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Sara Beery

Publications and source records attributed to Sara Beery.

At least 19 recordsLinked to original sources
arXiv2026

Targeted Review for AI-Assisted Biodiversity Surveys: Active Continuous-Score Occupancy Modeling

We increasingly use machine learning to label scientific datasets. The models we develop and deploy are improving all the time, but they are not and will likely never be perfect. Mistakes matter, as errors can propagate into our scientific understanding, particularly when systematically biased. Very reasonably, scientists thus review substantial proportions of ML-generated labels to verify or correct mistakes in pursuit of ensuring their scientific findings are not biased by ML. In this work, we focus on helping scientists optimally allocate this reviewing effort relative to their scientific goals. We focus on a specific class of scientists (ecologists) and a specific, widespread, and impactful modeling target (occupancy modeling, which estimates where species are likely to occur, conditioned on environmental factors). We introduce Active Continuous-Score Occupancy Modeling (ACORN), a method that incorporates ML predictions into occupancy models and strategically selects samples for expert review that are maximally informative for downstream ecological analysis. Across camera-trap and bioacoustic datasets, our method recovers ecological conclusions close to those obtained from fully human-labeled data, while requiring substantially fewer expert reviews than non-targeted review policies. Our results suggest that ML-assisted scientific workflows should optimize expert effort for downstream inference, rather than for classifier accuracy alone, especially when human review budget is limited. Our code is available at https://github.com/timmh/acorn

cs.LG↗
arXiv2026

BioDCASE: Active Learning for Bioacoustics

Ecological monitoring increasingly relies on machine learning models, whose performance depends on the quality and quantity of labelled data. However, obtaining these labels is costly, particularly in passive acoustic monitoring, where vast amounts of data are collected but only a small proportion can feasibly be annotated. Active learning addresses this bottleneck by prioritizing which samples should be labelled. However, progress is difficult to measure, because published methods are evaluated under different models, budgets, evaluation metrics and datasets. To address this challenge, we present the 2026 Active Learning for Bioacoustics BioDCASE challenge: a systematic evaluation of sampling methods designed to identify effective AL strategies. Participant methods were evaluated across four subsets composed of terrestrial and marine data. Across ten proposed sampling methods from seven teams, the top-ranked method achieved an area under the learning curve 26.4 % higher than random sampling at the same annotation budget, averaged over four data subsets. Significant variation in performance was observed across subsets, with the top-performing submission achieving a 67.1 % gain for the HSN subset over random sampling and a gain of 8 % for the ATBFL subset. Top-ranking submissions combined multiple acquisition signals, and diversity-based selection outperformed pure uncertainty sampling. Furthermore, there is evidence that transitioning from diversity-based to uncertainty-based selection and explicitly reducing redundancy within acquisition batches improve model training. There is also initial evidence that larger acquisition batch sizes may be increasingly beneficial later in the labelling process.

cs.LG↗
arXiv2026

MoveBench: A Benchmark for Global-Scale Wildlife Movement Forecasting

Understanding and predicting wildlife movement is critical for ecology and conservation. While trajectory forecasting has advanced for human and vehicle movement, wildlife trajectories present distinct challenges: they are unconstrained in space, highly stochastic, and influenced by environmental conditions. We introduce MoveBench, the first large-scale benchmark for probabilistic wildlife movement forecasting, containing 2.6M GPS locations from 800+ individuals across 110 species in 127 countries, paired with 1.6B environmental raster tiles capturing 160 covariates known or hypothesized to influence movement. We propose a probabilistic evaluation protocol for movement trajectory forecasts, addressing limitations of point-prediction metrics for inherently stochastic phenomena. Through comprehensive empirical evaluation of four method families across multiple temporal and spatial scales, we reveal that: (1) existing predictive methods generalize better to future timepoints than to unseen individuals, (2) deep learning approaches do not consistently outperform simpler baselines, and (3) environmental covariate selection significantly impacts performance. MoveBench enables standardized evaluation of movement forecasting methods and provides a foundation for methodological advances on this ecologically important task.

cs.LG↗
arXiv2026

Teach a Molmo2Fish: Towards interactive fish tracking with natural language guidance

Computer vision is increasingly used to automate recognition tasks in large ecological datasets, but more complex tasks such as multi-object tracking continue to pose challenges. As researchers seek to incorporate vision models in ecology workflows, various lines of research have explored how to make imperfect predictions useful through human-in-the-loop processes. We propose a new approach to working with imperfect tracking predictions through an interactive prediction correction workflow taking place as a conversation with a multimodal large language model, which we tailor to a sonar fish tracking dataset as an initial proof of concept. We investigate the performance of the tool, Molmo2Fish, across guided and unguided tasks, correcting its own predicted tracks and external tracks. We find that Molmo2Fish achieves high performance on fish tracking and track correction tasks, but there is still much room to improve on incorporating natural language guidance. The code and data are publicly available at https://github.com/tidalove/molmo2fish.

cs.CV↗
arXiv2026

Oh Deer, How Should I Handle This? Seasonal Priors for Selective Wildlife Annotation and Classification

Fine-grained wildlife classification in aerial imagery is limited not only by model performance, but also by unreliable labels: animals occupy few pixels, key visual cues vary seasonally, and modality-specific evidence can be ambiguous. We study adult-male identification in red deer ($\textit{Cervus elaphus}$), where the antler cycle defines predictable windows of reliable evidence for both annotation and prediction. Using 7,295 RGB-only, thermal-only, and matched RGB+thermal crop sets from low-altitude UAV surveys, labeled by three annotators, we show that seasonal structure links (I) annotation quality, (II) downstream classification, and (III) selective prediction. Matched RGB+thermal review resolves more samples than either single modality, recovering majority-male labels otherwise missed by RGB or thermal alone, in human-based as well as model-based classification. Months with high annotator abstention also show lower classifier confidence, and soft seasonal priors mainly benefit the season-limited thermal view. Uncertainty-band abstention further raises covered accuracy to 98.9%, though at reduced coverage and with deferral that falls disproportionately on males. Overall, a biologically grounded seasonal calendar predicts where annotation and prediction are unreliable, and can guide both annotation protocol design and modality weighting.

cs.CV↗
arXiv2026

When One Modality Is Not Enough: Multimodal Sex and Life-Stage Classification of Red Deer from Aerial RGB-Thermal Video

Aerial drone surveys increasingly support wildlife population estimation, yet a useful census is more than a count: population dynamics are defined by species composition, sex ratios and age structure, that is, by which species are present and how a herd splits into adult males, adult females and juveniles. We use red deer ($\textit{Cervus elaphus}$) as a test case, because managers act on these dynamics and because the visible cue defining adult males, the antlers, is seasonally variable. Surveys are flown nadir, high enough not to disturb the animals, so each deer occupies only a small, low-resolution patch. The two recording modalities fail in opposite conditions: in color a deer under canopy blends into the ground, while in thermal it becomes a bright blob that loses fine detail. Rather than trust either modality alone, we fuse them at every stage using self-supervised DINOv3 features. Our pipeline tracks animals in both modalities, treats an animal as confirmed only when the two cameras agree, keeps only the clear, non-occluded frames, and assigns species and sex by a vote across them; life stage is read separately from geo-referenced body size, since at survey resolution a juvenile often only differs from an adult female in size. Across four flights spanning the antler season the fused pipeline correctly classifies 25 of the 26 detected individuals (7 of 8 adult males, all 16 adult females and 2 juveniles), against 20 of 26 for either sensor alone. Multimodal species classification reaches 96.0%, while for sex classification fusing the two sensors matters most: the combined RGB+thermal model is the most robust across environments and seasons. Automating the demographic classification turns a drone flight from a count into a repeatable reading of herd structure, so the sex ratios and age structure that managers already act on can be gathered as often as a survey can be flown.

cs.CV↗
arXiv2026

DSeq-JEPA: Discriminative Sequential Joint-Embedding Predictive Architecture

Recent advances in self-supervised visual representation learning have demonstrated the effectiveness of predictive latent-space objectives for learning transferable features. In particular, Image-based Joint-Embedding Predictive Architecture (I-JEPA) learns representations by predicting latent embeddings of masked target regions from visible context. However, it predicts target regions in parallel and all at once, lacking ability to order predictions meaningfully. Inspired by human visual perception, which attends selectively and progressively from primary to secondary cues, we propose Dseq-JEPA, a Discriminative Sequential Joint-Embedding Predictive Architecture that bridges latent predictive and autoregressive self-supervised learning. Specifically, Dseq-JEPA integrates a discriminatively ordered sequential process with JEPA-style learning objective. This is achieved by (i) identifying primary discriminative regions using an attention-derived saliency map that serves as a proxy for visual importance, and (ii) predicting subsequent regions in discriminative order, inducing a curriculum-like semantic progression from primary to secondary cues in pre-training. Extensive experiments across tasks -- image classification (ImageNet), fine-grained visual categorization (iNaturalist21, CUB, Stanford Cars), detection/segmentation (MS-COCO, ADE20K), and low-level reasoning (CLEVR) -- show that Dseq-JEPA consistently learns more discriminative and generalizable representations compared to I-JEPA variants.

cs.CV↗
arXiv2026

INQUIRE-Search: Interactive Discovery in Large-Scale Biodiversity Databases

Many ecological questions center on complex phenomena, such as species interactions, behaviors, phenology, and responses to disturbance, that are inherently difficult to observe and sparsely documented. Community science platforms such as iNaturalist contain hundreds of millions of biodiversity images, which often contain evidence of these complex phenomena. However, current workflows that seek to discover and analyze this evidence often rely on manual inspection, leaving this information largely inaccessible at scale. We introduce INQUIRE-Search, an open-source system that uses natural language to enable scientists to rapidly search within an ecological image database like iNaturalist for specific phenomena, verify and export relevant observations, and use these outputs for downstream scientific analysis. Across five illustrative case studies, INQUIRE-Search concentrates relevant observations 3-25x more efficiently than comparable manual inspection budgets. These examples demonstrate how the system can be used for ecological inference, from analyzing seasonal variation in behavior across species to forest regrowth after wildfires. These examples illustrate a new paradigm for interactive, efficient, and scalable scientific discovery that can begin to unlock previously inaccessible scientific value in large-scale biodiversity datasets. Finally, we highlight how AI-enabled discovery tools for science require reframing aspects of the scientific process, including experiment design, data collection, survey effort, and uncertainty analysis.

cs.CV↗
arXiv2026

Autonomous Scientific Discovery via Iterative Meta-Reflection

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

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arXiv2026

Finding Needles in the Haystack: Transductive Active Labeling in Ecology

Active learning is now standard practice in labeling ecological data, enabling ecologists to quickly process large volumes of field data to understand and monitor natural environments. Current practices evaluate active learning inductively, estimating predictive performance on a held-out test set. We argue that this evaluation is misaligned with most ecological tasks, where the goal is to transductively label an entire pool of data as efficiently as possible. We demonstrate that ignoring the human-in-the-loop underestimates the importance of continuing to label, particularly for classes in the long tail which may be of disproportionate ecological importance (rare species, uncommon behaviors, etc.). Our analysis shows that, for this long tail, the transductive objective shifts importance from prediction to discovery: the true challenge becomes finding "needles in the haystack," examples of rare classes that are embedded within dense regions of abundant classes in the latent geometry, which we quantify with a novel metric of sampling difficulty. Finally, to translate these insights to practical ecological workflows, we propose a conservative hybrid stopping criterion inspired by ecological rarefaction curves, and show that combining predictive performance with discovery criteria reduces premature stopping on long-tailed pools, improving rare-class recovery when discovery, not classification, is the limiting factor.

cs.LG↗
arXiv2026

A Critical Look at Targeted Instruction Selection: Disentangling What Matters (and What Doesn't)

Instruction fine-tuning of large language models (LLMs) often involves selecting a subset of instruction training data from a large candidate pool, using a small query set from the target task. Despite growing interest, the literature on targeted instruction selection remains fragmented and opaque: methods vary widely in selection budgets, often omit zero-shot baselines, and frequently entangle the contributions of key components. As a result, practitioners lack actionable guidance on selecting instructions for their target tasks. In this work, we aim to bring clarity to this landscape by disentangling and systematically analyzing the two core ingredients: data representation and selection algorithms. Our framework enables controlled comparisons across models, tasks, and budgets. We find that only gradient-based data representations choose subsets whose similarity to the query consistently predicts performance across datasets, models, and candidate pools. While no single method dominates, gradient-based representations paired with greedy round-robin selection often perform best on average at low budgets, but these gains diminish at larger budgets. Finally, we unify several existing selection algorithms as forms of approximate distance minimization between the selected subset and the query set, and support this view with new generalization bounds. More broadly, our findings provide critical insights and a foundation for more principled data selection in LLM fine-tuning. The code is available at https://github.com/dcml-lab/targeted-instruction-selection.

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arXiv2026

Centering Ecological Goals in Automated Identification of Individual Animals

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.

q-bio.PE↗
arXiv2026

ReefNet: A Large-Scale Dataset and Benchmark for Fine-Grained Coral Reef Recognition

Coral reefs are rapidly declining under anthropogenic pressures (e.g., climate change), creating an urgent need for scalable and automated monitoring. Progress in data-driven coral analysis, however, is constrained by the scarcity of large-scale datasets with fine-grained labels that are taxonomically consistent across sites and studies. To address this gap, we introduce ReefNet, a large-scale public coral reef image dataset with point-level annotations mapped to the World Register of Marine Species (WoRMS) taxonomy. ReefNet aggregates imagery from 76 curated CoralNet sources and an additional reef site from Al-Wajh (Red Sea), totaling approximately 925K genus-level hard coral annotations. Through expert-driven verification and targeted filtering, we derive a high-confidence benchmark subset with 92% expert agreement over 39 hard-coral label classes, enabling reliable evaluation under realistic label noise and strong class imbalance. Beyond dataset construction, we establish a comprehensive benchmark spanning zero-shot, cross-domain few-shot adaptation, within-source evaluation, and cross-source transfer to the Al-Wajh dataset. Experiments with state-of-the-art vision-language models (VLMs), multimodal large language models (MLLMs), and vision-only backbones reveal substantial degradation in zero-shot and extremely few-shot regimes, while adaptation with in-domain supervision yields large gains yet still leaves a persistent gap under cross-source shift and on long-tail genera. These results highlight fundamental challenges in applying general-purpose multimodal models to biodiversity monitoring and underscore the importance of large-scale, taxonomically grounded, high-quality datasets. ReefNet serves as both a benchmark and a training resource for advancing fine-grained coral reef understanding.

cs.CV↗
arXiv2026

ID-Sim: An Identity-Focused Similarity Metric

Humans have remarkable selective sensitivity to identities -- easily distinguishing between highly similar identities, even across significantly different contexts such as diverse viewpoints or lighting. Vision models have struggled to match this capability, and progress toward identity-focused tasks such as personalized image generation is slowed by a lack of identity-focused evaluation metrics. To help facilitate progress, we propose ID-Sim, a feed-forward metric designed to faithfully reflect human selective sensitivity. To build ID-Sim, we curate a high-quality training set of images spanning diverse real-world domains, augmented with generative synthetic data that provides controlled, fine-grained identity and contextual variations. We evaluate our metric on a new unified evaluation benchmark for assessing consistency with human annotations across identity-focused recognition, retrieval, and generative tasks.

cs.CV↗
arXiv2026

TaxaAdapter: Vision Taxonomy Models are Key to Fine-grained Image Generation over the Tree of Life

Accurately generating images across the Tree of Life is difficult: there are over 10M distinct species on Earth, many of which differ only by subtle visual traits. Despite the remarkable progress in text-to-image synthesis, existing models often fail to capture the fine-grained visual cues that define species identity, even when their outputs appear photo-realistic. To this end, we propose TaxaAdapter, a simple and lightweight approach that incorporates Vision Taxonomy Models (VTMs) such as BioCLIP to guide fine-grained species generation. Our method injects VTM embeddings into a frozen text-to-image diffusion model, improving species-level fidelity while preserving flexible text control over attributes such as pose, style, and background. Extensive experiments demonstrate that TaxaAdapter consistently improves morphology fidelity and species-identity accuracy over strong baselines, with a cleaner architecture and training recipe. To better evaluate these improvements, we also introduce a multimodal Large Language Model-based metric that summarizes trait-level descriptions from generated and real images, providing a more interpretable measure of morphological consistency. Beyond this, we observe that TaxaAdapter exhibits strong generalization capabilities, enabling species synthesis in challenging regimes such as few-shot species with only a handful of training images and even species unseen during training. Overall, our results highlight that VTMs are a key ingredient for scalable, fine-grained species generation.

cs.CV↗
arXiv2026

Seeing Through the PRISM: Compound & Controllable Restoration of Scientific Images

Scientific and environmental imagery often suffer from complex mixtures of noise related to the sensor and the environment. Existing restoration methods typically remove one degradation at a time, leading to cascading artifacts, overcorrection, or loss of meaningful signal. In scientific applications, restoration must be able to simultaneously handle compound degradations while allowing experts to selectively remove subsets of distortions without erasing important features. To address these challenges, we present PRISM (Precision Restoration with Interpretable Separation of Mixtures). PRISM is a prompted conditional diffusion framework which combines compound-aware supervision over mixed degradations with a weighted contrastive disentanglement objective that aligns primitives and their mixtures in the latent space. This compositional geometry enables high-fidelity joint removal of overlapping distortions while also allowing flexible, targeted fixes through natural language prompts. Across microscopy, wildlife monitoring, remote sensing, and urban weather datasets, PRISM outperforms state-of-the-art baselines on complex compound degradations, including zero-shot mixtures not seen during training. Importantly, we show that selective restoration significantly improves downstream scientific accuracy in several domains over standard "black-box" restoration. These results establish PRISM as a generalizable and controllable framework for high-fidelity restoration in domains where scientific utility is a priority.

cs.CV↗
arXiv2026

Deep in the Jungle: Towards Automating Chimpanzee Population Estimation

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.

cs.CV↗
arXiv2025

Application-Driven Innovation in Machine Learning

In this position paper, we argue that application-driven research has been systemically under-valued in the machine learning community. As applications of machine learning proliferate, innovative algorithms inspired by specific real-world challenges have become increasingly important. Such work offers the potential for significant impact not merely in domains of application but also in machine learning itself. In this paper, we describe the paradigm of application-driven research in machine learning, contrasting it with the more standard paradigm of methods-driven research. We illustrate the benefits of application-driven machine learning and how this approach can productively synergize with methods-driven work. Despite these benefits, we find that reviewing, hiring, and teaching practices in machine learning often hold back application-driven innovation. We outline how these processes may be improved.

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