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Feb 18

LLM-Based Evaluation of Low-Resource Machine Translation: A Reference-less Dialect Guided Approach with a Refined Sylheti-English Benchmark

Evaluating machine translation (MT) for low-resource languages poses a persistent challenge, primarily due to the limited availability of high quality reference translations. This issue is further exacerbated in languages with multiple dialects, where linguistic diversity and data scarcity hinder robust evaluation. Large Language Models (LLMs) present a promising solution through reference-free evaluation techniques; however, their effectiveness diminishes in the absence of dialect-specific context and tailored guidance. In this work, we propose a comprehensive framework that enhances LLM-based MT evaluation using a dialect guided approach. We extend the ONUBAD dataset by incorporating Sylheti-English sentence pairs, corresponding machine translations, and Direct Assessment (DA) scores annotated by native speakers. To address the vocabulary gap, we augment the tokenizer vocabulary with dialect-specific terms. We further introduce a regression head to enable scalar score prediction and design a dialect-guided (DG) prompting strategy. Our evaluation across multiple LLMs shows that the proposed pipeline consistently outperforms existing methods, achieving the highest gain of +0.1083 in Spearman correlation, along with improvements across other evaluation settings. The dataset and the code are available at https://github.com/180041123-Atiq/MTEonLowResourceLanguage.

  • 3 authors
·
May 18, 2025

HumBugDB: A Large-scale Acoustic Mosquito Dataset

This paper presents the first large-scale multi-species dataset of acoustic recordings of mosquitoes tracked continuously in free flight. We present 20 hours of audio recordings that we have expertly labelled and tagged precisely in time. Significantly, 18 hours of recordings contain annotations from 36 different species. Mosquitoes are well-known carriers of diseases such as malaria, dengue and yellow fever. Collecting this dataset is motivated by the need to assist applications which utilise mosquito acoustics to conduct surveys to help predict outbreaks and inform intervention policy. The task of detecting mosquitoes from the sound of their wingbeats is challenging due to the difficulty in collecting recordings from realistic scenarios. To address this, as part of the HumBug project, we conducted global experiments to record mosquitoes ranging from those bred in culture cages to mosquitoes captured in the wild. Consequently, the audio recordings vary in signal-to-noise ratio and contain a broad range of indoor and outdoor background environments from Tanzania, Thailand, Kenya, the USA and the UK. In this paper we describe in detail how we collected, labelled and curated the data. The data is provided from a PostgreSQL database, which contains important metadata such as the capture method, age, feeding status and gender of the mosquitoes. Additionally, we provide code to extract features and train Bayesian convolutional neural networks for two key tasks: the identification of mosquitoes from their corresponding background environments, and the classification of detected mosquitoes into species. Our extensive dataset is both challenging to machine learning researchers focusing on acoustic identification, and critical to entomologists, geo-spatial modellers and other domain experts to understand mosquito behaviour, model their distribution, and manage the threat they pose to humans.

  • 16 authors
·
Oct 14, 2021

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

  • 17 authors
·
May 19, 2025

DengueNet: Dengue Prediction using Spatiotemporal Satellite Imagery for Resource-Limited Countries

Dengue fever presents a substantial challenge in developing countries where sanitation infrastructure is inadequate. The absence of comprehensive healthcare systems exacerbates the severity of dengue infections, potentially leading to life-threatening circumstances. Rapid response to dengue outbreaks is also challenging due to limited information exchange and integration. While timely dengue outbreak forecasts have the potential to prevent such outbreaks, the majority of dengue prediction studies have predominantly relied on data that impose significant burdens on individual countries for collection. In this study, our aim is to improve health equity in resource-constrained countries by exploring the effectiveness of high-resolution satellite imagery as a nontraditional and readily accessible data source. By leveraging the wealth of publicly available and easily obtainable satellite imagery, we present a scalable satellite extraction framework based on Sentinel Hub, a cloud-based computing platform. Furthermore, we introduce DengueNet, an innovative architecture that combines Vision Transformer, Radiomics, and Long Short-term Memory to extract and integrate spatiotemporal features from satellite images. This enables dengue predictions on an epi-week basis. To evaluate the effectiveness of our proposed method, we conducted experiments on five municipalities in Colombia. We utilized a dataset comprising 780 high-resolution Sentinel-2 satellite images for training and evaluation. The performance of DengueNet was assessed using the mean absolute error (MAE) metric. Across the five municipalities, DengueNet achieved an average MAE of 43.92. Our findings strongly support the efficacy of satellite imagery as a valuable resource for dengue prediction, particularly in informing public health policies within countries where manually collected data is scarce and dengue virus prevalence is severe.

  • 12 authors
·
Jan 19, 2024

A Labelled Dataset for Sentiment Analysis of Videos on YouTube, TikTok, and Other Sources about the 2024 Outbreak of Measles

The work of this paper presents a dataset that contains the data of 4011 videos about the ongoing outbreak of measles published on 264 websites on the internet between January 1, 2024, and May 31, 2024. The dataset is available at https://dx.doi.org/10.21227/40s8-xf63. These websites primarily include YouTube and TikTok, which account for 48.6% and 15.2% of the videos, respectively. The remainder of the websites include Instagram and Facebook as well as the websites of various global and local news organizations. For each of these videos, the URL of the video, title of the post, description of the post, and the date of publication of the video are presented as separate attributes in the dataset. After developing this dataset, sentiment analysis (using VADER), subjectivity analysis (using TextBlob), and fine-grain sentiment analysis (using DistilRoBERTa-base) of the video titles and video descriptions were performed. This included classifying each video title and video description into (i) one of the sentiment classes i.e. positive, negative, or neutral, (ii) one of the subjectivity classes i.e. highly opinionated, neutral opinionated, or least opinionated, and (iii) one of the fine-grain sentiment classes i.e. fear, surprise, joy, sadness, anger, disgust, or neutral. These results are presented as separate attributes in the dataset for the training and testing of machine learning algorithms for performing sentiment analysis or subjectivity analysis in this field as well as for other applications. Finally, this paper also presents a list of open research questions that may be investigated using this dataset.

  • 7 authors
·
Jun 11, 2024

Rapid Biomedical Research Classification: The Pandemic PACT Advanced Categorisation Engine

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

  • 14 authors
·
Jul 14, 2024

Extending the WILDS Benchmark for Unsupervised Adaptation

Machine learning systems deployed in the wild are often trained on a source distribution but deployed on a different target distribution. Unlabeled data can be a powerful point of leverage for mitigating these distribution shifts, as it is frequently much more available than labeled data and can often be obtained from distributions beyond the source distribution as well. However, existing distribution shift benchmarks with unlabeled data do not reflect the breadth of scenarios that arise in real-world applications. In this work, we present the WILDS 2.0 update, which extends 8 of the 10 datasets in the WILDS benchmark of distribution shifts to include curated unlabeled data that would be realistically obtainable in deployment. These datasets span a wide range of applications (from histology to wildlife conservation), tasks (classification, regression, and detection), and modalities (photos, satellite images, microscope slides, text, molecular graphs). The update maintains consistency with the original WILDS benchmark by using identical labeled training, validation, and test sets, as well as the evaluation metrics. On these datasets, we systematically benchmark state-of-the-art methods that leverage unlabeled data, including domain-invariant, self-training, and self-supervised methods, and show that their success on WILDS is limited. To facilitate method development and evaluation, we provide an open-source package that automates data loading and contains all of the model architectures and methods used in this paper. Code and leaderboards are available at https://wilds.stanford.edu.

  • 20 authors
·
Dec 9, 2021

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

  • 2 authors
·
Apr 19, 2024

FineBio: A Fine-Grained Video Dataset of Biological Experiments with Hierarchical Annotation

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

  • 7 authors
·
Jan 31, 2024

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

  • 16 authors
·
Jan 13, 2025 3

Crowdsourcing Dermatology Images with Google Search Ads: Creating a Real-World Skin Condition Dataset

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

  • 20 authors
·
Feb 28, 2024

Arboretum: A Large Multimodal Dataset Enabling AI for Biodiversity

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

  • 15 authors
·
Jun 25, 2024 1

The Audio-Visual BatVision Dataset for Research on Sight and Sound

Vision research showed remarkable success in understanding our world, propelled by datasets of images and videos. Sensor data from radar, LiDAR and cameras supports research in robotics and autonomous driving for at least a decade. However, while visual sensors may fail in some conditions, sound has recently shown potential to complement sensor data. Simulated room impulse responses (RIR) in 3D apartment-models became a benchmark dataset for the community, fostering a range of audiovisual research. In simulation, depth is predictable from sound, by learning bat-like perception with a neural network. Concurrently, the same was achieved in reality by using RGB-D images and echoes of chirping sounds. Biomimicking bat perception is an exciting new direction but needs dedicated datasets to explore the potential. Therefore, we collected the BatVision dataset to provide large-scale echoes in complex real-world scenes to the community. We equipped a robot with a speaker to emit chirps and a binaural microphone to record their echoes. Synchronized RGB-D images from the same perspective provide visual labels of traversed spaces. We sampled modern US office spaces to historic French university grounds, indoor and outdoor with large architectural variety. This dataset will allow research on robot echolocation, general audio-visual tasks and sound ph{\ae}nomena unavailable in simulated data. We show promising results for audio-only depth prediction and show how state-of-the-art work developed for simulated data can also succeed on our dataset. Project page: https://amandinebtto.github.io/Batvision-Dataset/

  • 4 authors
·
Mar 13, 2023

EduRABSA: An Education Review Dataset for Aspect-based Sentiment Analysis Tasks

Every year, most educational institutions seek and receive an enormous volume of text feedback from students on courses, teaching, and overall experience. Yet, turning this raw feedback into useful insights is far from straightforward. It has been a long-standing challenge to adopt automatic opinion mining solutions for such education review text data due to the content complexity and low-granularity reporting requirements. Aspect-based Sentiment Analysis (ABSA) offers a promising solution with its rich, sub-sentence-level opinion mining capabilities. However, existing ABSA research and resources are very heavily focused on the commercial domain. In education, they are scarce and hard to develop due to limited public datasets and strict data protection. A high-quality, annotated dataset is urgently needed to advance research in this under-resourced area. In this work, we present EduRABSA (Education Review ABSA), the first public, annotated ABSA education review dataset that covers three review subject types (course, teaching staff, university) in the English language and all main ABSA tasks, including the under-explored implicit aspect and implicit opinion extraction. We also share ASQE-DPT (Data Processing Tool), an offline, lightweight, installation-free manual data annotation tool that generates labelled datasets for comprehensive ABSA tasks from a single-task annotation. Together, these resources contribute to the ABSA community and education domain by removing the dataset barrier, supporting research transparency and reproducibility, and enabling the creation and sharing of further resources. The dataset, annotation tool, and scripts and statistics for dataset processing and sampling are available at https://github.com/yhua219/edurabsa_dataset_and_annotation_tool.

  • 4 authors
·
Aug 23, 2025 2

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

  • 34 authors
·
Oct 6, 2023

TrialPanorama: Database and Benchmark for Systematic Review and Design of Clinical Trials

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

  • 9 authors
·
May 21, 2025

SEWA DB: A Rich Database for Audio-Visual Emotion and Sentiment Research in the Wild

Natural human-computer interaction and audio-visual human behaviour sensing systems, which would achieve robust performance in-the-wild are more needed than ever as digital devices are increasingly becoming an indispensable part of our life. Accurately annotated real-world data are the crux in devising such systems. However, existing databases usually consider controlled settings, low demographic variability, and a single task. In this paper, we introduce the SEWA database of more than 2000 minutes of audio-visual data of 398 people coming from six cultures, 50% female, and uniformly spanning the age range of 18 to 65 years old. Subjects were recorded in two different contexts: while watching adverts and while discussing adverts in a video chat. The database includes rich annotations of the recordings in terms of facial landmarks, facial action units (FAU), various vocalisations, mirroring, and continuously valued valence, arousal, liking, agreement, and prototypic examples of (dis)liking. This database aims to be an extremely valuable resource for researchers in affective computing and automatic human sensing and is expected to push forward the research in human behaviour analysis, including cultural studies. Along with the database, we provide extensive baseline experiments for automatic FAU detection and automatic valence, arousal and (dis)liking intensity estimation.

  • 13 authors
·
Jan 9, 2019

Introducing CALMED: Multimodal Annotated Dataset for Emotion Detection in Children with Autism

Automatic Emotion Detection (ED) aims to build systems to identify users' emotions automatically. This field has the potential to enhance HCI, creating an individualised experience for the user. However, ED systems tend to perform poorly on people with Autism Spectrum Disorder (ASD). Hence, the need to create ED systems tailored to how people with autism express emotions. Previous works have created ED systems tailored for children with ASD but did not share the resulting dataset. Sharing annotated datasets is essential to enable the development of more advanced computer models for ED within the research community. In this paper, we describe our experience establishing a process to create a multimodal annotated dataset featuring children with a level 1 diagnosis of autism. In addition, we introduce CALMED (Children, Autism, Multimodal, Emotion, Detection), the resulting multimodal emotion detection dataset featuring children with autism aged 8-12. CALMED includes audio and video features extracted from recording files of study sessions with participants, together with annotations provided by their parents into four target classes. The generated dataset includes a total of 57,012 examples, with each example representing a time window of 200ms (0.2s). Our experience and methods described here, together with the dataset shared, aim to contribute to future research applications of affective computing in ASD, which has the potential to create systems to improve the lives of people with ASD.

  • 5 authors
·
Jul 24, 2023

Integrating Biological Data into Autonomous Remote Sensing Systems for In Situ Imageomics: A Case Study for Kenyan Animal Behavior Sensing with Unmanned Aerial Vehicles (UAVs)

In situ imageomics leverages machine learning techniques to infer biological traits from images collected in the field, or in situ, to study individuals organisms, groups of wildlife, and whole ecosystems. Such datasets provide real-time social and environmental context to inferred biological traits, which can enable new, data-driven conservation and ecosystem management. The development of machine learning techniques to extract biological traits from images are impeded by the volume and quality data required to train these models. Autonomous, unmanned aerial vehicles (UAVs), are well suited to collect in situ imageomics data as they can traverse remote terrain quickly to collect large volumes of data with greater consistency and reliability compared to manually piloted UAV missions. However, little guidance exists on optimizing autonomous UAV missions for the purposes of remote sensing for conservation and biodiversity monitoring. The UAV video dataset curated by KABR: In-Situ Dataset for Kenyan Animal Behavior Recognition from Drone Videos required three weeks to collect, a time-consuming and expensive endeavor. Our analysis of KABR revealed that a third of the videos gathered were unusable for the purposes of inferring wildlife behavior. We analyzed the flight telemetry data from portions of UAV videos that were usable for inferring wildlife behavior, and demonstrate how these insights can be integrated into an autonomous remote sensing system to track wildlife in real time. Our autonomous remote sensing system optimizes the UAV's actions to increase the yield of usable data, and matches the flight path of an expert pilot with an 87% accuracy rate, representing an 18.2% improvement in accuracy over previously proposed methods.

  • 6 authors
·
Jul 23, 2024

SpeakerVid-5M: A Large-Scale High-Quality Dataset for Audio-Visual Dyadic Interactive Human Generation

The rapid development of large-scale models has catalyzed significant breakthroughs in the digital human domain. These advanced methodologies offer high-fidelity solutions for avatar driving and rendering, leading academia to focus on the next major challenge: audio-visual dyadic interactive virtual human. To facilitate research in this emerging area, we present SpeakerVid-5M dataset, the first large-scale, high-quality dataset designed for audio-visual dyadic interactive virtual human generation. Totaling over 8,743 hours, SpeakerVid-5M contains more than 5.2 million video clips of human portraits. It covers diverse scales and interaction types, including monadic talking, listening, and dyadic conversations. Crucially, the dataset is structured along two key dimensions: interaction type and data quality. First, it is categorized into four types (dialogue branch, single branch, listening branch and multi-turn branch) based on the interaction scenario. Second, it is stratified into a large-scale pre-training subset and a curated, high-quality subset for Supervised Fine-Tuning (SFT). This dual structure accommodates a wide array of 2D virtual human tasks. In addition, we provide an autoregressive (AR)-based video chat baseline trained on this data, accompanied by a dedicated set of metrics and test data to serve as a benchmark VidChatBench for future work. Both the dataset and the corresponding data processing code will be publicly released. Project page: https://dorniwang.github.io/SpeakerVid-5M/

  • 9 authors
·
Jul 13, 2025 3

UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

  • 3 authors
·
Apr 9, 2025 2

LEMUR Neural Network Dataset: Towards Seamless AutoML

Neural networks are fundamental in artificial intelligence, driving progress in computer vision and natural language processing. High-quality datasets are crucial for their development, and there is growing interest in datasets composed of neural networks themselves to support benchmarking, automated machine learning (AutoML), and model analysis. We introduce LEMUR, an open source dataset of neural network models with well-structured code for diverse architectures across tasks such as object detection, image classification, segmentation, and natural language processing. LEMUR is primarily designed to provide a rich source of structured model representations and associated performance data, enabling the fine-tuning of large language models for AutoML applications. Leveraging Python and PyTorch, LEMUR enables seamless extension to new datasets and models while maintaining consistency. It integrates an Optuna-powered framework for evaluation, hyperparameter optimization, statistical analysis, and graphical insights. LEMUR VR extension enables the seamless deployment of models in virtual reality, optimizing their performance on resource-constrained devices. Providing tools for model evaluation, preprocessing, and database management, LEMUR supports researchers and practitioners in developing, testing, and analyzing neural networks. It offers an API that delivers comprehensive information about neural network models and their complete performance statistics with a single request, which can be used in experiments with code-generating large language models. The LEMUR and its plugins are accessible as open source projects under the MIT license at https://github.com/ABrain-One/nn-dataset, https://github.com/ABrain-One/nn-plots and https://github.com/ABrain-One/nn-vr.

  • 10 authors
·
Apr 14, 2025

RFUAV: A Benchmark Dataset for Unmanned Aerial Vehicle Detection and Identification

In this paper, we propose RFUAV as a new benchmark dataset for radio-frequency based (RF-based) unmanned aerial vehicle (UAV) identification and address the following challenges: Firstly, many existing datasets feature a restricted variety of drone types and insufficient volumes of raw data, which fail to meet the demands of practical applications. Secondly, existing datasets often lack raw data covering a broad range of signal-to-noise ratios (SNR), or do not provide tools for transforming raw data to different SNR levels. This limitation undermines the validity of model training and evaluation. Lastly, many existing datasets do not offer open-access evaluation tools, leading to a lack of unified evaluation standards in current research within this field. RFUAV comprises approximately 1.3 TB of raw frequency data collected from 37 distinct UAVs using the Universal Software Radio Peripheral (USRP) device in real-world environments. Through in-depth analysis of the RF data in RFUAV, we define a drone feature sequence called RF drone fingerprint, which aids in distinguishing drone signals. In addition to the dataset, RFUAV provides a baseline preprocessing method and model evaluation tools. Rigorous experiments demonstrate that these preprocessing methods achieve state-of-the-art (SOTA) performance using the provided evaluation tools. The RFUAV dataset and baseline implementation are publicly available at https://github.com/kitoweeknd/RFUAV/.

  • 7 authors
·
Mar 11, 2025

STARSS22: A dataset of spatial recordings of real scenes with spatiotemporal annotations of sound events

This report presents the Sony-TAu Realistic Spatial Soundscapes 2022 (STARS22) dataset for sound event localization and detection, comprised of spatial recordings of real scenes collected in various interiors of two different sites. The dataset is captured with a high resolution spherical microphone array and delivered in two 4-channel formats, first-order Ambisonics and tetrahedral microphone array. Sound events in the dataset belonging to 13 target sound classes are annotated both temporally and spatially through a combination of human annotation and optical tracking. The dataset serves as the development and evaluation dataset for the Task 3 of the DCASE2022 Challenge on Sound Event Localization and Detection and introduces significant new challenges for the task compared to the previous iterations, which were based on synthetic spatialized sound scene recordings. Dataset specifications are detailed including recording and annotation process, target classes and their presence, and details on the development and evaluation splits. Additionally, the report presents the baseline system that accompanies the dataset in the challenge with emphasis on the differences with the baseline of the previous iterations; namely, introduction of the multi-ACCDOA representation to handle multiple simultaneous occurences of events of the same class, and support for additional improved input features for the microphone array format. Results of the baseline indicate that with a suitable training strategy a reasonable detection and localization performance can be achieved on real sound scene recordings. The dataset is available in https://zenodo.org/record/6387880.

  • 10 authors
·
Jun 4, 2022

BaboonLand Dataset: Tracking Primates in the Wild and Automating Behaviour Recognition from Drone Videos

Using drones to track multiple individuals simultaneously in their natural environment is a powerful approach for better understanding group primate behavior. Previous studies have demonstrated that it is possible to automate the classification of primate behavior from video data, but these studies have been carried out in captivity or from ground-based cameras. To understand group behavior and the self-organization of a collective, the whole troop needs to be seen at a scale where behavior can be seen in relation to the natural environment in which ecological decisions are made. This study presents a novel dataset from drone videos for baboon detection, tracking, and behavior recognition. The baboon detection dataset was created by manually annotating all baboons in drone videos with bounding boxes. A tiling method was subsequently applied to create a pyramid of images at various scales from the original 5.3K resolution images, resulting in approximately 30K images used for baboon detection. The tracking dataset is derived from the detection dataset, where all bounding boxes are assigned the same ID throughout the video. This process resulted in half an hour of very dense tracking data. The behavior recognition dataset was generated by converting tracks into mini-scenes, a video subregion centered on each animal; each mini-scene was manually annotated with 12 distinct behavior types, resulting in over 20 hours of data. Benchmark results show mean average precision (mAP) of 92.62\% for the YOLOv8-X detection model, multiple object tracking precision (MOTA) of 63.81\% for the BotSort tracking algorithm, and micro top-1 accuracy of 63.97\% for the X3D behavior recognition model. Using deep learning to classify wildlife behavior from drone footage facilitates non-invasive insight into the collective behavior of an entire group.

  • 12 authors
·
May 27, 2024

Datasheets Aren't Enough: DataRubrics for Automated Quality Metrics and Accountability

High-quality datasets are fundamental to training and evaluating machine learning models, yet their creation-especially with accurate human annotations-remains a significant challenge. Many dataset paper submissions lack originality, diversity, or rigorous quality control, and these shortcomings are often overlooked during peer review. Submissions also frequently omit essential details about dataset construction and properties. While existing tools such as datasheets aim to promote transparency, they are largely descriptive and do not provide standardized, measurable methods for evaluating data quality. Similarly, metadata requirements at conferences promote accountability but are inconsistently enforced. To address these limitations, this position paper advocates for the integration of systematic, rubric-based evaluation metrics into the dataset review process-particularly as submission volumes continue to grow. We also explore scalable, cost-effective methods for synthetic data generation, including dedicated tools and LLM-as-a-judge approaches, to support more efficient evaluation. As a call to action, we introduce DataRubrics, a structured framework for assessing the quality of both human- and model-generated datasets. Leveraging recent advances in LLM-based evaluation, DataRubrics offers a reproducible, scalable, and actionable solution for dataset quality assessment, enabling both authors and reviewers to uphold higher standards in data-centric research. We also release code to support reproducibility of LLM-based evaluations at https://github.com/datarubrics/datarubrics.

  • 20 authors
·
Jun 2, 2025 2

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

  • 3 authors
·
Nov 10, 2023

A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

  • 12 authors
·
Aug 14, 2025

DataComp: In search of the next generation of multimodal datasets

Large multimodal datasets have been instrumental in recent breakthroughs such as CLIP, Stable Diffusion, and GPT-4. At the same time, datasets rarely receive the same research attention as model architectures or training algorithms. To address this shortcoming in the machine learning ecosystem, we introduce DataComp, a benchmark where the training code is fixed and researchers innovate by proposing new training sets. We provide a testbed for dataset experiments centered around a new candidate pool of 12.8B image-text pairs from Common Crawl. Participants in our benchmark design new filtering techniques or curate new data sources and then evaluate their new dataset by running our standardized CLIP training code and testing on 38 downstream test sets. Our benchmark consists of multiple scales, with four candidate pool sizes and associated compute budgets ranging from 12.8M to 12.8B samples seen during training. This multi-scale design facilitates the study of scaling trends and makes the benchmark accessible to researchers with varying resources. Our baseline experiments show that the DataComp workflow is a promising way of improving multimodal datasets. We introduce DataComp-1B, a dataset created by applying a simple filtering algorithm to the 12.8B candidate pool. The resulting 1.4B subset enables training a CLIP ViT-L/14 from scratch to 79.2% zero-shot accuracy on ImageNet. Our new ViT-L/14 model outperforms a larger ViT-g/14 trained on LAION-2B by 0.7 percentage points while requiring 9x less training compute. We also outperform OpenAI's CLIP ViT-L/14 by 3.7 percentage points, which is trained with the same compute budget as our model. These gains highlight the potential for improving model performance by carefully curating training sets. We view DataComp-1B as only the first step and hope that DataComp paves the way toward the next generation of multimodal datasets.

  • 34 authors
·
Apr 27, 2023

VideoUFO: A Million-Scale User-Focused Dataset for Text-to-Video Generation

Text-to-video generative models convert textual prompts into dynamic visual content, offering wide-ranging applications in film production, gaming, and education. However, their real-world performance often falls short of user expectations. One key reason is that these models have not been trained on videos related to some topics users want to create. In this paper, we propose VideoUFO, the first Video dataset specifically curated to align with Users' FOcus in real-world scenarios. Beyond this, our VideoUFO also features: (1) minimal (0.29%) overlap with existing video datasets, and (2) videos searched exclusively via YouTube's official API under the Creative Commons license. These two attributes provide future researchers with greater freedom to broaden their training sources. The VideoUFO comprises over 1.09 million video clips, each paired with both a brief and a detailed caption (description). Specifically, through clustering, we first identify 1,291 user-focused topics from the million-scale real text-to-video prompt dataset, VidProM. Then, we use these topics to retrieve videos from YouTube, split the retrieved videos into clips, and generate both brief and detailed captions for each clip. After verifying the clips with specified topics, we are left with about 1.09 million video clips. Our experiments reveal that (1) current 16 text-to-video models do not achieve consistent performance across all user-focused topics; and (2) a simple model trained on VideoUFO outperforms others on worst-performing topics. The dataset is publicly available at https://huggingface.co/datasets/WenhaoWang/VideoUFO under the CC BY 4.0 License.

  • 2 authors
·
Mar 3, 2025 2

OIDA-QA: A Multimodal Benchmark for Analyzing the Opioid Industry Documents Archive

The opioid crisis represents a significant moment in public health that reveals systemic shortcomings across regulatory systems, healthcare practices, corporate governance, and public policy. Analyzing how these interconnected systems simultaneously failed to protect public health requires innovative analytic approaches for exploring the vast amounts of data and documents disclosed in the UCSF-JHU Opioid Industry Documents Archive (OIDA). The complexity, multimodal nature, and specialized characteristics of these healthcare-related legal and corporate documents necessitate more advanced methods and models tailored to specific data types and detailed annotations, ensuring the precision and professionalism in the analysis. In this paper, we tackle this challenge by organizing the original dataset according to document attributes and constructing a benchmark with 400k training documents and 10k for testing. From each document, we extract rich multimodal information-including textual content, visual elements, and layout structures-to capture a comprehensive range of features. Using multiple AI models, we then generate a large-scale dataset comprising 360k training QA pairs and 10k testing QA pairs. Building on this foundation, we develop domain-specific multimodal Large Language Models (LLMs) and explore the impact of multimodal inputs on task performance. To further enhance response accuracy, we incorporate historical QA pairs as contextual grounding for answering current queries. Additionally, we incorporate page references within the answers and introduce an importance-based page classifier, further improving the precision and relevance of the information provided. Preliminary results indicate the improvements with our AI assistant in document information extraction and question-answering tasks. The dataset is available at: https://huggingface.co/datasets/opioidarchive/oida-qa

  • 15 authors
·
Nov 12, 2025

Representation-Centric Survey of Skeletal Action Recognition and the ANUBIS Benchmark

3D skeleton-based human action recognition has emerged as a powerful alternative to traditional RGB and depth-based approaches, offering robustness to environmental variations, computational efficiency, and enhanced privacy. Despite remarkable progress, current research remains fragmented across diverse input representations and lacks evaluation under scenarios that reflect modern real-world challenges. This paper presents a representation-centric survey of skeleton-based action recognition, systematically categorizing state-of-the-art methods by their input feature types: joint coordinates, bone vectors, motion flows, and extended representations, and analyzing how these choices influence spatial-temporal modeling strategies. Building on the insights from this review, we introduce ANUBIS, a large-scale, challenging skeleton action dataset designed to address critical gaps in existing benchmarks. ANUBIS incorporates multi-view recordings with back-view perspectives, complex multi-person interactions, fine-grained and violent actions, and contemporary social behaviors. We benchmark a diverse set of state-of-the-art models on ANUBIS and conduct an in-depth analysis of how different feature types affect recognition performance across 102 action categories. Our results show strong action-feature dependencies, highlight the limitations of na\"ive multi-representational fusion, and point toward the need for task-aware, semantically aligned integration strategies. This work offers both a comprehensive foundation and a practical benchmarking resource, aiming to guide the next generation of robust, generalizable skeleton-based action recognition systems for complex real-world scenarios. The dataset website, benchmarking framework, and download link are available at https://yliu1082.github.io/ANUBIS/{https://yliu1082.github.io/ANUBIS/

  • 11 authors
·
May 4, 2022

Data Filtering Networks

Large training sets have become a cornerstone of machine learning and are the foundation for recent advances in language modeling and multimodal learning. While data curation for pre-training is often still ad-hoc, one common paradigm is to first collect a massive pool of data from the Web and then filter this candidate pool down to an actual training set via various heuristics. In this work, we study the problem of learning a data filtering network (DFN) for this second step of filtering a large uncurated dataset. Our key finding is that the quality of a network for filtering is distinct from its performance on downstream tasks: for instance, a model that performs well on ImageNet can yield worse training sets than a model with low ImageNet accuracy that is trained on a small amount of high-quality data. Based on our insights, we construct new data filtering networks that induce state-of-the-art image-text datasets. Specifically, our best performing dataset DFN-5B enables us to train state-of-the-art models for their compute budgets: among other improvements on a variety of tasks, a ViT-H trained on our dataset achieves 83.0% zero-shot transfer accuracy on ImageNet, out-performing models trained on other datasets such as LAION-2B, DataComp-1B, or OpenAI's WIT. In order to facilitate further research in dataset design, we also release a new 2 billion example dataset DFN-2B and show that high performance data filtering networks can be trained from scratch using only publicly available data.

  • 6 authors
·
Sep 29, 2023 1

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

  • 7 authors
·
Jan 3, 2025 2

DatasetResearch: Benchmarking Agent Systems for Demand-Driven Dataset Discovery

The rapid advancement of large language models has fundamentally shifted the bottleneck in AI development from computational power to data availability-with countless valuable datasets remaining hidden across specialized repositories, research appendices, and domain platforms. As reasoning capabilities and deep research methodologies continue to evolve, a critical question emerges: can AI agents transcend conventional search to systematically discover any dataset that meets specific user requirements, enabling truly autonomous demand-driven data curation? We introduce DatasetResearch, the first comprehensive benchmark evaluating AI agents' ability to discover and synthesize datasets from 208 real-world demands across knowledge-intensive and reasoning-intensive tasks. Our tri-dimensional evaluation framework reveals a stark reality: even advanced deep research systems achieve only 22% score on our challenging DatasetResearch-pro subset, exposing the vast gap between current capabilities and perfect dataset discovery. Our analysis uncovers a fundamental dichotomy-search agents excel at knowledge tasks through retrieval breadth, while synthesis agents dominate reasoning challenges via structured generation-yet both catastrophically fail on "corner cases" outside existing distributions. These findings establish the first rigorous baseline for dataset discovery agents and illuminate the path toward AI systems capable of finding any dataset in the digital universe. Our benchmark and comprehensive analysis provide the foundation for the next generation of self-improving AI systems and are publicly available at https://github.com/GAIR-NLP/DatasetResearch.

  • 7 authors
·
Aug 9, 2025

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, and geographical 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/zahrag/BIOSCAN-5M}

  • 13 authors
·
Jun 18, 2024

How We Won BraTS-SSA 2025: Brain Tumor Segmentation in the Sub-Saharan African Population Using Segmentation-Aware Data Augmentation and Model Ensembling

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

  • 8 authors
·
Oct 3, 2025

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

  • 11 authors
·
May 23, 2025 2

Animal Kingdom: A Large and Diverse Dataset for Animal Behavior Understanding

Understanding animals' behaviors is significant for a wide range of applications. However, existing animal behavior datasets have limitations in multiple aspects, including limited numbers of animal classes, data samples and provided tasks, and also limited variations in environmental conditions and viewpoints. To address these limitations, we create a large and diverse dataset, Animal Kingdom, that provides multiple annotated tasks to enable a more thorough understanding of natural animal behaviors. The wild animal footages used in our dataset record different times of the day in extensive range of environments containing variations in backgrounds, viewpoints, illumination and weather conditions. More specifically, our dataset contains 50 hours of annotated videos to localize relevant animal behavior segments in long videos for the video grounding task, 30K video sequences for the fine-grained multi-label action recognition task, and 33K frames for the pose estimation task, which correspond to a diverse range of animals with 850 species across 6 major animal classes. Such a challenging and comprehensive dataset shall be able to facilitate the community to develop, adapt, and evaluate various types of advanced methods for animal behavior analysis. Moreover, we propose a Collaborative Action Recognition (CARe) model that learns general and specific features for action recognition with unseen new animals. This method achieves promising performance in our experiments. Our dataset can be found at https://sutdcv.github.io/Animal-Kingdom.

  • 6 authors
·
Apr 17, 2022

The SourceData-NLP dataset: integrating curation into scientific publishing for training large language models

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

  • 4 authors
·
Oct 31, 2023

IndraEye: Infrared Electro-Optical UAV-based Perception Dataset for Robust Downstream Tasks

Deep neural networks (DNNs) have shown exceptional performance when trained on well-illuminated images captured by Electro-Optical (EO) cameras, which provide rich texture details. However, in critical applications like aerial perception, it is essential for DNNs to maintain consistent reliability across all conditions, including low-light scenarios where EO cameras often struggle to capture sufficient detail. Additionally, UAV-based aerial object detection faces significant challenges due to scale variability from varying altitudes and slant angles, adding another layer of complexity. Existing methods typically address only illumination changes or style variations as domain shifts, but in aerial perception, correlation shifts also impact DNN performance. In this paper, we introduce the IndraEye dataset, a multi-sensor (EO-IR) dataset designed for various tasks. It includes 5,612 images with 145,666 instances, encompassing multiple viewing angles, altitudes, seven backgrounds, and different times of the day across the Indian subcontinent. The dataset opens up several research opportunities, such as multimodal learning, domain adaptation for object detection and segmentation, and exploration of sensor-specific strengths and weaknesses. IndraEye aims to advance the field by supporting the development of more robust and accurate aerial perception systems, particularly in challenging conditions. IndraEye dataset is benchmarked with object detection and semantic segmentation tasks. Dataset and source codes are available at https://bit.ly/indraeye.

  • 7 authors
·
Oct 28, 2024

WIT-UAS: A Wildland-fire Infrared Thermal Dataset to Detect Crew Assets From Aerial Views

We present the Wildland-fire Infrared Thermal (WIT-UAS) dataset for long-wave infrared sensing of crew and vehicle assets amidst prescribed wildland fire environments. While such a dataset is crucial for safety monitoring in wildland fire applications, to the authors' awareness, no such dataset focusing on assets near fire is publicly available. Presumably, this is due to the barrier to entry of collaborating with fire management personnel. We present two related data subsets: WIT-UAS-ROS consists of full ROS bag files containing sensor and robot data of UAS flight over the fire, and WIT-UAS-Image contains hand-labeled long-wave infrared (LWIR) images extracted from WIT-UAS-ROS. Our dataset is the first to focus on asset detection in a wildland fire environment. We show that thermal detection models trained without fire data frequently detect false positives by classifying fire as people. By adding our dataset to training, we show that the false positive rate is reduced significantly. Yet asset detection in wildland fire environments is still significantly more challenging than detection in urban environments, due to dense obscuring trees, greater heat variation, and overbearing thermal signal of the fire. We publicize this dataset to encourage the community to study more advanced models to tackle this challenging environment. The dataset, code and pretrained models are available at https://github.com/castacks/WIT-UAS-Dataset.

  • 7 authors
·
Dec 14, 2023

REFUGE2 Challenge: A Treasure Trove for Multi-Dimension Analysis and Evaluation in Glaucoma Screening

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge -- Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application.

  • 28 authors
·
Feb 17, 2022

ECOSoundSet: a finely annotated dataset for the automated acoustic identification of Orthoptera and Cicadidae in North, Central and temperate Western Europe

Currently available tools for the automated acoustic recognition of European insects in natural soundscapes are limited in scope. Large and ecologically heterogeneous acoustic datasets are currently needed for these algorithms to cross-contextually recognize the subtle and complex acoustic signatures produced by each species, thus making the availability of such datasets a key requisite for their development. Here we present ECOSoundSet (European Cicadidae and Orthoptera Sound dataSet), a dataset containing 10,653 recordings of 200 orthopteran and 24 cicada species (217 and 26 respective taxa when including subspecies) present in North, Central, and temperate Western Europe (Andorra, Belgium, Denmark, mainland France and Corsica, Germany, Ireland, Luxembourg, Monaco, Netherlands, United Kingdom, Switzerland), collected partly through targeted fieldwork in South France and Catalonia and partly through contributions from various European entomologists. The dataset is composed of a combination of coarsely labeled recordings, for which we can only infer the presence, at some point, of their target species (weak labeling), and finely annotated recordings, for which we know the specific time and frequency range of each insect sound present in the recording (strong labeling). We also provide a train/validation/test split of the strongly labeled recordings, with respective approximate proportions of 0.8, 0.1 and 0.1, in order to facilitate their incorporation in the training and evaluation of deep learning algorithms. This dataset could serve as a meaningful complement to recordings already available online for the training of deep learning algorithms for the acoustic classification of orthopterans and cicadas in North, Central, and temperate Western Europe.

  • 26 authors
·
Apr 29, 2025

MEVA: A Large-Scale Multiview, Multimodal Video Dataset for Activity Detection

We present the Multiview Extended Video with Activities (MEVA) dataset, a new and very-large-scale dataset for human activity recognition. Existing security datasets either focus on activity counts by aggregating public video disseminated due to its content, which typically excludes same-scene background video, or they achieve persistence by observing public areas and thus cannot control for activity content. Our dataset is over 9300 hours of untrimmed, continuous video, scripted to include diverse, simultaneous activities, along with spontaneous background activity. We have annotated 144 hours for 37 activity types, marking bounding boxes of actors and props. Our collection observed approximately 100 actors performing scripted scenarios and spontaneous background activity over a three-week period at an access-controlled venue, collecting in multiple modalities with overlapping and non-overlapping indoor and outdoor viewpoints. The resulting data includes video from 38 RGB and thermal IR cameras, 42 hours of UAV footage, as well as GPS locations for the actors. 122 hours of annotation are sequestered in support of the NIST Activity in Extended Video (ActEV) challenge; the other 22 hours of annotation and the corresponding video are available on our website, along with an additional 306 hours of ground camera data, 4.6 hours of UAV data, and 9.6 hours of GPS logs. Additional derived data includes camera models geo-registering the outdoor cameras and a dense 3D point cloud model of the outdoor scene. The data was collected with IRB oversight and approval and released under a CC-BY-4.0 license.

  • 4 authors
·
Dec 1, 2020

Sparks of Science: Hypothesis Generation Using Structured Paper Data

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of scientifically informed hypotheses. However, current foundation models often struggle to produce scientific ideas that are both novel and feasible. One reason is the lack of a dedicated dataset that frames Scientific Hypothesis Generation (SHG) as a Natural Language Generation (NLG) task. In this paper, we introduce HypoGen, the first dataset of approximately 5500 structured problem-hypothesis pairs extracted from top-tier computer science conferences structured with a Bit-Flip-Spark schema, where the Bit is the conventional assumption, the Spark is the key insight or conceptual leap, and the Flip is the resulting counterproposal. HypoGen uniquely integrates an explicit Chain-of-Reasoning component that reflects the intellectual process from Bit to Flip. We demonstrate that framing hypothesis generation as conditional language modelling, with the model fine-tuned on Bit-Flip-Spark and the Chain-of-Reasoning (and where, at inference, we only provide the Bit), leads to improvements in the overall quality of the hypotheses. Our evaluation employs automated metrics and LLM judge rankings for overall quality assessment. We show that by fine-tuning on our HypoGen dataset we improve the novelty, feasibility, and overall quality of the generated hypotheses. The HypoGen dataset is publicly available at huggingface.co/datasets/UniverseTBD/hypogen-dr1.

  • 7 authors
·
Apr 17, 2025

The Urban Vision Hackathon Dataset and Models: Towards Image Annotations and Accurate Vision Models for Indian Traffic

This report describes the UVH-26 dataset, the first public release by AIM@IISc of a large-scale dataset of annotated traffic-camera images from India. The dataset comprises 26,646 high-resolution (1080p) images sampled from 2800 Bengaluru's Safe-City CCTV cameras over a 4-week period, and subsequently annotated through a crowdsourced hackathon involving 565 college students from across India. In total, 1.8 million bounding boxes were labeled across 14 vehicle classes specific to India: Cycle, 2-Wheeler (Motorcycle), 3-Wheeler (Auto-rickshaw), LCV (Light Commercial Vehicles), Van, Tempo-traveller, Hatchback, Sedan, SUV, MUV, Mini-bus, Bus, Truck and Other. Of these, 283k-316k consensus ground truth bounding boxes and labels were derived for distinct objects in the 26k images using Majority Voting and STAPLE algorithms. Further, we train multiple contemporary detectors, including YOLO11-S/X, RT-DETR-S/X, and DAMO-YOLO-T/L using these datasets, and report accuracy based on mAP50, mAP75 and mAP50:95. Models trained on UVH-26 achieve 8.4-31.5% improvements in mAP50:95 over equivalent baseline models trained on COCO dataset, with RT-DETR-X showing the best performance at 0.67 (mAP50:95) as compared to 0.40 for COCO-trained weights for common classes (Car, Bus, and Truck). This demonstrates the benefits of domain-specific training data for Indian traffic scenarios. The release package provides the 26k images with consensus annotations based on Majority Voting (UVH-26-MV) and STAPLE (UVH-26-ST) and the 6 fine-tuned YOLO and DETR models on each of these datasets. By capturing the heterogeneity of Indian urban mobility directly from operational traffic-camera streams, UVH-26 addresses a critical gap in existing global benchmarks, and offers a foundation for advancing detection, classification, and deployment of intelligent transportation systems in emerging nations with complex traffic conditions.

  • 13 authors
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Nov 4, 2025

Thousand Voices of Trauma: A Large-Scale Synthetic Dataset for Modeling Prolonged Exposure Therapy Conversations

The advancement of AI systems for mental health support is hindered by limited access to therapeutic conversation data, particularly for trauma treatment. We present Thousand Voices of Trauma, a synthetic benchmark dataset of 3,000 therapy conversations based on Prolonged Exposure therapy protocols for Post-traumatic Stress Disorder (PTSD). The dataset comprises 500 unique cases, each explored through six conversational perspectives that mirror the progression of therapy from initial anxiety to peak distress to emotional processing. We incorporated diverse demographic profiles (ages 18-80, M=49.3, 49.4% male, 44.4% female, 6.2% non-binary), 20 trauma types, and 10 trauma-related behaviors using deterministic and probabilistic generation methods. Analysis reveals realistic distributions of trauma types (witnessing violence 10.6%, bullying 10.2%) and symptoms (nightmares 23.4%, substance abuse 20.8%). Clinical experts validated the dataset's therapeutic fidelity, highlighting its emotional depth while suggesting refinements for greater authenticity. We also developed an emotional trajectory benchmark with standardized metrics for evaluating model responses. This privacy-preserving dataset addresses critical gaps in trauma-focused mental health data, offering a valuable resource for advancing both patient-facing applications and clinician training tools.

  • 5 authors
·
Apr 16, 2025

EmotionTalk: An Interactive Chinese Multimodal Emotion Dataset With Rich Annotations

In recent years, emotion recognition plays a critical role in applications such as human-computer interaction, mental health monitoring, and sentiment analysis. While datasets for emotion analysis in languages such as English have proliferated, there remains a pressing need for high-quality, comprehensive datasets tailored to the unique linguistic, cultural, and multimodal characteristics of Chinese. In this work, we propose EmotionTalk, an interactive Chinese multimodal emotion dataset with rich annotations. This dataset provides multimodal information from 19 actors participating in dyadic conversational settings, incorporating acoustic, visual, and textual modalities. It includes 23.6 hours of speech (19,250 utterances), annotations for 7 utterance-level emotion categories (happy, surprise, sad, disgust, anger, fear, and neutral), 5-dimensional sentiment labels (negative, weakly negative, neutral, weakly positive, and positive) and 4-dimensional speech captions (speaker, speaking style, emotion and overall). The dataset is well-suited for research on unimodal and multimodal emotion recognition, missing modality challenges, and speech captioning tasks. To our knowledge, it represents the first high-quality and versatile Chinese dialogue multimodal emotion dataset, which is a valuable contribution to research on cross-cultural emotion analysis and recognition. Additionally, we conduct experiments on EmotionTalk to demonstrate the effectiveness and quality of the dataset. It will be open-source and freely available for all academic purposes. The dataset and codes will be made available at: https://github.com/NKU-HLT/EmotionTalk.

  • 12 authors
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May 28, 2025

Biomed-Enriched: A Biomedical Dataset Enriched with LLMs for Pretraining and Extracting Rare and Hidden Content

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

  • 3 authors
·
Jun 25, 2025 1

SemEval-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

  • 6 authors
·
May 4, 2023

COVID-BLUeS -- A Prospective Study on the Value of AI in Lung Ultrasound Analysis

As a lightweight and non-invasive imaging technique, lung ultrasound (LUS) has gained importance for assessing lung pathologies. The use of Artificial intelligence (AI) in medical decision support systems is promising due to the time- and expertise-intensive interpretation, however, due to the poor quality of existing data used for training AI models, their usability for real-world applications remains unclear. In a prospective study, we analyze data from 63 COVID-19 suspects (33 positive) collected at Maastricht University Medical Centre. Ultrasound recordings at six body locations were acquired following the BLUE protocol and manually labeled for severity of lung involvement. Several AI models were applied and trained for detection and severity of pulmonary infection. The severity of the lung infection, as assigned by human annotators based on the LUS videos, is not significantly different between COVID-19 positive and negative patients (p = 0.89). Nevertheless, the predictions of image-based AI models identify a COVID-19 infection with 65% accuracy when applied zero-shot (i.e., trained on other datasets), and up to 79% with targeted training, whereas the accuracy based on human annotations is at most 65%. Multi-modal models combining images and CBC improve significantly over image-only models. Although our analysis generally supports the value of AI in LUS assessment, the evaluated models fall short of the performance expected from previous work. We find this is due to 1) the heterogeneity of LUS datasets, limiting the generalization ability to new data, 2) the frame-based processing of AI models ignoring video-level information, and 3) lack of work on multi-modal models that can extract the most relevant information from video-, image- and variable-based inputs. To aid future research, we publish the dataset at: https://github.com/NinaWie/COVID-BLUES.

  • 13 authors
·
Sep 9, 2025

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

  • 6 authors
·
Dec 20, 2024

8-Calves Image dataset

We introduce the 8-Calves dataset, a benchmark for evaluating object detection and identity classification in occlusion-rich, temporally consistent environments. The dataset comprises a 1-hour video (67,760 frames) of eight Holstein Friesian calves in a barn, with ground truth bounding boxes and identities, alongside 900 static frames for detection tasks. Each calf exhibits a unique coat pattern, enabling precise identity distinction. For cow detection, we fine-tuned 28 models (25 YOLO variants, 3 transformers) on 600 frames, testing on the full video. Results reveal smaller YOLO models (e.g., YOLOV9c) outperform larger counterparts despite potential bias from a YOLOv8m-based labeling pipeline. For identity classification, embeddings from 23 pretrained vision models (ResNet, ConvNextV2, ViTs) were evaluated via linear classifiers and KNN. Modern architectures like ConvNextV2 excelled, while larger models frequently overfit, highlighting inefficiencies in scaling. Key findings include: (1) Minimal, targeted augmentations (e.g., rotation) outperform complex strategies on simpler datasets; (2) Pretraining strategies (e.g., BEiT, DinoV2) significantly boost identity recognition; (3) Temporal continuity and natural motion patterns offer unique challenges absent in synthetic or domain-specific benchmarks. The dataset's controlled design and extended sequences (1 hour vs. prior 10-minute benchmarks) make it a pragmatic tool for stress-testing occlusion handling, temporal consistency, and efficiency. The link to the dataset is https://github.com/tonyFang04/8-calves.

  • 3 authors
·
Mar 17, 2025

Comprehensive Benchmarking of YOLOv11 Architectures for Scalable and Granular Peripheral Blood Cell Detection

Manual peripheral blood smear (PBS) analysis is labor intensive and subjective. While deep learning offers a promising alternative, a systematic evaluation of state of the art models such as YOLOv11 for fine grained PBS detection is still lacking. In this work, we make two key contributions. First, we curate a large scale annotated dataset for blood cell detection and classification, comprising 16,891 images across 12 peripheral blood cell (PBC) classes, along with the red blood cell class, all carefully re annotated for object detection tasks. In total, the dataset contains 298,850 annotated cells. Second, we leverage this dataset to conduct a comprehensive evaluation of five YOLOv11 variants (ranging from Nano to XLarge). These models are rigorously benchmarked under two data splitting strategies (70:20:10 and 80:10:10) and systematically assessed using multiple performance criteria, including mean Average Precision (mAP), precision, recall, F1 score, and computational efficiency. Our experiments show that the YOLOv11 Medium variant achieves the best trade off, reaching a mAP@0.5 of 0.934 under the 8:1:1 split. Larger models (Large and XLarge) provide only marginal accuracy gains at substantially higher computational cost. Moreover, the 8:1:1 split consistently outperforms the 7:2:1 split across all models. These findings highlight YOLOv11, particularly the Medium variant, as a highly effective framework for automated, fine grained PBS detection. Beyond benchmarking, our publicly released dataset (github.com/Mohamad-AbouAli/OI-PBC-Dataset) offers a valuable resource to advance research on blood cell detection and classification in hematology.

  • 7 authors
·
Sep 29, 2025