Mikko Impiö

Mikko Impiö, Pekka Härmä, Anna Tammilehto et al.

Remote sensing benefits habitat conservation by making monitoring of large areas easier compared to field surveying especially if the remote sensed data can be automatically analyzed. An important aspect of monitoring is classifying and mapping habitat types present in the monitored area. Automatic classification is a difficult task, as classes have fine-grained differences and their distributions are long-tailed and unbalanced. Usually training data used for automatic land cover classification relies on fully annotated segmentation maps, annotated from remote sensed imagery to a fairly high-level taxonomy, i.e., classes such as forest, farmland, or urban area. A challenge with automatic habitat classification is that reliable data annotation requires field-surveys. Therefore, full segmentation maps are expensive to produce, and training data is often sparse, point-like, and limited to areas accessible by foot. Methods for utilizing these limited data more efficiently are needed. We address these problems by proposing a method for habitat classification and mapping, and apply this method to classify the entire northern Finnish Lapland area into Natura2000 classes. The method is characterized by using finely-grained, sparse, single-pixel annotations collected from the field, combined with large amounts of unannotated data to produce segmentation maps. Supervised, unsupervised and semi-supervised methods are compared, and the benefits of transfer learning from a larger out-of-domain dataset are demonstrated. We propose a \ac{CNN} biased towards center pixel classification ensembled with a random forest classifier, that produces higher quality classifications than the models themselves alone. We show that cropping augmentations, test-time augmentation and semi-supervised learning can help classification even further.

Mikko Impiö, Jenni Raitoharju

Image-based species identification could help scaling biodiversity monitoring to a global scale. Many challenges still need to be solved in order to implement these systems in real-world applications. A reliable image-based monitoring system must detect out-of-distribution (OOD) classes it has not been presented before. This is challenging especially with fine-grained classes. Emerging environmental monitoring techniques, DNA metabarcoding and eDNA, can help by providing information on OOD classes that are present in a sample. In this paper, we study if DNA barcodes can also support in finding the outlier images based on the outlier DNA sequence's similarity to the seen classes. We propose a re-ordering approach that can be easily applied on any pre-trained models and existing OOD detection methods. We experimentally show that the proposed approach improves taxonomic OOD detection compared to all common baselines. We also show that the method works thanks to a correlation between visual similarity and DNA barcode proximity. The code and data are available at https://github.com/mikkoim/dnaimg-ood.

Mikko Impiö, Philipp M. Rehsen, Jenni Raitoharju

The amount of image datasets collected for environmental monitoring purposes has increased in the past years as computer vision assisted methods have gained interest. Computer vision applications rely on high-quality datasets, making data curation important. However, data curation is often done ad-hoc and the methods used are rarely published. We present a method for curating large-scale image datasets of invertebrates that contain multiple images of the same taxa and/or specimens and have relatively uniform background in the images. Our approach is based on extracting feature embeddings with pretrained deep neural networks, and using these embeddings to find visually most distinct images by comparing their embeddings to the group prototype embedding. Also, we show that a simple area-based size comparison approach is able to find a lot of common erroneous images, such as images containing detached body parts and misclassified samples. In addition to the method, we propose using novel metrics for evaluating human-in-the-loop outlier detection methods. The implementations of the proposed curation methods, as well as a benchmark dataset containing annotated erroneous images, are publicly available in https://github.com/mikkoim/taxonomist-studio.

Mikko Impiö, Philipp M. Rehsen, Jarrett Blair et al.

The ability to estimate invertebrate biomass using only images could help scaling up quantitative biodiversity monitoring efforts. Computer vision-based methods have the potential to omit the manual, time-consuming, and destructive process of dry weighing specimens. We present two approaches for dry mass estimation that do not require additional manual effort apart from imaging the specimens: fitting a linear model with novel predictors, automatically calculated by an imaging device, and training a family of end-to-end deep neural networks for the task, using single-view, multi-view, and metadata-aware architectures. We propose using area and sinking speed as predictors. These can be calculated with BIODISCOVER, which is a dual-camera system that captures image sequences of specimens sinking in an ethanol column. For this study, we collected a large dataset of dry mass measurement and image sequence pairs to train and evaluate models. We show that our methods can estimate specimen dry mass even with complex and visually diverse specimen morphologies. Combined with automatic taxonomic classification, our approach is an accurate method for group-level dry mass estimation, with a median percentage error of 10-20% for individuals. We highlight the importance of choosing appropriate evaluation metrics, and encourage using both percentage errors and absolute errors as metrics, because they measure different properties. We also explore different optimization losses, data augmentation methods, and model architectures for training deep-learning models.

Mikko Impiö, Philipp M. Rehsen, Tiina Laamanen et al.

This paper presents the AquaMonitor dataset, the first large computer vision dataset of aquatic invertebrates collected during routine environmental monitoring. While several large species identification datasets exist, they are rarely collected using standardized collection protocols, and none focus on aquatic invertebrates, which are particularly laborious to collect. For AquaMonitor, we imaged all specimens from two years of monitoring whenever imaging was possible given practical limitations. The dataset enables the evaluation of automated identification methods for real-life monitoring purposes using a realistically challenging and unbiased setup. The dataset has 2.7M images from 43,189 specimens, DNA sequences for 1358 specimens, and dry mass and size measurements for 1494 specimens, making it also one of the largest biological multi-view and multimodal datasets to date. We define three benchmark tasks and provide strong baselines for these: 1) Monitoring benchmark, reflecting real-life deployment challenges such as open-set recognition, distribution shift, and extreme class imbalance, 2) Classification benchmark, which follows a standard fine-grained visual categorization setup, and 3) Few-shot benchmark, which targets classes with only few training examples from very fine-grained categories. Advancements on the Monitoring benchmark can directly translate to improvement of aquatic biodiversity monitoring, which is an important component of regular legislative water quality assessment in many countries.

Mikko Impiö, Mehmet Yamaç, Jenni Raitoharju

Privacy concerns in healthcare have gained interest recently via GDPR, with a rising need for privacy-preserving data collection methods that keep personal information hidden in otherwise usable data. Sometimes data needs to be encrypted for several authentication levels, where a semi-authorized user gains access to data stripped of personal or sensitive information, while a fully-authorized user can recover the full signal. In this paper, we propose a compressive sensing based multi-level encryption to ECG signals to mask possible heartbeat anomalies from semi-authorized users, while preserving the beat structure for heart rate monitoring. Masking is performed both in time and frequency domains. Masking effectiveness is validated using 1D convolutional neural networks for heartbeat anomaly classification, while masked signal usefulness is validated comparing heartbeat detection accuracy between masked and recovered signals. The proposed multi-level encryption method can decrease classification accuracy of heartbeat anomalies by up to 50%, while maintaining a fairly high R-peak detection accuracy.