Because of their close relationship with humans, non-human apes (chimpanzees, bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great scientific interest. The goal of understanding their complex behavior would be greatly advanced by the ability to perform video-based pose tracking. Tracking, however, requires high-quality annotated datasets of ape photographs. Here we present OpenApePose, a new public dataset of 71,868 photographs, annotated with 16 body landmarks, of six ape species in naturalistic contexts. We show that a standard deep net (HRNet-W48) trained on ape photos can reliably track out-of-sample ape photos better than networks trained on monkeys (specifically, the OpenMonkeyPose dataset) and on humans (COCO) can. This trained network can track apes almost as well as the other networks can track their respective taxa, and models trained without one of the six ape species can track the held out species better than the monkey and human models can. Ultimately, the results of our analyses highlight the importance of large specialized databases for animal tracking systems and confirm the utility of our new ape database.

Neural Representations have recently been shown to effectively reconstruct a wide range of signals from 3D meshes and shapes to images and videos. We show that, when adapted correctly, neural representations can be used to directly represent the weights of a pre-trained convolutional neural network, resulting in a Neural Representation for Neural Networks (NeRN). Inspired by coordinate inputs of previous neural representation methods, we assign a coordinate to each convolutional kernel in our network based on its position in the architecture, and optimize a predictor network to map coordinates to their corresponding weights. Similarly to the spatial smoothness of visual scenes, we show that incorporating a smoothness constraint over the original network's weights aids NeRN towards a better reconstruction. In addition, since slight perturbations in pre-trained model weights can result in a considerable accuracy loss, we employ techniques from the field of knowledge distillation to stabilize the learning process. We demonstrate the effectiveness of NeRN in reconstructing widely used architectures on CIFAR-10, CIFAR-100, and ImageNet. Finally, we present two applications using NeRN, demonstrating the capabilities of the learned representations.

Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the underlying spatial structure of the given data. In our work, we apply a spatially aware graph neural network model consisting of GraphSAGE layers to forecast the presence of West Nile virus in Illinois, to aid mosquito surveillance and abatement efforts within the state. More generally, we show that graph neural networks applied to irregularly sampled geospatial data can exceed the performance of a range of baseline methods including logistic regression, XGBoost, and fully-connected neural networks.

Recent methods demonstrate that data augmentation using counterfactual knowledge can teach models the causal structure of a task, leading to robust and generalizable models. However, such counterfactual data often has a limited scale and diversity if crowdsourced and is computationally expensive to extend to new perturbation types if generated using supervised methods. To address this, we introduce a new framework called DISCO for automatically generating high-quality counterfactual data at scale. DISCO engineers prompts to generate phrasal perturbations with a large general language model. Then, a task-specific teacher model filters the generation to distill high-quality counterfactual data. We show that learning with this counterfactual data yields a comparatively small student model that is 6% (absolute) more robust and generalizes 5% better across distributions than baselines on various challenging evaluations. This model is also 15% more sensitive in differentiating original and counterfactual examples, on three evaluation sets written by human workers and via human-AI collaboration.

Recent work has reported that AI classifiers trained on audio recordings can accurately predict severe acute respiratory syndrome coronavirus 2 (SARSCoV2) infection status. Here, we undertake a large scale study of audio-based deep learning classifiers, as part of the UK governments pandemic response. We collect and analyse a dataset of audio recordings from 67,842 individuals with linked metadata, including reverse transcription polymerase chain reaction (PCR) test outcomes, of whom 23,514 tested positive for SARS CoV 2. Subjects were recruited via the UK governments National Health Service Test-and-Trace programme and the REal-time Assessment of Community Transmission (REACT) randomised surveillance survey. In an unadjusted analysis of our dataset AI classifiers predict SARS-CoV-2 infection status with high accuracy (Receiver Operating Characteristic Area Under the Curve (ROCAUC) 0.846 [0.838, 0.854]) consistent with the findings of previous studies. However, after matching on measured confounders, such as age, gender, and self reported symptoms, our classifiers performance is much weaker (ROC-AUC 0.619 [0.594, 0.644]). Upon quantifying the utility of audio based classifiers in practical settings, we find them to be outperformed by simple predictive scores based on user reported symptoms.

The UK COVID-19 Vocal Audio Dataset is designed for the training and evaluation of machine learning models that classify SARS-CoV-2 infection status or associated respiratory symptoms using vocal audio. The UK Health Security Agency recruited voluntary participants through the national Test and Trace programme and the REACT-1 survey in England from March 2021 to March 2022, during dominant transmission of the Alpha and Delta SARS-CoV-2 variants and some Omicron variant sublineages. Audio recordings of volitional coughs, exhalations, and speech were collected in the 'Speak up to help beat coronavirus' digital survey alongside demographic, self-reported symptom and respiratory condition data, and linked to SARS-CoV-2 test results. The UK COVID-19 Vocal Audio Dataset represents the largest collection of SARS-CoV-2 PCR-referenced audio recordings to date. PCR results were linked to 70,794 of 72,999 participants and 24,155 of 25,776 positive cases. Respiratory symptoms were reported by 45.62% of participants. This dataset has additional potential uses for bioacoustics research, with 11.30% participants reporting asthma, and 27.20% with linked influenza PCR test results.

Electronic Health Records (EHRs) hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Temporal modelling of this medical history, which considers the sequence of events, can be used to forecast and simulate future events, estimate risk, suggest alternative diagnoses or forecast complications. While most prediction approaches use mainly structured data or a subset of single-domain forecasts and outcomes, we processed the entire free-text portion of EHRs for longitudinal modelling. We present Foresight, a novel GPT3-based pipeline that uses NER+L tools (i.e. MedCAT) to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, medications, symptoms and interventions. Since large portions of EHR data are in text form, such an approach benefits from a granular and detailed view of a patient while introducing modest additional noise. On tests in two large UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by 5 clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. Foresight can be easily trained and deployed locally as it only requires free-text data (as a minimum). As a generative model, it can simulate follow-on disorders, medications and interventions for as many steps as required. Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk estimation, virtual trials and clinical research to study the progression of diseases, simulate interventions and counterfactuals, and for educational purposes.

A clustering termination procedure which is locally adaptive (with respect to the hierarchical tree of sets representative of the agglomerative merging) is proposed, for agglomerative hierarchical clustering on a set equipped with a distance function. It represents a multi-scale alternative to conventional scale dependent threshold based termination criteria.

Knowledge of the symmetries of reinforcement learning (RL) systems can be used to create compressed and semantically meaningful representations of a low-level state space. We present a method of automatically detecting RL symmetries directly from raw trajectory data without requiring active control of the system. Our method generates candidate symmetries and trains a recurrent neural network (RNN) to discriminate between the original trajectories and the transformed trajectories for each candidate symmetry. The RNN discriminator's accuracy for each candidate reveals how symmetric the system is under that transformation. This information can be used to create high-level representations that are invariant to all symmetries on a dataset level and to communicate properties of the RL behavior to users. We show in experiments on two simulated RL use cases (a pusher robot and a UAV flying in wind) that our method can determine the symmetries underlying both the environment physics and the trained RL policy.

Hidden parameters are latent variables in reinforcement learning (RL) environments that are constant over the course of a trajectory. Understanding what, if any, hidden parameters affect a particular environment can aid both the development and appropriate usage of RL systems. We present an unsupervised method to map RL trajectories into a feature space where distance represents the relative difference in system behavior due to hidden parameters. Our approach disentangles the effects of hidden parameters by leveraging a recurrent neural network (RNN) world model as used in model-based RL. First, we alter the standard world model training algorithm to isolate the hidden parameter information in the world model memory. Then, we use a metric learning approach to map the RNN memory into a space with a distance metric approximating a bisimulation metric with respect to the hidden parameters. The resulting disentangled feature space can be used to meaningfully relate trajectories to each other and analyze the hidden parameter. We demonstrate our approach on four hidden parameters across three RL environments. Finally we present two methods to help identify and understand the effects of hidden parameters on systems.