First, it may be a good idea to check whether your alleged core point $y^0$ is actually in the relative interior of the integer hull $\mathrm{conv}(Y)$. A sufficient condition is that, when you substitute $y^0$ into the constraints, all inequality constraints including variable bounds have positive slack. (Equality constraints obviously will not have slack.) In particular, do not forget that nonnegativity restrictions count as bounds. If you specify $0\le y_i \le u_i$, then you are looking for $\epsilon \le y^0_i \le u_i - \epsilon$ for some $\epsilon > 0$ (and $\epsilon$ greater than your tolerance for rounding error).
Second, while the presence of equality constraints will definitely make the feasible region less than full dimension, it can occur even in a problem with only inequality constraints. Consider a problem with nonnegative general integer variables and the following constraints (as well as others, and other variables): \begin{align*} y_{1}+y_{2} +y_{3} & \le 2\\ y_{2}+y_{4} + y_{5} & \le 4\\ y_{1}+y_{3} + y_{4} + y_{5}& \ge 6 \end{align*} Although all the constraints are inequalities, the feasible region will live in the hyperplane $y_2 = 0$, and thus be less than full dimension. This points to why I said the condition in the previous paragraph is sufficient rather than necessary and sufficient for $y^0$ to be in the relative interior of the integer hull. In this example, there is no way to get positive slack in all three of the constraints (or, in fact, in any one of them) without violating the nonnegativity restriction on $y_2$.
Yesterday, I listed a few things one could try in the hope of getting a core point $y^0$ in the relative interior of the integer hull. Here are a few others that occurred to me. (Warning: I'm going to use the term "slack variable" for both slacks and surpluses.)
- Tighten all inequality constraints (including variable bounds) and solve the LP relaxation of the tightened problem. (Feel free to change the objective function if you wish.) If you find a feasible solution $y^0$, it will be in the relative interior of the LP hull, and quite possibly in the integer hull. Good news: It's easy to do. Bad news: Even a modest tightening might make the problem infeasible (see example above).
- Insert slack variables in all constraints, including variable bounds. That means $0 \le y_i \le u_i$ would become \begin{align*} y_{i}-s_{i} & \ge0\\ y_{i}+t_{i} & \le u_{i} \end{align*} where $s_i \ge 0$ and $t_i \ge 0$ are slack variables. Maximize the minimum value of the slacks over the LP relaxation of the modified problem. Good news: If the solution has positive objective value (meaning all slacks are positive), you have a relative interior point of at least the LP hull. Bad news: An unfortunate combination of inequalities, like the example above, may prevent you from getting all slacks positive.
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