraging advances in graph neural networks, we propose a hypernetwork that can predict performant parameters in a single forward pass taking a fraction of a second, even on a CPU. The proposed model achieves surprisingly good performance on unseen and diverse networks. For example, it is able to predict all 24 million parameters of a ResNet-50 achieving a 60% accuracy on CIFAR-10. On ImageNet, top-5 accuracy of some of our networks approaches 50%. Our task along with the model and results can potentially lead to a new, more computationally efficient paradigm of training networks. Our model also learns a strong representation of neural architectures enabling their analysis.

Terrance DeVries, Miguel Angel Bautista, Nitish Srivastava et al.

We tackle the challenge of learning a distribution over complex, realistic, indoor scenes. In this paper, we introduce Generative Scene Networks (GSN), which learns to decompose scenes into a collection of many local radiance fields that can be rendered from a free moving camera. Our model can be used as a prior to generate new scenes, or to complete a scene given only sparse 2D observations. Recent work has shown that generative models of radiance fields can capture properties such as multi-view consistency and view-dependent lighting. However, these models are specialized for constrained viewing of single objects, such as cars or faces. Due to the size and complexity of realistic indoor environments, existing models lack the representational capacity to adequately capture them. Our decomposition scheme scales to larger and more complex scenes while preserving details and diversity, and the learned prior enables high-quality rendering from viewpoints that are significantly different from observed viewpoints. When compared to existing models, GSN produces quantitatively higher-quality scene renderings across several different scene datasets.

Eu Wern Teh, Terrance DeVries, Brendan Duke et al.

We consider the task of semi-supervised semantic segmentation, where we aim to produce pixel-wise semantic object masks given only a small number of human-labeled training examples. We focus on iterative self-training methods in which we explore the behavior of self-training over multiple refinement stages. We show that iterative self-training leads to performance degradation if done naïvely with a fixed ratio of human-labeled to pseudo-labeled training examples. We propose Greedy Iterative Self-Training (GIST) and Random Iterative Self-Training (RIST) strategies that alternate between training on either human-labeled data or pseudo-labeled data at each refinement stage, resulting in a performance boost rather than degradation. We further show that GIST and RIST can be combined with existing semi-supervised learning methods to boost performance.

Michal Lisicki, Arash Afkanpour, Graham W. Taylor

Neural combinatorial optimization (NCO) aims at designing problem-independent and efficient neural network-based strategies for solving combinatorial problems. The field recently experienced growth by successfully adapting architectures originally designed for machine translation. Even though the results are promising, a large gap still exists between NCO models and classic deterministic solvers, both in terms of accuracy and efficiency. One of the drawbacks of current approaches is the inefficiency of training on multiple problem sizes. Curriculum learning strategies have been shown helpful in increasing performance in the multi-task setting. In this work, we focus on designing a curriculum learning-based training procedure that can help existing architectures achieve competitive performance on a large range of problem sizes simultaneously. We provide a systematic investigation of several training procedures and use the insights gained to motivate application of a psychologically-inspired approach to improve upon the classic curriculum method.

Boris Knyazev, Harm de Vries, Cătălina Cangea et al.

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.