An interpretable framework using foundation models for fish sex identification

Correct identification of fish species is highly significant for food security, economic development, and climate resilience in Bangladesh. Protein sequences directly reflect functional and evolutionary constraints which are important for species authentication and biodiversity monitoring. Yet there exists no benchmark for native Bangladeshi fish species identification from protein sequence. In this study, we addressed this gap by introducing the first curated dataset for nine native Bangladeshi fish species of 2845 high quality protein sequences. We also established the first protein sequence classification baseline for this domain through a systematic benchmarking of seven architectural paradigms. Moreover, we propose a realistic deployable novel hybrid architecture of MotifCNN and Transformer with Terminal-Aware Positional-Encoding (MotifCNN-Transformer+TA-PE). Our novel architecture achieves 79.80% accuracy with macro-F1 of 0.80. The highest 83.04% accuracy is achieved by finetuned protein language model ProtBERT that has 420M parameters and requires dual 16GB GPUs for inference. According to McNemar's test, ProtBERT's 3.24% accuracy gain over our MotifCNN-Transformer+TA-PE is statistically insignificant (p = 0.1120). Our novel architecture beats it among six of the nine classes in per class identification. Also our MotifCNN-Transformer+TA-PE is approximately 5x faster, 42x smaller, and supports 16x larger batch size than ProtBERT and has GPU free inference, making it more practical for deployment in resources constrained areas such as rural Bangladesh. Beyond this, our foundational work shows effects of phylogenetic relationships on sequence similarity and establishes pathways for fisheries management, food authentication and biodiversity conservation in South Asia's protein dependent economy.

Recent advances in field technology have led to a massive influx of in-the-wild video data for ecological science. The primary bottleneck in leveraging this data is the high cost of expert annotation. While computer vision offers a potential solution, current models frequently fail when deployed in complex marine environments. To characterize these failures, we introduce WildFin, a novel benchmark for fish behavior recognition collected and annotated by ecologists. WildFin spans two critical real-world paradigms: stationary cameras monitoring groups of fish and dynamic divers following individual subjects. The dataset represents a massive curation effort, involving 1,350 hours of fieldwork and 600 hours of expert annotation to produce 9 hours of behavioral data with over 2 million frame-by-frame labels. We benchmark modern vision foundation models and quantify tradeoffs between static and spatiotemporal architectures, revealing the substantial gap that remains between current model capabilities and the demands of real-world underwater behavioral analysis. Project website: https://team-wildfin.github.io/.

With the continuous expansion of aquaculture, precise and efficient monitoring of fish behavior has become increasingly critical for improving farming efficiency and reducing economic losses. In particular, with the ongoing enhancement of computational capabilities in deep learning models, vision-based fish segmentation methods are garnering growing attention. By analyzing video segmentation results, fish behavior can be effectively tracked, thereby providing reliable data support for the precise regulation of aquaculture environments. However, existing deep learning-based video segmentation methods for aquaculture scenarios often overlook the dynamic correlations between video frames. In contrast, Interactive Video Object Segmentation (IVOS) employs an interaction-propagation scheme to achieve high-precision segmentation while minimizing user effort, thereby enhancing monitoring efficiency. Yet, IVOS applications in aquaculture remain limited due to data scarcity, and are susceptible to error accumulation and mask loss over long sequence propagation due to high intra-class similarity. In response, this paper proposes an improved interactive video object segmentation method (FiVOS) and constructs two fish-specific datasets. FiVOS utilizes a mask block filter to enable early detection and correction of erroneous propagated mask blocks, enhancing filtering accuracy through a rule-based thresholding approach. Additionally, it serializes noise filters to further eliminate erroneous mask noise, thereby improving model robustness. Experimental results demonstrate that FiVOS achieves state-of-the-art (SOTA) performance in fish video segmentation tasks, providing robust technical support for fish behavior research.