Force sensing in robotic-assisted minimally invasive surgery (RMIS) is crucial for performing dedicated surgical procedures, such as bilateral teleoperation and palpation. Due to the bio-compatibility and sterilization requirements, a specially designed surgical tool/shaft is normally attached to the sensor while contacting the organ targets. Through this design, the measured force from the sensor usually contains uncertainties, such as noise, inertial force etc., and thus cannot reflect the actual interaction force with the tissue environment. Motivated to provide the authentic contact force between a robotic tool and soft tissue, we proposed a data-driven force compensation scheme without intricate modeling to reduce the effects of force measurement uncertainties. In this paper, a neural-network-based approach is utilized to automatically model the inertial force subject to noise during the robotic palpation procedure, then the exact contact force can be obtained through the force compensation method which cancels the noise and inertial force. Following this approach, the genuine interaction force during the palpation task can be achieved furthermore to improve the appraisal of the tumor surrounded by the soft tissue. Experiments are conducted with robotic-assisted palpation tasks on a silicone-based soft tissue phantom and the results verify the effectiveness of the suggested method.