Dataset Information

A benchmark dataset for machine learning in ecotoxicology.

ABSTRACT: The use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, which we consider a barrier of entry for this kind of research. Additionally, model performances can only be compared across studies when the same dataset, cleaning, and splittings were used. Therefore, we provide ADORE, an extensive and well-described dataset on acute aquatic toxicity in three relevant taxonomic groups (fish, crustaceans, and algae). The core dataset describes ecotoxicological experiments and is expanded with phylogenetic and species-specific data on the species as well as chemical properties and molecular representations. Apart from challenging other researchers to try and achieve the best model performances across the whole dataset, we propose specific relevant challenges on subsets of the data and include datasets and splittings corresponding to each of these challenge as well as in-depth characterization and discussion of train-test splitting approaches.

SUBMITTER: Schur C

PROVIDER: S-EPMC10584858 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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A benchmark dataset for machine learning in ecotoxicology.

Schür Christoph C Gasser Lilian L Perez-Cruz Fernando F Schirmer Kristin K Baity-Jesi Marco M

Scientific data 20231018 1

The use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, which we consider a barrier of entry for this kind of research. Additionally, model performances can only be compared across studies when the same dataset, cleaning, and splittings were used. Therefore, we provide ADORE, an extensive and well- ...[more]

PMID: 37853023

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Project description:ObjectiveTracking seizures is crucial for epilepsy monitoring and treatment evaluation. Current epilepsy care relies on caretaker seizure diaries, but clinical seizure monitoring may miss seizures. Wearable devices may be better tolerated and more suitable for long-term ambulatory monitoring. This study evaluates the seizure detection performance of custom-developed machine learning (ML) algorithms across a broad spectrum of epileptic seizures utilizing wrist- and ankle-worn multisignal biosensors.MethodsWe enrolled patients admitted to the epilepsy monitoring unit and asked them to wear a wearable sensor on either their wrists or ankles. The sensor recorded body temperature, electrodermal activity, accelerometry (ACC), and photoplethysmography, which provides blood volume pulse (BVP). We used electroencephalographic seizure onset and offset as determined by a board-certified epileptologist as a standard comparison. We trained and validated ML for two different algorithms: Algorithm 1, ML methods for developing seizure type-specific detection models for nine individual seizure types; and Algorithm 2, ML methods for building general seizure type-agnostic detection, lumping together all seizure types.ResultsWe included 94 patients (57.4% female, median age = 9.9 years) and 548 epileptic seizures (11 066 h of sensor data) for a total of 930 seizures and nine seizure types. Algorithm 1 detected eight of nine seizure types better than chance (area under the receiver operating characteristic curve [AUC-ROC] = .648-.976). Algorithm 2 detected all nine seizure types better than chance (AUC-ROC = .642-.995); a fusion of ACC and BVP modalities achieved the best AUC-ROC (.752) when combining all seizure types together.SignificanceAutomatic seizure detection using ML from multimodal wearable sensor data is feasible across a broad spectrum of epileptic seizures. Preliminary results show better than chance seizure detection. The next steps include validation of our results in larger datasets, evaluation of the detection utility tool for additional clinical seizure types, and integration of additional clinical information.

Dataset Information

A benchmark dataset for machine learning in ecotoxicology.

Publications

A benchmark dataset for machine learning in ecotoxicology.

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