Nicholas Pellegrino

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.

Nicholas Pellegrino, Zahra Gharaee, Paul Fieguth

The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In addition to genetically barcoding insects, over 1.5 million images per year will be collected, each needing taxonomic classification. With the immense volume of incoming images, relying solely on expert taxonomists to label the images would be impossible; however, artificial intelligence and computer vision technology may offer a viable high-throughput solution. Additional tasks including manually weighing individual insects to determine biomass, remain tedious and costly. Here again, computer vision may offer an efficient and compelling alternative. While the use of computer vision methods is appealing for addressing these problems, significant challenges resulting from biological factors present themselves. These challenges are formulated in the context of machine learning in this paper.

Emma Croxford, Yanjun Gao, Nicholas Pellegrino et al.

Large Language Models have advanced clinical Natural Language Generation, creating opportunities to manage the volume of medical text. However, the high-stakes nature of medicine requires reliable evaluation, which remains a challenge. In this narrative review, we assess the current evaluation state for clinical summarization tasks and propose future directions to address the resource constraints of expert human evaluation.

Amir Nazemi, Mohammad Hadi Sepanj, Nicholas Pellegrino et al.

Current strategies for solving image-based inverse problems apply latent diffusion models to perform posterior sampling.However, almost all approaches make no explicit attempt to explore the solution space, instead drawing only a single sample from a Gaussian distribution from which to generate their solution. In this paper, we introduce a particle-filtering-based framework for a nonlinear exploration of the solution space in the initial stages of reverse SDE methods. Our proposed particle-filtering-based latent diffusion (PFLD) method and proposed problem formulation and framework can be applied to any diffusion-based solution for linear or nonlinear inverse problems. Our experimental results show that PFLD outperforms the SoTA solver PSLD on the FFHQ-1K and ImageNet-1K datasets on inverse problem tasks of super resolution, Gaussian debluring and inpainting.

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.

Emma Croxford, Yanjun Gao, Nicholas Pellegrino et al.

As Large Language Models (LLMs) are integrated into electronic health record (EHR) workflows, validated instruments are essential to evaluate their performance before implementation. Existing instruments for provider documentation quality are often unsuitable for the complexities of LLM-generated text and lack validation on real-world data. The Provider Documentation Summarization Quality Instrument (PDSQI-9) was developed to evaluate LLM-generated clinical summaries. Multi-document summaries were generated from real-world EHR data across multiple specialties using several LLMs (GPT-4o, Mixtral 8x7b, and Llama 3-8b). Validation included Pearson correlation for substantive validity, factor analysis and Cronbach's alpha for structural validity, inter-rater reliability (ICC and Krippendorff's alpha) for generalizability, a semi-Delphi process for content validity, and comparisons of high-versus low-quality summaries for discriminant validity. Seven physician raters evaluated 779 summaries and answered 8,329 questions, achieving over 80% power for inter-rater reliability. The PDSQI-9 demonstrated strong internal consistency (Cronbach's alpha = 0.879; 95% CI: 0.867-0.891) and high inter-rater reliability (ICC = 0.867; 95% CI: 0.867-0.868), supporting structural validity and generalizability. Factor analysis identified a 4-factor model explaining 58% of the variance, representing organization, clarity, accuracy, and utility. Substantive validity was supported by correlations between note length and scores for Succinct (rho = -0.200, p = 0.029) and Organized ($ρ= -0.190$, $p = 0.037$). Discriminant validity distinguished high- from low-quality summaries ($p < 0.001$). The PDSQI-9 demonstrates robust construct validity, supporting its use in clinical practice to evaluate LLM-generated summaries and facilitate safer integration of LLMs into healthcare workflows.

Nicholas Pellegrino, David Szczecina, Paul Fieguth

Methods for detecting label errors in training data require models that are robust to label errors (i.e., not fit to erroneously labelled data points). However, acquiring such models often involves training on corrupted data, which presents a challenge. Adjustments to the loss function present an opportunity for improvement. Motivated by Focal Loss (which emphasizes difficult-to-classify samples), two novel, yet simple, loss functions are proposed that de-weight or ignore these difficult samples (i.e., those likely to have label errors). Results on artificially corrupted data show promise, such that F1 scores for detecting errors are improved from the baselines of conventional categorical Cross Entropy and Focal Loss.

David Szczecina, Nicholas Pellegrino, Paul Fieguth

Training deep networks with noisy labels leads to poor generalization and degraded accuracy due to overfitting to label noise. Existing approaches for learning with noisy labels often rely on the availability of a clean subset of data. By pre-training a feature extractor backbone without labels using self-supervised learning (SSL), followed by standard supervised training on the noisy dataset, we can train a more noise robust model without requiring a subset with clean labels. We evaluate the use of SimCLR and Barlow~Twins as SSL methods on CIFAR-10 and CIFAR-100 under synthetic and real world noise. Across all noise rates, self-supervised pre-training consistently improves classification accuracy and enhances downstream label-error detection (F1 and Balanced Accuracy). The performance gap widens as the noise rate increases, demonstrating improved robustness. Notably, our approach achieves comparable results to ImageNet pre-trained models at low noise levels, while substantially outperforming them under high noise conditions.

Nicholas Pellegrino, David Szczecina, Paul W. Fieguth

Untrained large neural networks, just after random initialization, tend to favour a small subset of classes, assigning high predicted probabilities to these few classes and approximately zero probability to all others. This bias, termed Initial Guessing Bias, affects the early training dynamics, when the model is fitting to the coarse structure of the data. The choice of loss function against which to train the model has a large impact on how these early dynamics play out. Two recent loss functions, Blurry and Piecewise-zero loss, were designed for robustness to label errors but can become unable to steer the direction of training when exposed to this initial bias. Results indicate that the choice of loss function has a dramatic effect on the early phase training of networks, and highlights the need for careful consideration of how Initial Guessing Bias may interact with various components of the training scheme.

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.

Nicholas Pellegrino, Paul Fieguth, Parsin Haji Reza

Many measurement modalities which perform imaging by probing an object pixel-by-pixel, such as via Photoacoustic Microscopy, produce a multi-dimensional feature (typically a time-domain signal) at each pixel. In principle, the many degrees of freedom in the time-domain signal would admit the possibility of significant multi-modal information being implicitly present, much more than a single scalar "brightness", regarding the underlying targets being observed. However, the measured signal is neither a weighted-sum of basis functions (such as principal components) nor one of a set of prototypes (K-means), which has motivated the novel clustering method proposed here. Signals are clustered based on their shape, but not amplitude, via angular distance and centroids are calculated as the direction of maximal intra-cluster variance, resulting in a clustering algorithm capable of learning centroids (signal shapes) that are related to the underlying, albeit unknown, target characteristics in a scalable and noise-robust manner.