Abstract: Inertial Measurement Unit (IMU) sensors are becoming increasingly ubiquitous in everyday devices such as smartphones, fitness watches, etc. As a result, the array of health-related applications that tap onto this data has been growing, as well as the importance of designing accurate prediction models for tasks such as human activity recognition (HAR). However, one important task that has received little attention is the prediction of an individual's heart rate when undergoing a physical activity using IMU data. This could be used, for example, to determine which activities are safe for a person without having him/her actually perform them. We propose a neural architecture for this task composed of convolutional and LSTM layers, similarly to the state-of-the-art techniques for the closely related task of HAR. However, our model includes a convolutional network that extracts, based on sensor data from a previously executed activity, a physical conditioning embedding (PCE) of the individual to be used as the LSTM's initial hidden state. We evaluate the proposed model, dubbed PCE-LSTM, when predicting the heart rate of 23 subjects performing a variety of physical activities from IMU-sensor data available in public datasets (PAMAP2, PPG-DaLiA). For comparison, we use as baselines the only model specifically proposed for this task, and an adapted state-of-the-art model for HAR. PCE-LSTM yields over 10% lower mean absolute error. We demonstrate empirically that this error reduction is in part due to the use of the PCE. Last, we use the two datasets (PPG-DaLiA, WESAD) to show that PCE-LSTM can also be successfully applied when photoplethysmography (PPG) sensors are available to rectify heart rate measurement errors caused by movement, outperforming the state-of-the-art deep learning baselines by more than 30%.