Scott Lowe

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.

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.

Isaac Xu, Scott Lowe, Thomas Trappenberg

Self-supervised learning (SSL) is an effective method for exploiting unlabelled data to learn a high-level embedding space that can be used for various downstream tasks. However, existing methods to monitor the quality of the encoder -- either during training for one model or to compare several trained models -- still rely on access to annotated data. When SSL methodologies are applied to new data domains, a sufficiently large labelled dataset may not always be available. In this study, we propose several evaluation metrics which can be applied on the embeddings of unlabelled data and investigate their viability by comparing them to linear probe accuracy (a common metric which utilizes an annotated dataset). In particular, we apply $k$-means clustering and measure the clustering quality with the silhouette score and clustering agreement. We also measure the entropy of the embedding distribution. We find that while the clusters did correspond better to the ground truth annotations as training of the network progressed, label-free clustering metrics correlated with the linear probe accuracy only when training with SSL methods SimCLR and MoCo-v2, but not with SimSiam. Additionally, although entropy did not always have strong correlations with LP accuracy, this appears to be due to instability arising from early training, with the metric stabilizing and becoming more reliable at later stages of learning. Furthermore, while entropy generally decreases as learning progresses, this trend reverses for SimSiam. More research is required to establish the cause for this unexpected behaviour. Lastly, we find that while clustering based approaches are likely only viable for same-architecture comparisons, entropy may be architecture-independent.

Isaac Xu, Benjamin Misiuk, Scott C. Lowe et al.

In this work, we apply state-of-the-art self-supervised learning techniques on a large dataset of seafloor imagery, \textit{BenthicNet}, and study their performance for a complex hierarchical multi-label (HML) classification downstream task. In particular, we demonstrate the capacity to conduct HML training in scenarios where there exist multiple levels of missing annotation information, an important scenario for handling heterogeneous real-world data collected by multiple research groups with differing data collection protocols. We find that, when using smaller one-hot image label datasets typical of local or regional scale benthic science projects, models pre-trained with self-supervision on a larger collection of in-domain benthic data outperform models pre-trained on ImageNet. In the HML setting, we find the model can attain a deeper and more precise classification if it is pre-trained with self-supervision on in-domain data. We hope this work can establish a benchmark for future models in the field of automated underwater image annotation tasks and can guide work in other domains with hierarchical annotations of mixed resolution.

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/}.

Scott C. Lowe, Benjamin Misiuk, Isaac Xu et al.

Advances in underwater imaging enable collection of extensive seafloor image datasets necessary for monitoring important benthic ecosystems. The ability to collect seafloor imagery has outpaced our capacity to analyze it, hindering mobilization of this crucial environmental information. Machine learning approaches provide opportunities to increase the efficiency with which seafloor imagery is analyzed, yet large and consistent datasets to support development of such approaches are scarce. Here we present BenthicNet: a global compilation of seafloor imagery designed to support the training and evaluation of large-scale image recognition models. An initial set of over 11.4 million images was collected and curated to represent a diversity of seafloor environments using a representative subset of 1.3 million images. These are accompanied by 3.1 million annotations translated to the CATAMI scheme, which span 190,000 of the images. A large deep learning model was trained on this compilation and preliminary results suggest it has utility for automating large and small-scale image analysis tasks. The compilation and model are made openly available for reuse at https://doi.org/10.20383/103.0614.

Alyson East, Elizabeth G. Campolongo, Luke Meyers et al.

1) Biological collections house millions of specimens with digital images increasingly available through open-access platforms. However, most imaging protocols were developed for human interpretation without considering automated analysis requirements. As computer vision applications revolutionize taxonomic identification and trait extraction, a critical gap exists between current digitization practices and computational analysis needs. This review provides the first comprehensive practical framework for optimizing biological specimen imaging for computer vision applications. 2) Through interdisciplinary collaboration between taxonomists, collection managers, ecologists, and computer scientists, we synthesized evidence-based recommendations addressing fundamental computer vision concepts and practical imaging considerations. We provide immediately actionable implementation guidance while identifying critical areas requiring community standards development. 3) Our framework encompasses ten interconnected considerations for optimizing image capture for computer vision-powered taxonomic identification and trait extraction. We translate these into practical implementation checklists, equipment selection guidelines, and a roadmap for community standards development including filename conventions, pixel density requirements, and cross-institutional protocols. 4)By bridging biological and computational disciplines, this approach unlocks automated analysis potential for millions of existing specimens and guides future digitization efforts toward unprecedented analytical capabilities.

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.

Scott C. Lowe, Louise P. McGarry, Jessica Douglas et al.

Understanding the abundance and distribution of fish in tidal energy streams is important to assess risks presented by introducing tidal energy devices to the habitat. However tidal current flows suitable for tidal energy are often highly turbulent, complicating the interpretation of echosounder data. The portion of the water column contaminated by returns from entrained air must be excluded from data used for biological analyses. Application of a single conventional algorithm to identify the depth-of-penetration of entrained air is insufficient for a boundary that is discontinuous, depth-dynamic, porous, and varies with tidal flow speed. Using a case study at a tidal energy demonstration site in the Bay of Fundy, we describe the development and application of a deep machine learning model with a U-Net based architecture. Our model, Echofilter, was highly responsive to the dynamic range of turbulence conditions and sensitive to the fine-scale nuances in the boundary position, producing an entrained-air boundary line with an average error of 0.33m on mobile downfacing and 0.5-1.0m on stationary upfacing data, less than half that of existing algorithmic solutions. The model's overall annotations had a high level of agreement with the human segmentation, with an intersection-over-union score of 99% for mobile downfacing recordings and 92-95% for stationary upfacing recordings. This resulted in a 50% reduction in the time required for manual edits when compared to the time required to manually edit the line placement produced by the currently available algorithms. Because of the improved initial automated placement, the implementation of the models permits an increase in the standardization and repeatability of line placement.

Scott C. Lowe, Thomas Trappenberg, Sageev Oore

We seek to improve the pooling operation in neural networks, by applying a more theoretically justified operator. We demonstrate that LogSumExp provides a natural OR operator for logits. When one corrects for the number of elements inside the pooling operator, this becomes $\text{LogAvgExp} := \log(\text{mean}(\exp(x)))$. By introducing a single temperature parameter, LogAvgExp smoothly transitions from the max of its operands to the mean (found at the limiting cases $t \to 0^+$ and $t \to +\infty$). We experimentally tested LogAvgExp, both with and without a learnable temperature parameter, in a variety of deep neural network architectures for computer vision.

Scott C. Lowe, Robert Earle, Jason d'Eon et al.

The choice of activation functions and their motivation is a long-standing issue within the neural network community. Neuronal representations within artificial neural networks are commonly understood as logits, representing the log-odds score of presence of features within the stimulus. We derive logit-space operators equivalent to probabilistic Boolean logic-gates AND, OR, and XNOR for independent probabilities. Such theories are important to formalize more complex dendritic operations in real neurons, and these operations can be used as activation functions within a neural network, introducing probabilistic Boolean-logic as the core operation of the neural network. Since these functions involve taking multiple exponents and logarithms, they are computationally expensive and not well suited to be directly used within neural networks. Consequently, we construct efficient approximations named $\text{AND}_\text{AIL}$ (the AND operator Approximate for Independent Logits), $\text{OR}_\text{AIL}$, and $\text{XNOR}_\text{AIL}$, which utilize only comparison and addition operations, have well-behaved gradients, and can be deployed as activation functions in neural networks. Like MaxOut, $\text{AND}_\text{AIL}$ and $\text{OR}_\text{AIL}$ are generalizations of ReLU to two-dimensions. While our primary aim is to formalize dendritic computations within a logit-space probabilistic-Boolean framework, we deploy these new activation functions, both in isolation and in conjunction to demonstrate their effectiveness on a variety of tasks including image classification, transfer learning, abstract reasoning, and compositional zero-shot learning.

Lu Yihe, Scott C. Lowe, Penelope A. Lewis et al.

Despite remarkable advances in automated visual recognition by machines, some visual tasks remain challenging for machines. Fleuret et al. (2011) introduced the Synthetic Visual Reasoning Test (SVRT) to highlight this point, which required classification of images consisting of randomly generated shapes based on hidden abstract rules using only a few examples. Ellis et al. (2015) demonstrated that a program synthesis approach could solve some of the SVRT problems with unsupervised, few-shot learning, whereas they remained challenging for several convolutional neural networks trained with thousands of examples. Here we re-considered the human and machine experiments, because they followed different protocols and yielded different statistics. We thus proposed a quantitative reintepretation of the data between the protocols, so that we could make fair comparison between human and machine performance. We improved the program synthesis classifier by correcting the image parsings, and compared the results to the performance of other machine agents and human subjects. We grouped the SVRT problems into different types by the two aspects of the core characteristics for classification: shape specification and location relation. We found that the program synthesis classifier could not solve problems involving shape distances, because it relied on symbolic computation which scales poorly with input dimension and adding distances into such computation would increase the dimension combinatorially with the number of shapes in an image. Therefore, although the program synthesis classifier is capable of abstract reasoning, its performance is highly constrained by the accessible information in image parsings.

Nicholas Meade, Nicholas Barreyre, Scott C. Lowe et al.

Performance RNN is a machine-learning system designed primarily for the generation of solo piano performances using an event-based (rather than audio) representation. More specifically, Performance RNN is a long short-term memory (LSTM) based recurrent neural network that models polyphonic music with expressive timing and dynamics (Oore et al., 2018). The neural network uses a simple language model based on the Musical Instrument Digital Interface (MIDI) file format. Performance RNN is trained on the e-Piano Junior Competition Dataset (International Piano e-Competition, 2018), a collection of solo piano performances by expert pianists. As an artistic tool, one of the limitations of the original model has been the lack of useable controls. The standard form of Performance RNN can generate interesting pieces, but little control is provided over what specifically is generated. This paper explores a set of conditioning-based controls used to influence the generation process.