State of health (SOH) estimation of lithium-ion batteries has typically been focused on estimating present cell capacity relative to initial cell capacity. While many successes have been achieved in this area, it is generally more advantageous to not only estimate cell capacity, but also the underlying degradation modes which cause capacity fade because these modes give further insight into maximizing cell usage. There have been some successes in estimating cell degradation modes, however, these methods either require long-term degradation data, are demonstrated solely on artificially constructed cells, or exhibit high error in estimating late-life degradation. To address these shortfalls and alleviate the need for long-term cycling data, we propose a method for estimating the capacity of a battery cell and diagnosing its primary degradation mechanisms using limited early-life degradation data. The proposed method uses simulation data from a physics-based half-cell model and early-life degradation data from 16 cells cycled under two temperatures and C rates to train a machine learning model. Results obtained from a four-fold cross validation study indicate that the proposed physics-informed machine learning method trained with only 60 early life data (five data from each of the 12 training cells) and 30 high-degradation simulated data can decrease estimation error by up to a total of 9.77 root mean square error % when compared to models which were trained only on the early-life experimental data.