arXiv subjects

Graham W. Taylor

Publications and source records attributed to Graham W. Taylor.

At least 37 records · Page 2Linked to original sources

arXiv2025

Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning and RAG for Interpretable Classification

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.

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arXiv2025

BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity

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.

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arXiv2025

Enhancing DNA Foundation Models to Address Masking Inefficiencies

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.

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arXiv2024

BarcodeMamba: State Space Models for Biodiversity Analysis

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.

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arXiv2024

Food for thought: How can machine learning help better predict and understand changes in food prices?

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.

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arXiv2024

LoSA: Long-Short-range Adapter for Scaling End-to-End Temporal Action Localization

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.

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arXiv2024

Agglomerative Token Clustering

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.

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arXiv2024

Open-Vocabulary Temporal Action Localization using Multimodal Guidance

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.

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arXiv2023

A Step Towards Worldwide Biodiversity Assessment: The BIOSCAN-1M Insect Dataset

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.

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arXiv2023

Bandit-Driven Batch Selection for Robust Learning under Label Noise

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.

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arXiv2023

Which Tokens to Use? Investigating Token Reduction in Vision Transformers

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.

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arXiv2023

Empirically Validating Conformal Prediction on Modern Vision Architectures Under Distribution Shift and Long-tailed Data

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.

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arXiv2023

Sparsifiner: Learning Sparse Instance-Dependent Attention for Efficient Vision Transformers

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%.

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arXiv2023

GCNet: Probing Self-Similarity Learning for Generalized Counting Network

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.

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arXiv2022

Empirical analysis of representation learning and exploration in neural kernel bandits

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.

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arXiv2022

Bounding generalization error with input compression: An empirical study with infinite-width networks

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.

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arXiv2022

Monitoring Shortcut Learning using Mutual Information

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.

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arXiv2022

The GIST and RIST of Iterative Self-Training for Semi-Supervised Segmentation

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.

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