We present Transfer Orthology Networks (TRON), a novel neural network architecture designed for cross-species transfer learning. TRON leverages orthologous relationships, represented as a bipartite graph between species, to guide knowledge transfer. Specifically, we prepend a learned species conversion layer, whose weights are masked by the biadjacency matrix of this bipartite graph, to a pre-trained feedforward neural network that predicts a phenotype from gene expression data in a source species. This allows for efficient transfer of knowledge to a target species by learning a linear transformation that maps gene expression from the source to the target species' gene space. The learned weights of this conversion layer offer a potential avenue for interpreting functional orthology, providing insights into how genes across species contribute to the phenotype of interest. TRON offers a biologically grounded and interpretable approach to cross-species transfer learning, paving the way for more effective utilization of available transcriptomic data. We are in the process of collecting cross-species transcriptomic/phenotypic data to gain experimental validation of the TRON architecture.

The Xeno -Canto bird audio repository is an invaluable resource for those interested in vocalizations and other sounds made by birds around the world. This is particularly the case for machine learning researchers attempting to improve on the bird species r ecognition accuracy of classification models. However, the task of extracting labeled datasets from th e recordings found in this crowd -sourced repository faces several challenges. One challenge of particular significance to machine learning practitioners i s that one bird species label is applied to each audio recording, but frequently other sounds are also captured including other bird species, other animal sounds, anthropogenic and other ambient sounds . These non -target bird species sounds can result in dataset labeling discrepanc ies referred to as label noise . In this work we present a cleaning process consisting of audio preprocessing followed by dimensionality reduction and unsupervised outlier detection (UOD) to reduce the label noise in a dataset derived from Xeno -Canto recordings . We investigate three neural network dimensionality reduction techniques: two flavors of convolutional autoencoder s and variational deep embedding (VaDE (Jiang, 2017)) . While both methods show some degree of effectiveness at detecting outliers for most bird species datasets, we f ound significant variation in the performance of the methods from one species to the next. We believe that the results of this investigation demonstrate that the application of our cleaning process can meaningfully reduce the label noise of bird species datasets derived from Xeno-Canto audio repository but results vary across species.

The diagnostic processes of epilepsy are often hindered by the transient and unpredictable nature of seizures. Here we propose a multi-space alignment approach based on cross-species and cross-modality electroencephalogram (EEG) data to enhance the detection capabilities and understanding of epileptic seizures. By employing deep learning techniques, including domain adaptation and knowledge distillation, our framework aligns cross-species and cross-modality EEG signals to enhance the detection capability beyond traditional within-species and with-modality models. Experiments on multiple surface and intracranial EEG datasets of humans and canines demonstrated substantial improvements in the detection accuracy, achieving over 90% AUC scores for cross-species and cross-modality seizure detection with extremely limited labeled data from the target species/modality. To our knowledge, this is the first study that demonstrates the effectiveness of integrating heterogeneous data from different species and modalities to improve EEG-based seizure detection performance. The approach may also be generalizable to different brain-computer interface paradigms, and suggests the possibility to combine data from different species/modalities to increase the amount of training data for large EEG models.

Passive acoustic monitoring (PAM) studies generate thousands of hours of audio, which may be used to monitor specific animal populations, conduct broad biodiversity surveys, detect threats such as poachers, and more. Machine learning classifiers for species identification are increasingly being used to process the vast amount of audio generated by bioacoustic surveys, expediting analysis and increasing the utility of PAM as a management tool. In common practice, a threshold is applied to classifier output scores, and scores above the threshold are aggregated into a detection count. The choice of threshold produces biased counts of vocalizations, which are subject to false positive/negative rates that may vary across subsets of the dataset. In this work, we advocate for directly estimating call density: The proportion of detection windows containing the target vocalization, regardless of classifier score. Our approach targets a desirable ecological estimator and provides a more rigorous grounding for identifying the core problems caused by distribution shifts -- when the defining characteristics of the data distribution change -- and designing strategies to mitigate them. We propose a validation scheme for estimating call density in a body of data and obtain, through Bayesian reasoning, probability distributions of confidence scores for both the positive and negative classes. We use these distributions to predict site-level densities, which may be subject to distribution shifts. We test our proposed methods on a real-world study of Hawaiian birds and provide simulation results leveraging existing fully annotated datasets, demonstrating robustness to variations in call density and classifier model quality.

Passive acoustic monitoring can be an effective way of monitoring wildlife populations that are acoustically active but difficult to survey visually. Digital recorders allow surveyors to gather large volumes of data at low cost, but identifying target species vocalisations in these data is non-trivial. Machine learning (ML) methods are often used to do the identification. They can process large volumes of data quickly, but they do not detect all vocalisations and they do generate some false positives (vocalisations that are not from the target species). Existing wildlife abundance survey methods have been designed specifically to deal with the first of these mistakes, but current methods of dealing with false positives are not well-developed. They do not take account of features of individual vocalisations, some of which are more likely to be false positives than others. We propose three methods for acoustic spatial capture-recapture inference that integrate individual-level measures of confidence from ML vocalisation identification into the likelihood and hence integrate ML uncertainty into inference. The methods include a mixture model in which species identity is a latent variable. We test the methods by simulation and find that in a scenario based on acoustic data from Hainan gibbons, in which ignoring false positives results in 17% positive bias, our methods give negligible bias and coverage probabilities that are close to the nominal 95% level.

The evolution of drug-resistant microbial species is one of the major challenges to global health. The development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the discovery of novel antimicrobial peptides is hampered by low-throughput biochemical assays. Computational techniques can be used for rapid screening of promising antimicrobial peptide candidates prior to testing in the wet lab. The vast majority of existing antimicrobial peptide predictors are non-targeted in nature, i.e., they can predict whether a given peptide sequence is antimicrobial, but they are unable to predict whether the sequence can target a particular microbial species. In this work, we have developed a targeted antimicrobial peptide activity predictor that can predict whether a peptide is effective against a given microbial species or not. This has been made possible through zero-shot and few-shot machine learning. The proposed predictor called AMP0 takes in the peptide amino acid sequence and any N/C-termini modifications together with the genomic sequence of a target microbial species to generate targeted predictions. It is important to note that the proposed method can generate predictions for species that are not part of its training set. The accuracy of predictions for novel test species can be further improved by providing a few example peptides for that species. Our computational cross-validation results show that the pro-posed scheme is particularly effective for targeted antimicrobial prediction in comparison to existing approaches and can be used for screening potential antimicrobial peptides in a targeted manner especially for cases in which the number of training examples is small. The webserver of the method is available at http://ampzero.pythonanywhere.com.