Tilo Burghardt

Xinyu Yang, Tilo Burghardt, Majid Mirmehdi

We propose a novel end-to-end curriculum learning approach for sparsely labelled animal datasets leveraging large volumes of unlabelled data to improve supervised species detectors. We exemplify the method in detail on the task of finding great apes in camera trap footage taken in challenging real-world jungle environments. In contrast to previous semi-supervised methods, our approach adjusts learning parameters dynamically over time and gradually improves detection quality by steering training towards virtuous self-reinforcement. To achieve this, we propose integrating pseudo-labelling with curriculum learning policies and show how learning collapse can be avoided. We discuss theoretical arguments, ablations, and significant performance improvements against various state-of-the-art systems when evaluating on the Extended PanAfrican Dataset holding approx. 1.8M frames. We also demonstrate our method can outperform supervised baselines with significant margins on sparse label versions of other animal datasets such as Bees and Snapshot Serengeti. We note that performance advantages are strongest for smaller labelled ratios common in ecological applications. Finally, we show that our approach achieves competitive benchmarks for generic object detection in MS-COCO and PASCAL-VOC indicating wider applicability of the dynamic learning concepts introduced. We publish all relevant source code, network weights, and data access details for full reproducibility. The code is available at https://github.com/youshyee/DCL-Detection.

Chengxi Zeng, Xinyu Yang, David Smithard et al.

This paper presents a deep learning framework for medical video segmentation. Convolution neural network (CNN) and transformer-based methods have achieved great milestones in medical image segmentation tasks due to their incredible semantic feature encoding and global information comprehension abilities. However, most existing approaches ignore a salient aspect of medical video data - the temporal dimension. Our proposed framework explicitly extracts features from neighbouring frames across the temporal dimension and incorporates them with a temporal feature blender, which then tokenises the high-level spatio-temporal feature to form a strong global feature encoded via a Swin Transformer. The final segmentation results are produced via a UNet-like encoder-decoder architecture. Our model outperforms other approaches by a significant margin and improves the segmentation benchmarks on the VFSS2022 dataset, achieving a dice coefficient of 0.8986 and 0.8186 for the two datasets tested. Our studies also show the efficacy of the temporal feature blending scheme and cross-dataset transferability of learned capabilities. Code and models are fully available at https://github.com/SimonZeng7108/Video-SwinUNet.

Toby Perrett, Saptarshi Sinha, Tilo Burghardt et al.

This paper presents an investigation into long-tail video recognition. We demonstrate that, unlike naturally-collected video datasets and existing long-tail image benchmarks, current video benchmarks fall short on multiple long-tailed properties. Most critically, they lack few-shot classes in their tails. In response, we propose new video benchmarks that better assess long-tail recognition, by sampling subsets from two datasets: SSv2 and VideoLT. We then propose a method, Long-Tail Mixed Reconstruction, which reduces overfitting to instances from few-shot classes by reconstructing them as weighted combinations of samples from head classes. LMR then employs label mixing to learn robust decision boundaries. It achieves state-of-the-art average class accuracy on EPIC-KITCHENS and the proposed SSv2-LT and VideoLT-LT. Benchmarks and code at: tobyperrett.github.io/lmr

Otto Brookes, Majid Mirmehdi, Hjalmar Kühl et al.

We propose the first metric learning system for the recognition of great ape behavioural actions. Our proposed triple stream embedding architecture works on camera trap videos taken directly in the wild and demonstrates that the utilisation of an explicit DensePose-C chimpanzee body part segmentation stream effectively complements traditional RGB appearance and optical flow streams. We evaluate system variants with different feature fusion techniques and long-tail recognition approaches. Results and ablations show performance improvements of ~12% in top-1 accuracy over previous results achieved on the PanAf-500 dataset containing 180,000 manually annotated frames across nine behavioural actions. Furthermore, we provide a qualitative analysis of our findings and augment the metric learning system with long-tail recognition techniques showing that average per class accuracy -- critical in the domain -- can be improved by ~23% compared to the literature on that dataset. Finally, since our embedding spaces are constructed as metric, we provide first data-driven visualisations of the great ape behavioural action spaces revealing emerging geometry and topology. We hope that the work sparks further interest in this vital application area of computer vision for the benefit of endangered great apes.

Chengxi Zeng, Xinyu Yang, Majid Mirmehdi et al.

We propose Video-TransUNet, a deep architecture for instance segmentation in medical CT videos constructed by integrating temporal feature blending into the TransUNet deep learning framework. In particular, our approach amalgamates strong frame representation via a ResNet CNN backbone, multi-frame feature blending via a Temporal Context Module (TCM), non-local attention via a Vision Transformer, and reconstructive capabilities for multiple targets via a UNet-based convolutional-deconvolutional architecture with multiple heads. We show that this new network design can significantly outperform other state-of-the-art systems when tested on the segmentation of bolus and pharynx/larynx in Videofluoroscopic Swallowing Study (VFSS) CT sequences. On our VFSS2022 dataset it achieves a dice coefficient of 0.8796 and an average surface distance of 1.0379 pixels. Note that tracking the pharyngeal bolus accurately is a particularly important application in clinical practice since it constitutes the primary method for diagnostics of swallowing impairment. Our findings suggest that the proposed model can indeed enhance the TransUNet architecture via exploiting temporal information and improving segmentation performance by a significant margin. We publish key source code, network weights, and ground truth annotations for simplified performance reproduction.

Maria Stennett, Daniel I. Rubenstein, Tilo Burghardt

This paper combines deep learning techniques for species detection, 3D model fitting, and metric learning in one pipeline to perform individual animal identification from photographs by exploiting unique coat patterns. This is the first work to attempt this and, compared to traditional 2D bounding box or segmentation based CNN identification pipelines, the approach provides effective and explicit view-point normalisation and allows for a straight forward visualisation of the learned biometric population space. Note that due to the use of metric learning the pipeline is also readily applicable to open set and zero shot re-identification scenarios. We apply the proposed approach to individual Grevy's zebra (Equus grevyi) identification and show in a small study on the SMALST dataset that the use of 3D model fitting can indeed benefit performance. In particular, back-projected textures from 3D fitted models improve identification accuracy from 48.0% to 56.8% compared to 2D bounding box approaches for the dataset. Whilst the study is far too small accurately to estimate the full performance potential achievable in larger-scale real-world application settings and in comparisons against polished tools, our work lays the conceptual and practical foundations for a next step in animal biometrics towards deep metric learning driven, fully 3D-aware animal identification in open population settings. We publish network weights and relevant facilitating source code with this paper for full reproducibility and as inspiration for further research.

Jing Gao, Tilo Burghardt, Neill W. Campbell

We describe a practically evaluated approach for training visual cattle ID systems for a whole farm requiring only ten minutes of labelling effort. In particular, for the task of automatic identification of individual Holstein-Friesians in real-world farm CCTV, we show that self-supervision, metric learning, cluster analysis, and active learning can complement each other to significantly reduce the annotation requirements usually needed to train cattle identification frameworks. Evaluating the approach on the test portion of the publicly available Cows2021 dataset, for training we use 23,350 frames across 435 single individual tracklets generated by automated oriented cattle detection and tracking in operational farm footage. Self-supervised metric learning is first employed to initialise a candidate identity space where each tracklet is considered a distinct entity. Grouping entities into equivalence classes representing cattle identities is then performed by automated merging via cluster analysis and active learning. Critically, we identify the inflection point at which automated choices cannot replicate improvements based on human intervention to reduce annotation to a minimum. Experimental results show that cluster analysis and a few minutes of labelling after automated self-supervision can improve the test identification accuracy of 153 identities to 92.44% (ARI=0.93) from the 74.9% (ARI=0.754) obtained by self-supervision only. These promising results indicate that a tailored combination of human and machine reasoning in visual cattle ID pipelines can be highly effective whilst requiring only minimal labelling effort. We provide all key source code and network weights with this paper for easy result reproduction.

Alessandro Masullo, Toby Perrett, Tilo Burghardt et al.

We propose a novel approach to multimodal sensor fusion for Ambient Assisted Living (AAL) which takes advantage of learning using privileged information (LUPI). We address two major shortcomings of standard multimodal approaches, limited area coverage and reduced reliability. Our new framework fuses the concept of modality hallucination with triplet learning to train a model with different modalities to handle missing sensors at inference time. We evaluate the proposed model on inertial data from a wearable accelerometer device, using RGB videos and skeletons as privileged modalities, and show an improvement of accuracy of an average 6.6% on the UTD-MHAD dataset and an average 5.5% on the Berkeley MHAD dataset, reaching a new state-of-the-art for inertial-only classification accuracy on these datasets. We validate our framework through several ablation studies.

Tom Raynes, Otto Brookes, Timm Haucke et al.

The estimation of abundance and density in unmarked populations of great apes relies on statistical frameworks that require animal-to-camera distance measurements. In practice, acquiring these distances depends on labour-intensive manual interpretation of animal observations across large camera trap video corpora. This study introduces and evaluates an only sparsely explored alternative: the integration of computer vision-based monocular depth estimation (MDE) pipelines directly into ecological camera trap workflows for great ape conservation. Using a real-world dataset of 220 camera trap videos documenting a wild chimpanzee population, we combine two MDE models, Dense Prediction Transformers and Depth Anything, with multiple distance sampling strategies. These components are used to generate detection distance estimates, from which population density and abundance are inferred. Comparative analysis against manually derived ground-truth distances shows that calibrated DPT consistently outperforms Depth Anything. This advantage is observed in both distance estimation accuracy and downstream density and abundance inference. Nevertheless, both models exhibit systematic biases. We show that, given complex forest environments, they tend to overestimate detection distances and consequently underestimate density and abundance relative to conventional manual approaches. We further find that failures in animal detection across distance ranges are a primary factor limiting estimation accuracy. Overall, this work provides a case study that shows MDE-driven camera trap distance sampling is a viable and practical alternative to manual distance estimation. The proposed approach yields population estimates within 22% of those obtained using traditional methods.

Kejia Zhang, Mingyu Yang, Stephen D. J. Lang et al.

African penguins (Spheniscus demersus) are an endangered species. Little is known regarding their underwater hunting strategies and associated predation success rates, yet this is essential for guiding conservation. Modern bio-logging technology has the potential to provide valuable insights, but manually analysing large amounts of data from animal-borne video recorders (AVRs) is time-consuming. In this paper, we publish an animal-borne underwater video dataset of penguins and introduce a ready-to-deploy deep learning system capable of robustly detecting penguins (mAP50@98.0%) and also instances of fish (mAP50@73.3%). We note that the detectors benefit explicitly from air-bubble learning to improve accuracy. Extending this detector towards a dual-stream behaviour recognition network, we also provide the first results for identifying predation behaviour in penguin underwater videos. Whilst results are promising, further work is required for useful applicability of predation behaviour detection in field scenarios. In summary, we provide a highly reliable underwater penguin detector, a fish detector, and a valuable first attempt towards an automated visual detection of complex behaviours in a marine predator. We publish the networks, the DivingWithPenguins video dataset, annotations, splits, and weights for full reproducibility and immediate usability by practitioners.

Wenshuo Li, Majid Mirmehdi, Tilo Burghardt

Biologists have long combined visuals with textual field notes to re-identify (Re-ID) animals. Contemporary AI tools automate this for species with distinctive morphological features but remain largely image-based. Here, we extend Re-ID methodologies by incorporating precise dermatoglyphic textual descriptors-an approach used in forensics but new to ecology. We demonstrate that these specialist semantics abstract and encode animal coat topology using human-interpretable language tags. Drawing on 84,264 manually labelled minutiae across 3,355 images of 185 tigers (Panthera tigris), we evaluate this visual-textual methodology, revealing novel capabilities for cross-modal identity retrieval. To optimise performance, we developed a text-image co-synthesis pipeline to generate 'virtual individuals', each comprising dozens of life-like visuals paired with dermatoglyphic text. Benchmarking against real-world scenarios shows this augmentation significantly boosts AI accuracy in cross-modal retrieval while alleviating data scarcity. We conclude that dermatoglyphic language-guided biometrics can overcome vision-only limitations, enabling textual-to-visual identity recovery underpinned by human-verifiable matchings. This represents a significant advance towards explainability in Re-ID and a language-driven unification of descriptive modalities in ecological monitoring.

Phoenix Yu, Tilo Burghardt, Andrew W Dowsey et al.

Holstein-Friesian detection and re-identification (Re-ID) methods capture individuals well when targets are spatially separate. However, existing approaches, including YOLO-based species detection, break down when cows group closely together. This is particularly prevalent for species which have outline-breaking coat patterns. To boost both effectiveness and transferability in this setting, we propose a new detect-segment-identify pipeline that leverages the Open-Vocabulary Weight-free Localisation and the Segment Anything models as pre-processing stages alongside Re-ID networks. To evaluate our approach, we publish a collection of nine days CCTV data filmed on a working dairy farm. Our methodology overcomes detection breakdown in dense animal groupings, resulting in a 98.93% accuracy. This significantly outperforms current oriented bounding box-driven, as well as SAM species detection baselines with accuracy improvements of 47.52% and 27.13%, respectively. We show that unsupervised contrastive learning can build on this to yield 94.82% Re-ID accuracy on our test data. Our work demonstrates that Re-ID in crowded scenarios is both practical as well as reliable in working farm settings with no manual intervention. Code and dataset are provided for reproducibility.

Jess Jones, Leonardo Bertini, Kenneth Johnson et al.

The life history of an individual coral is archived within the accreting skeleton of the colony. While reef-forming coral colonies (e.g. massive \emph{Porites} sp.) may live for hundreds of years and deposit calcareous structures many metres in height and width, their living tissue is a thin outer surface layer comprised of asexually-dividing polyps that only survive a few years. To understand the rate and timing of polyp division and the consequences for colony skeletal growth, scientists need to track the skeletal corallite deposited around each polyp. Here we propose CoralLite, an annotated μCT scan dataset of entire calcareous skeletons and an associated, first corallite deep learning reconstruction baseline. CoralLite combines fully quantified volumetric segmentations with cross-slice linking for visualisations of 3D models for each corallite up to colony scale. For segmentation, we propose and evaluate in detail a hybrid V-Trans-UNet architecture applicable to segmenting tiled μCT virtual slabs of \emph{Porites} sp. colonies. The model is pre-trained on weakly annotated data and topology-aware fine-tuned using fully annotated slice sections with 8k+ manual corallite region annotations. On unseen slices of the same colony, the resulting model reaches 0.94 topological accuracy at mean Dice scores of 0.77 on the same colony and projection axis, and 0.63 mean Dice scores on a different, biologically unrelated specimen. Whilst our experiments are limited in scale and context, our results show for the first time that visual machine learning can effectively support full 3D individual corallite modelling from μCT scans of coral skeletons alone. For reproducibility and as a baseline for future research we publish our full dataset of 697 μCT slices, 37 partial or full slice annotations, and all network weights and source code with this paper.

Dante Francisco Wasmuht, Otto Brookes, Maximillian Schall et al.

Automated video analysis is critical for wildlife conservation. A foundational task in this domain is multi-animal tracking (MAT), which underpins applications such as individual re-identification and behavior recognition. However, existing datasets are limited in scale, constrained to a few species, or lack sufficient temporal and geographical diversity - leaving no suitable benchmark for training general-purpose MAT models applicable across wild animal populations. To address this, we introduce SA-FARI, the largest open-source MAT dataset for wild animals. It comprises 11,609 camera trap videos collected over approximately 10 years (2014-2024) from 741 locations across 4 continents, spanning 99 species categories. Each video is exhaustively annotated culminating in ~46 hours of densely annotated footage containing 16,224 masklet identities and 942,702 individual bounding boxes, segmentation masks, and species labels. Alongside the task-specific annotations, we publish anonymized camera trap locations for each video. Finally, we present comprehensive benchmarks on SA-FARI using state-of-the-art vision-language models for detection and tracking, including SAM 3, evaluated with both species-specific and generic animal prompts. We also compare against vision-only methods developed specifically for wildlife analysis. SA-FARI is the first large-scale dataset to combine high species diversity, multi-region coverage, and high-quality spatio-temporal annotations, offering a new foundation for advancing generalizable multianimal tracking in the wild. The dataset is available at $\href{https://www.conservationxlabs.com/sa-fari}{\text{conservationxlabs.com/SA-FARI}}$.

Lukas Picek, Timm Haucke, Lukáš Adam et al.

Recognizing individual animals over time is central to many ecological and conservation questions, including estimating abundance, survival, movement, and social structure. Recent advances in automated identification from images and even acoustic data suggest that this process could be greatly accelerated, yet their promise has not translated well into ecological practice. We argue that the main barrier is not the performance of the automated methods themselves, but a mismatch between how those methods are typically developed and evaluated, and how ecological data is actually collected, processed, reviewed, and used. Future progress, therefore, will depend less on algorithmic gains alone than on recognizing that the usefulness of automated identification is grounded in ecological context: it depends on what question is being asked, what data are available, and what kinds of mistakes matter. Only by centering these questions can we move toward automated identification of individuals that is not only accurate but also ecologically useful, transparent, and trustworthy.

Nguyen Ngoc Dat, Tom Richardson, Matthew Watson et al.

Live tracking of wildlife via high-resolution video processing directly onboard drones is widely unexplored and most existing solutions rely on streaming video to ground stations to support navigation. Yet, both autonomous animal-reactive flight control beyond visual line of sight and/or mission-specific individual and behaviour recognition tasks rely to some degree on this capability. In response, we introduce WildLive - a near real-time animal detection and tracking framework for high-resolution imagery running directly onboard uncrewed aerial vehicles (UAVs). The system performs multi-animal detection and tracking at 17.81fps for HD and 7.53fps on 4K video streams suitable for operation during higher altitude flights to minimise animal disturbance. Our system is optimised for Jetson Orin AGX onboard hardware. It integrates the efficiency of sparse optical flow tracking and mission-specific sampling with device-optimised and proven YOLO-driven object detection and segmentation techniques. Essentially, computational resource is focused onto spatio-temporal regions of high uncertainty to significantly improve UAV processing speeds. Alongside, we introduce our WildLive dataset, which comprises 200K+ annotated animal instances across 19K+ frames from 4K UAV videos collected at the Ol Pejeta Conservancy in Kenya. All frames contain ground truth bounding boxes, segmentation masks, as well as individual tracklets and tracking point trajectories. We compare our system against current object tracking approaches including OC-SORT, ByteTrack, and SORT. Our multi-animal tracking experiments with onboard hardware confirm that near real-time high-resolution wildlife tracking is possible on UAVs whilst maintaining high accuracy levels as needed for future navigational and mission-specific animal-centric operational autonomy. Our materials are available at: https://dat-nguyenvn.github.io/WildLive/

Otto Brookes, Majid Mirmehdi, Hjalmar Kuhl et al.

We show that chimpanzee behaviour understanding from camera traps can be enhanced by providing visual architectures with access to an embedding of text descriptions that detail species behaviours. In particular, we present a vision-language model which employs multi-modal decoding of visual features extracted directly from camera trap videos to process query tokens representing behaviours and output class predictions. Query tokens are initialised using a standardised ethogram of chimpanzee behaviour, rather than using random or name-based initialisations. In addition, the effect of initialising query tokens using a masked language model fine-tuned on a text corpus of known behavioural patterns is explored. We evaluate our system on the PanAf500 and PanAf20K datasets and demonstrate the performance benefits of our multi-modal decoding approach and query initialisation strategy on multi-class and multi-label recognition tasks, respectively. Results and ablations corroborate performance improvements. We achieve state-of-the-art performance over vision and vision-language models in top-1 accuracy (+6.34%) on PanAf500 and overall (+1.1%) and tail-class (+2.26%) mean average precision on PanAf20K. We share complete source code and network weights for full reproducibility of results and easy utilisation.

Asheesh Sharma, Lucy Randewich, William Andrew et al.

This paper proposes and evaluates, for the first time, a top-down (dorsal view), depth-only deep learning system for accurately identifying individual cattle and provides associated code, datasets, and training weights for immediate reproducibility. An increase in herd size skews the cow-to-human ratio at the farm and makes the manual monitoring of individuals more challenging. Therefore, real-time cattle identification is essential for the farms and a crucial step towards precision livestock farming. Underpinned by our previous work, this paper introduces a deep-metric learning method for cattle identification using depth data from an off-the-shelf 3D camera. The method relies on CNN and MLP backbones that learn well-generalised embedding spaces from the body shape to differentiate individuals -- requiring neither species-specific coat patterns nor close-up muzzle prints for operation. The network embeddings are clustered using a simple algorithm such as $k$-NN for highly accurate identification, thus eliminating the need to retrain the network for enrolling new individuals. We evaluate two backbone architectures, ResNet, as previously used to identify Holstein Friesians using RGB images, and PointNet, which is specialised to operate on 3D point clouds. We also present CowDepth2023, a new dataset containing 21,490 synchronised colour-depth image pairs of 99 cows, to evaluate the backbones. Both ResNet and PointNet architectures, which consume depth maps and point clouds, respectively, led to high accuracy that is on par with the coat pattern-based backbone.

Chengxi Zeng, Tilo Burghardt, Alberto M Gambaruto

While many recent Physics-Informed Neural Networks (PINNs) variants have had considerable success in solving Partial Differential Equations, the empirical benefits of feature mapping drawn from the broader Neural Representations research have been largely overlooked. We highlight the limitations of widely used Fourier-based feature mapping in certain situations and suggest the use of the conditionally positive definite Radial Basis Function. The empirical findings demonstrate the effectiveness of our approach across a variety of forward and inverse problem cases. Our method can be seamlessly integrated into coordinate-based input neural networks and contribute to the wider field of PINNs research.

Chengxi Zeng, Yuxuan Jiang, Fan Zhang et al.

The deployment of foundation models for medical imaging has demonstrated considerable success. However, their training overheads associated with downstream tasks remain substantial due to the size of the image encoders employed, and the inference complexity is also significantly high. Although lightweight variants have been obtained for these foundation models, their performance is constrained by their limited model capacity and suboptimal training strategies. In order to achieve an improved tradeoff between complexity and performance, we propose a new framework to improve the performance of low complexity models via knowledge distillation from multiple large medical foundation models (e.g., MedSAM, RAD-DINO, MedCLIP), each specializing in different vision tasks, with the goal to effectively bridge the performance gap for medical image segmentation tasks. The agglomerated model demonstrates superior generalization across 12 segmentation tasks, whereas specialized models require explicit training for each task. Our approach achieved an average performance gain of 2\% in Dice coefficient compared to simple distillation.

Otto Brookes, Maksim Kukushkin, Majid Mirmehdi et al.

Computer vision analysis of camera trap video footage is essential for wildlife conservation, as captured behaviours offer some of the earliest indicators of changes in population health. Recently, several high-impact animal behaviour datasets and methods have been introduced to encourage their use; however, the role of behaviour-correlated background information and its significant effect on out-of-distribution generalisation remain unexplored. In response, we present the PanAf-FGBG dataset, featuring 20 hours of wild chimpanzee behaviours, recorded at over 350 individual camera locations. Uniquely, it pairs every video with a chimpanzee (referred to as a foreground video) with a corresponding background video (with no chimpanzee) from the same camera location. We present two views of the dataset: one with overlapping camera locations and one with disjoint locations. This setup enables, for the first time, direct evaluation of in-distribution and out-of-distribution conditions, and for the impact of backgrounds on behaviour recognition models to be quantified. All clips come with rich behavioural annotations and metadata including unique camera IDs and detailed textual scene descriptions. Additionally, we establish several baselines and present a highly effective latent-space normalisation technique that boosts out-of-distribution performance by +5.42% mAP for convolutional and +3.75% mAP for transformer-based models. Finally, we provide an in-depth analysis on the role of backgrounds in out-of-distribution behaviour recognition, including the so far unexplored impact of background durations (i.e., the count of background frames within foreground videos).

Chengxi Zeng, David Smithard, Alberto M Gambaruto et al.

Vision foundation models have demonstrated exceptional generalization capabilities in segmentation tasks for both generic and specialized images. However, a performance gap persists between foundation models and task-specific, specialized models. Fine-tuning foundation models on downstream datasets is often necessary to bridge this gap. Unfortunately, obtaining fully annotated ground truth for downstream datasets is both challenging and costly. To address this limitation, we propose a novel test-time training paradigm that enhances the performance of foundation models on downstream datasets without requiring full annotations. Specifically, our method employs simple point prompts to guide a test-time semi-self-supervised training task. The model learns by resolving the ambiguity of the point prompt through various augmentations. This approach directly tackles challenges in the medical imaging field, where acquiring annotations is both time-intensive and expensive. We conducted extensive experiments on our new Videofluoroscopy dataset (VFSS-5k) for the instance segmentation task, achieving an average Dice coefficient of 0.868 across 12 anatomies with a single model.

Phoenix Yu, Tilo Burghardt, Andrew W Dowsey et al.

We present MultiCamCows2024, a farm-scale image dataset filmed across multiple cameras for the biometric identification of individual Holstein-Friesian cattle exploiting their unique black and white coat-patterns. Captured by three ceiling-mounted visual sensors covering adjacent barn areas over seven days on a working dairy farm, the dataset comprises 101,329 images of 90 cows, plus underlying original CCTV footage. The dataset is provided with full computer vision recognition baselines, that is both a supervised and self-supervised learning framework for individual cow identification trained on cattle tracklets. We report a performance above 96% single image identification accuracy from the dataset and demonstrate that combining data from multiple cameras during learning enhances self-supervised identification. We show that our framework enables automatic cattle identification, barring only the simple human verification of tracklet integrity during data collection. Crucially, our study highlights that multi-camera, supervised and self-supervised components in tandem not only deliver highly accurate individual cow identification, but also achieve this efficiently with no labelling of cattle identities by humans. We argue that this improvement in efficacy has practical implications for livestock management, behaviour analysis, and agricultural monitoring. For reproducibility and practical ease of use, we publish all key software and code including re-identification components and the species detector with this paper, available at https://tinyurl.com/MultiCamCows2024.

Chengxi Zeng, Tilo Burghardt, Alberto M Gambaruto

In this paper, the training dynamics of PINNs with a feature mapping layer via the limiting Conjugate Kernel and Neural Tangent Kernel is investigated, shedding light on the convergence of PINNs; Although the commonly used Fourier-based feature mapping has achieved great success, we show its inadequacy in some physics scenarios. Via these two scopes, we propose conditionally positive definite Radial Basis Function as a better alternative. Lastly, we explore the feature mapping numerically in wide neural networks. Our empirical results reveal the efficacy of our method in diverse forward and inverse problem sets. Composing feature functions is found to be a practical way to address the expressivity and generalisability trade-off, viz., tuning the bandwidth of the kernels and the surjectivity of the feature mapping function. This simple technique can be implemented for coordinate inputs and benefits the broader PINNs research.

Zehua Liu, Tilo Burghardt

As most ''in the wild'' data collections of the natural world, the North America Camera Trap Images (NACTI) dataset shows severe long-tailed class imbalance, noting that the largest 'Head' class alone covers >50% of the 3.7M images in the corpus. Building on the PyTorch Wildlife model, we present a systematic study of Long-Tail Recognition methodologies for species recognition on the NACTI dataset covering experiments on various LTR loss functions plus LTR-sensitive regularisation. Our best configuration achieves 99.40% Top-1 accuracy on our NACTI test data split, substantially improving over a 95.51% baseline using standard cross-entropy with Adam. This also improves on previously reported top performance in MLWIC2 at 96.8% albeit using partly unpublished (potentially different) partitioning, optimiser, and evaluation protocols. To evaluate domain shifts (e.g. night-time captures, occlusion, motion-blur) towards other datasets we construct a Reduced-Bias Test set from the ENA-Detection dataset where our experimentally optimised long-tail enhanced model achieves leading 52.55% accuracy (up from 51.20% with WCE loss), demonstrating stronger generalisation capabilities under distribution shift. We document the consistent improvements of LTR-enhancing scheduler choices in this NACTI wildlife domain, particularly when in tandem with state-of-the-art LTR losses. We finally discuss qualitative and quantitative shortcomings that LTR methods cannot sufficiently address, including catastrophic breakdown for 'Tail' classes under severe domain shift. For maximum reproducibility we publish all dataset splits, key code, and full network weights.

Alex Hoi Hang Chan, Otto Brookes, Urs Waldmann et al.

Computer vision methods have demonstrated considerable potential to streamline ecological and biological workflows, with a growing number of datasets and models becoming available to the research community. However, these resources focus predominantly on evaluation using machine learning metrics, with relatively little emphasis on how their application impacts downstream analysis. We argue that models should be evaluated using application-specific metrics that directly represent model performance in the context of its final use case. To support this argument, we present two disparate case studies: (1) estimating chimpanzee abundance and density with camera trap distance sampling when using a video-based behaviour classifier and (2) estimating head rotation in pigeons using a 3D posture estimator. We show that even models with strong machine learning performance (e.g., 87% mAP) can yield data that leads to discrepancies in abundance estimates compared to expert-derived data. Similarly, the highest-performing models for posture estimation do not produce the most accurate inferences of gaze direction in pigeons. Motivated by these findings, we call for researchers to integrate application-specific metrics in ecological/biological datasets, allowing for models to be benchmarked in the context of their downstream application and to facilitate better integration of models into application workflows.

Jenna Kline, Samuel Stevens, Guy Maalouf et al.

Real-time wildlife detection in drone imagery supports critical ecological and conservation monitoring. However, standard detection models like YOLO often fail to generalize across locations and struggle with rare species, limiting their use in automated drone deployments. We present MMLA, a novel multi-environment, multi-species, low-altitude drone dataset collected across three sites (Ol Pejeta Conservancy and Mpala Research Centre in Kenya, and The Wilds in Ohio), featuring six species (zebras, giraffes, onagers, and African wild dogs). The dataset contains 811K annotations from 37 high-resolution videos. Baseline YOLO models show performance disparities across locations while fine-tuning YOLOv11m on MMLA improves mAP50 to 82%, a 52-point gain over baseline. Our results underscore the need for diverse training data to enable robust animal detection in autonomous drone systems.

Otto Brookes, Majid Mirmehdi, Colleen Stephens et al.

We present the PanAf20K dataset, the largest and most diverse open-access annotated video dataset of great apes in their natural environment. It comprises more than 7 million frames across ~20,000 camera trap videos of chimpanzees and gorillas collected at 14 field sites in tropical Africa as part of the Pan African Programme: The Cultured Chimpanzee. The footage is accompanied by a rich set of annotations and benchmarks making it suitable for training and testing a variety of challenging and ecologically important computer vision tasks including ape detection and behaviour recognition. Furthering AI analysis of camera trap information is critical given the International Union for Conservation of Nature now lists all species in the great ape family as either Endangered or Critically Endangered. We hope the dataset can form a solid basis for engagement of the AI community to improve performance, efficiency, and result interpretation in order to support assessments of great ape presence, abundance, distribution, and behaviour and thereby aid conservation efforts.

Tayfun Karaderi, Tilo Burghardt, Raphael Morard et al.

Visual as well as genetic biometrics are routinely employed to identify species and individuals in biological applications. However, no attempts have been made in this domain to computationally enhance visual classification of rare classes with little image data via genetics. In this paper, we thus propose aligned visual-genetic inference spaces with the aim to implicitly encode cross-domain associations for improved performance. We demonstrate for the first time that such alignment can be achieved via deep embedding models and that the approach is directly applicable to boosting long-tailed recognition (LTR) particularly for rare species. We experimentally demonstrate the efficacy of the concept via application to microscopic imagery of 30k+ planktic foraminifer shells across 32 species when used together with independent genetic data samples. Most importantly for practitioners, we show that visual-genetic alignment can significantly benefit visual-only recognition of the rarest species. Technically, we pre-train a visual ResNet50 deep learning model using triplet loss formulations to create an initial embedding space. We re-structure this space based on genetic anchors embedded via a Sequence Graph Transform (SGT) and linked to visual data by cross-domain cosine alignment. We show that an LTR approach improves the state-of-the-art across all benchmarks and that adding our visual-genetic alignment improves per-class and particularly rare tail class benchmarks significantly further. We conclude that visual-genetic alignment can be a highly effective tool for complementing visual biological data containing rare classes. The concept proposed may serve as an important future tool for integrating genetics and imageomics towards a more complete scientific representation of taxonomic spaces and life itself. Code, weights, and data splits are published for full reproducibility.

Tayfun Karaderi, Tilo Burghardt, Allison Y. Hsiang et al.

We apply deep metric learning for the first time to the problem of classifying planktic foraminifer shells on microscopic images. This species recognition task is an important information source and scientific pillar for reconstructing past climates. All foraminifer CNN recognition pipelines in the literature produce black-box classifiers that lack visualization options for human experts and cannot be applied to open-set problems. Here, we benchmark metric learning against these pipelines, produce the first scientific visualization of the phenotypic planktic foraminifer morphology space, and demonstrate that metric learning can be used to cluster species unseen during training. We show that metric learning outperforms all published CNN-based state-of-the-art benchmarks in this domain. We evaluate our approach on the 34,640 expert-annotated images of the Endless Forams public library of 35 modern planktic foraminifera species. Our results on this data show leading 92% accuracy (at 0.84 F1-score) in reproducing expert labels on withheld test data, and 66.5% accuracy (at 0.70 F1-score) when clustering species never encountered in training. We conclude that metric learning is highly effective for this domain and serves as an important tool towards expert-in-the-loop automation of microfossil identification. Keycode, network weights, and data splits are published with this paper for full reproducibility.

Mowen Xue, Theo Greenslade, Majid Mirmehdi et al.

Visuals captured by high-flying aerial drones are increasingly used to assess biodiversity and animal population dynamics around the globe. Yet, challenging acquisition scenarios and tiny animal depictions in airborne imagery, despite ultra-high resolution cameras, have so far been limiting factors for applying computer vision detectors successfully with high confidence. In this paper, we address the problem for the first time by combining deep object detectors with super-resolution techniques and altitude data. In particular, we show that the integration of a holistic attention network based super-resolution approach and a custom-built altitude data exploitation network into standard recognition pipelines can considerably increase the detection efficacy in real-world settings. We evaluate the system on two public, large aerial-capture animal datasets, SAVMAP and AED. We find that the proposed approach can consistently improve over ablated baselines and the state-of-the-art performance for both datasets. In addition, we provide a systematic analysis of the relationship between animal resolution and detection performance. We conclude that super-resolution and altitude knowledge exploitation techniques can significantly increase benchmarks across settings and, thus, should be used routinely when detecting minutely resolved animals in aerial imagery.

Devis Tuia, Benjamin Kellenberger, Sara Beery et al.

Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold great potential for large-scale environmental monitoring and understanding, but are limited by current data processing approaches which are inefficient in how they ingest, digest, and distill data into relevant information. We argue that machine learning, and especially deep learning approaches, can meet this analytic challenge to enhance our understanding, monitoring capacity, and conservation of wildlife species. Incorporating machine learning into ecological workflows could improve inputs for population and behavior models and eventually lead to integrated hybrid modeling tools, with ecological models acting as constraints for machine learning models and the latter providing data-supported insights. In essence, by combining new machine learning approaches with ecological domain knowledge, animal ecologists can capitalize on the abundance of data generated by modern sensor technologies in order to reliably estimate population abundances, study animal behavior and mitigate human/wildlife conflicts. To succeed, this approach will require close collaboration and cross-disciplinary education between the computer science and animal ecology communities in order to ensure the quality of machine learning approaches and train a new generation of data scientists in ecology and conservation.

Jing Gao, Tilo Burghardt, William Andrew et al.

In this paper we publish the largest identity-annotated Holstein-Friesian cattle dataset Cows2021 and a first self-supervision framework for video identification of individual animals. The dataset contains 10,402 RGB images with labels for localisation and identity as well as 301 videos from the same herd. The data shows top-down in-barn imagery, which captures the breed's individually distinctive black and white coat pattern. Motivated by the labelling burden involved in constructing visual cattle identification systems, we propose exploiting the temporal coat pattern appearance across videos as a self-supervision signal for animal identity learning. Using an individual-agnostic cattle detector that yields oriented bounding-boxes, rotation-normalised tracklets of individuals are formed via tracking-by-detection and enriched via augmentations. This produces a `positive' sample set per tracklet, which is paired against a `negative' set sampled from random cattle of other videos. Frame-triplet contrastive learning is then employed to construct a metric latent space. The fitting of a Gaussian Mixture Model to this space yields a cattle identity classifier. Results show an accuracy of Top-1 57.0% and Top-4: 76.9% and an Adjusted Rand Index: 0.53 compared to the ground truth. Whilst supervised training surpasses this benchmark by a large margin, we conclude that self-supervision can nevertheless play a highly effective role in speeding up labelling efforts when initially constructing supervision information. We provide all data and full source code alongside an analysis and evaluation of the system.

Toby Perrett, Alessandro Masullo, Tilo Burghardt et al.

We propose a novel approach to few-shot action recognition, finding temporally-corresponding frame tuples between the query and videos in the support set. Distinct from previous few-shot works, we construct class prototypes using the CrossTransformer attention mechanism to observe relevant sub-sequences of all support videos, rather than using class averages or single best matches. Video representations are formed from ordered tuples of varying numbers of frames, which allows sub-sequences of actions at different speeds and temporal offsets to be compared. Our proposed Temporal-Relational CrossTransformers (TRX) achieve state-of-the-art results on few-shot splits of Kinetics, Something-Something V2 (SSv2), HMDB51 and UCF101. Importantly, our method outperforms prior work on SSv2 by a wide margin (12%) due to the its ability to model temporal relations. A detailed ablation showcases the importance of matching to multiple support set videos and learning higher-order relational CrossTransformers.

Otto Brookes, Tilo Burghardt

We put forward a video dataset with 5k+ facial bounding box annotations across a troop of 7 western lowland gorillas at Bristol Zoo Gardens. Training on this dataset, we implement and evaluate a standard deep learning pipeline on the task of facially recognising individual gorillas in a zoo environment. We show that a basic YOLOv3-powered application is able to perform identifications at 92% mAP when utilising single frames only. Tracking-by-detection-association and identity voting across short tracklets yields an improved robust performance of 97% mAP. To facilitate easy utilisation for enriching the research capabilities of zoo environments, we publish the code, video dataset, weights, and ground-truth annotations at data.bris.ac.uk.

Faizaan Sakib, Tilo Burghardt

We propose a first great ape-specific visual behaviour recognition system utilising deep learning that is capable of detecting nine core ape behaviours.

Xinyu Yang, Majid Mirmehdi, Tilo Burghardt

In this paper we show that learning video feature spaces in which temporal cycles are maximally predictable benefits action classification. In particular, we propose a novel learning approach termed Cycle Encoding Prediction (CEP) that is able to effectively represent high-level spatio-temporal structure of unlabelled video content. CEP builds a latent space wherein the concept of closed forward-backward as well as backward-forward temporal loops is approximately preserved. As a self-supervision signal, CEP leverages the bi-directional temporal coherence of the video stream and applies loss functions that encourage both temporal cycle closure as well as contrastive feature separation. Architecturally, the underpinning network structure utilises a single feature encoder for all video snippets, adding two predictive modules that learn temporal forward and backward transitions. We apply our framework for pretext training of networks for action recognition tasks. We report significantly improved results for the standard datasets UCF101 and HMDB51. Detailed ablation studies support the effectiveness of the proposed components. We publish source code for the CEP components in full with this paper.

Toby Perrett, Alessandro Masullo, Tilo Burghardt et al.

Meta-learning approaches have addressed few-shot problems by finding initialisations suited for fine-tuning to target tasks. Often there are additional properties within training data (which we refer to as context), not relevant to the target task, which act as a distractor to meta-learning, particularly when the target task contains examples from a novel context not seen during training. We address this oversight by incorporating a context-adversarial component into the meta-learning process. This produces an initialisation for fine-tuning to target which is both context-agnostic and task-generalised. We evaluate our approach on three commonly used meta-learning algorithms and two problems. We demonstrate our context-agnostic meta-learning improves results in each case. First, we report on Omniglot few-shot character classification, using alphabets as context. An average improvement of 4.3% is observed across methods and tasks when classifying characters from an unseen alphabet. Second, we evaluate on a dataset for personalised energy expenditure predictions from video, using participant knowledge as context. We demonstrate that context-agnostic meta-learning decreases the average mean square error by 30%.

William Andrew, Jing Gao, Siobhan Mullan et al.

Holstein-Friesian cattle exhibit individually-characteristic black and white coat patterns visually akin to those arising from Turing's reaction-diffusion systems. This work takes advantage of these natural markings in order to automate visual detection and biometric identification of individual Holstein-Friesians via convolutional neural networks and deep metric learning techniques. Existing approaches rely on markings, tags or wearables with a variety of maintenance requirements, whereas we present a totally hands-off method for the automated detection, localisation, and identification of individual animals from overhead imaging in an open herd setting, i.e. where new additions to the herd are identified without re-training. We propose the use of SoftMax-based reciprocal triplet loss to address the identification problem and evaluate the techniques in detail against fixed herd paradigms. We find that deep metric learning systems show strong performance even when many cattle unseen during system training are to be identified and re-identified -- achieving 93.8% accuracy when trained on just half of the population. This work paves the way for facilitating the non-intrusive monitoring of cattle applicable to precision farming and surveillance for automated productivity, health and welfare monitoring, and to veterinary research such as behavioural analysis, disease outbreak tracing, and more. Key parts of the source code, network weights and datasets are available publicly.

Alessandro Masullo, Tilo Burghardt, Toby Perrett et al.

We present the first fully automated Sit-to-Stand or Stand-to-Sit (StS) analysis framework for long-term monitoring of patients in free-living environments using video silhouettes. Our method adopts a coarse-to-fine time localisation approach, where a deep learning classifier identifies possible StS sequences from silhouettes, and a smart peak detection stage provides fine localisation based on 3D bounding boxes. We tested our method on data from real homes of participants and monitored patients undergoing total hip or knee replacement. Our results show 94.4% overall accuracy in the coarse localisation and an error of 0.026 m/s in the speed of ascent measurement, highlighting important trends in the recuperation of patients who underwent surgery.

Xinyu Yang, Majid Mirmehdi, Tilo Burghardt

We propose the first multi-frame video object detection framework trained to detect great apes. It is applicable to challenging camera trap footage in complex jungle environments and extends a traditional feature pyramid architecture by adding self-attention driven feature blending in both the spatial as well as the temporal domain. We demonstrate that this extension can detect distinctive species appearance and motion signatures despite significant partial occlusion. We evaluate the framework using 500 camera trap videos of great apes from the Pan African Programme containing 180K frames, which we manually annotated with accurate per-frame animal bounding boxes. These clips contain significant partial occlusions, challenging lighting, dynamic backgrounds, and natural camouflage effects. We show that our approach performs highly robustly and significantly outperforms frame-based detectors. We also perform detailed ablation studies and validation on the full ILSVRC 2015 VID data corpus to demonstrate wider applicability at adequate performance levels. We conclude that the framework is ready to assist human camera trap inspection efforts. We publish code, weights, and ground truth annotations with this paper.

William Andrew, Colin Greatwood, Tilo Burghardt

This paper describes a computationally-enhanced M100 UAV platform with an onboard deep learning inference system for integrated computer vision and navigation able to autonomously find and visually identify by coat pattern individual Holstein Friesian cattle in freely moving herds. We propose an approach that utilises three deep convolutional neural network architectures running live onboard the aircraft; that is, a YoloV2-based species detector, a dual-stream CNN delivering exploratory agency and an InceptionV3-based biometric LRCN for individual animal identification. We evaluate the performance of each of the components offline, and also online via real-world field tests comprising 146.7 minutes of autonomous low altitude flight in a farm environment over a dispersed herd of 17 heifer dairy cows. We report error-free identification performance on this online experiment. The presented proof-of-concept system is the first of its kind and a successful step towards autonomous biometric identification of individual animals from the air in open pasture environments for tag-less AI support in farming and ecology.

Rory Smith, Tilo Burghardt

This paper describes DeepKey, an end-to-end deep neural architecture capable of taking a digital RGB image of an 'everyday' scene containing a pin tumbler key (e.g. lying on a table or carpet) and fully automatically inferring a printable 3D key model. We report on the key detection performance and describe how candidates can be transformed into physical prints. We show an example opening a real-world lock. Our system is described in detail, providing a breakdown of all components including key detection, pose normalisation, bitting segmentation and 3D model inference. We provide an in-depth evaluation and conclude by reflecting on limitations, applications, potential security risks and societal impact. We contribute the DeepKey Datasets of 5, 300+ images covering a few test keys with bounding boxes, pose and unaligned mask data.

Alessandro Masullo, Tilo Burghardt, Dima Damen et al.

We propose a novel deep fusion architecture, CaloriNet, for the online estimation of energy expenditure for free living monitoring in private environments, where RGB data is discarded and replaced by silhouettes. Our fused convolutional neural network architecture is trainable end-to-end, to estimate calorie expenditure, using temporal foreground silhouettes alongside accelerometer data. The network is trained and cross-validated on a publicly available dataset, SPHERE_RGBD + Inertial_calorie. Results show state-of-the-art minimum error on the estimation of energy expenditure (calories per minute), outperforming alternative, standard and single-modal techniques.

Víctor Ponce-López, Tilo Burghardt, Sion Hannunna et al.

We present a deep person re-identification approach that combines semantically selective, deep data augmentation with clustering-based network compression to generate high performance, light and fast inference networks. In particular, we propose to augment limited training data via sampling from a deep convolutional generative adversarial network (DCGAN), whose discriminator is constrained by a semantic classifier to explicitly control the domain specificity of the generation process. Thereby, we encode information in the classifier network which can be utilized to steer adversarial synthesis, and which fuels our CondenseNet ID-network training. We provide a quantitative and qualitative analysis of the approach and its variants on a number of datasets, obtaining results that outperform the state-of-the-art on the LIMA dataset for long-term monitoring in indoor living spaces.

Benjamin Hughes, Tilo Burghardt

This paper discusses the automated visual identification of individual great white sharks from dorsal fin imagery. We propose a computer vision photo ID system and report recognition results over a database of thousands of unconstrained fin images. To the best of our knowledge this line of work establishes the first fully automated contour-based visual ID system in the field of animal biometrics. The approach put forward appreciates shark fins as textureless, flexible and partially occluded objects with an individually characteristic shape. In order to recover animal identities from an image we first introduce an open contour stroke model, which extends multi-scale region segmentation to achieve robust fin detection. Secondly, we show that combinatorial, scale-space selective fingerprinting can successfully encode fin individuality. We then measure the species-specific distribution of visual individuality along the fin contour via an embedding into a global `fin space'. Exploiting this domain, we finally propose a non-linear model for individual animal recognition and combine all approaches into a fine-grained multi-instance framework. We provide a system evaluation, compare results to prior work, and report performance and properties in detail.

Lili Tao, Tilo Burghardt, Majid Mirmehdi et al.

We present a new framework for vision-based estimation of calorific expenditure from RGB-D data - the first that is validated on physical gas exchange measurements and applied to daily living scenarios. Deriving a person's energy expenditure from sensors is an important tool in tracking physical activity levels for health and lifestyle monitoring. Most existing methods use metabolic lookup tables (METs) for a manual estimate or systems with inertial sensors which ultimately require users to wear devices. In contrast, the proposed pose-invariant and individual-independent vision framework allows for a remote estimation of calorific expenditure. We introduce, and evaluate our approach on, a new dataset called SPHERE-calorie, for which visual estimates can be compared against simultaneously obtained, indirect calorimetry measures based on gas exchange. % based on per breath gas exchange. We conclude from our experiments that the proposed vision pipeline is suitable for home monitoring in a controlled environment, with calorific expenditure estimates above accuracy levels of commonly used manual estimations via METs. With the dataset released, our work establishes a baseline for future research for this little-explored area of computer vision.

Massimo Camplani, Adeline Paiement, Majid Mirmehdi et al.

Multiple human tracking (MHT) is a fundamental task in many computer vision applications. Appearance-based approaches, primarily formulated on RGB data, are constrained and affected by problems arising from occlusions and/or illumination variations. In recent years, the arrival of cheap RGB-Depth (RGB-D) devices has {led} to many new approaches to MHT, and many of these integrate color and depth cues to improve each and every stage of the process. In this survey, we present the common processing pipeline of these methods and review their methodology based (a) on how they implement this pipeline and (b) on what role depth plays within each stage of it. We identify and introduce existing, publicly available, benchmark datasets and software resources that fuse color and depth data for MHT. Finally, we present a brief comparative evaluation of the performance of those works that have applied their methods to these datasets.