Social security assurance contributions will be deducted from your stipend for as long as you receive it - because it is mandatory under legal regulations. 

Please report any change in your data (name, address, starting or quitting an employment contract) to the Doctoral Schools Centre to update your profile in the state-run system.

Is this the same as health insurance?

The said commissions do not include health assurance. 
However, they can be seen as a starting point for other NFZ schemes you might consider. It is only after having registered for social security purpose (which is done shortly after your arrival at the Doctoral Schools) that you will be able to sign up for NFZ/ZUS state health service plans on your own (this requires having a Polish PESEL number issued and signing up an agreement at an external office in town) in order to use state health services freely. Then, it should be noted that while an NFZ/ZUS agreement is voluntary, you may find it helpful for many reasons, including temporary residence formalities. Please note that this remark concerns non-EU newcomers (EU citizens may use EHIC card and their stay generally follows different procedures).
Also, in any case, you may decide for private health insurance plan as an alternative or in addition to NFZ scheme.