The PANDA (anti-Proton ANnihilation at DArmstadt) experiment at FAIR (Facility for Anti-proton and Ion Research) aims to study strong interactions in the confinement domain. In PANDA, a continuous beam of anti-protons will impinge on a fixed hydrogen target inside the High Energy Storage Ring (HESR), a feature intended to attain high interaction rates for various physics studies e.g. hyperon production. This thesis addresses the challenges of running PANDA under realistic conditions. The focus is two-fold: developing deep learning methods to reconstruct particle trajectories and reconstruct hyperons using realistic target profiles. Two approaches are used: (i) standard deep learning model such as dense network, and (ii) geometric deep leaning model such as interaction graph neural networks. The deep learning methods have given promising results, especially when it comes to (i) reconstruction of low-momentum particles that frequently occur in hadron physics experiments and (ii) reconstruction of tracks originating far from the interaction point. Both points are critical in many hyperon studies. However, further studies are needed to mitigate e.g. high clone rate. For the realistic target profiles, these pioneering simulations address the effect of residual gas on hyperon reconstruction. The results have shown that the signal-to-background ratio becomes worse by about a factor of 2 compared to the ideal target, however, the background level is still sufficiently low for these studies to be feasible. Further improvements can be made on the target side to achieve a better vacuum in the beam pipe and on the analysis side to improve the event selection. Finally, solutions are suggested to improve results, especially for the geometric deep learning method in handling low-momentum particles contributing to the high clone rate. In addition, a better way to build ground truth can improve the performance of our approach.