Recently, I come up with the following conjecture, which is proved to be true for small matrices and false for large matrices.
Conjecture. Let $E \in \mathbb{R}^{d\times d}$ be the matrix of ones and $M \in \mathbb{R}^{d\times d}$ be a bounded matrix representing a metric. That is, $M$ satisfies the following conditions:
- $1 \geq M_{ij} \geq 0\ $ for $\ 1 \leq i, j \leq d$
- $M_{ij} = 0\ \Leftrightarrow\ i = j$
- $M_{ij} = M_{ji}$
- $M_{ij} + M_{jk} \geq M_{ik}$ for $1 \leq i, j, k \leq d$
Then the matrix $A = E - M$ is positive semi-definite.
When $d = 2$, $M$ and $A$ respectively have the form
$$
M = \begin{bmatrix} 0 & a \\ a & 0 \end{bmatrix},\quad
A = \begin{bmatrix} 1 & 1 - a \\ 1 - a & 1 \end{bmatrix}
$$
with $0 < a \leq 1$. For any $x \in \mathbb{R}^2$,
$$
x^TAx = x_1^2 + x_2^2 + 2(1-a)x_1x_2 = (1-a)(x_1 + x_2)^2 + ax_1^2 + ax_2^2 \geq 0
$$
Thus the conjecture is true for $d = 2$.
When $d = 3$, $M$ and $A$ respectively have the form
$$
M = \begin{bmatrix} 0 & a & b \\ a & 0 & c \\ b & c & 0 \end{bmatrix},\quad
A = \begin{bmatrix} 1 & 1 - a & 1 - b \\ 1 - a & 1 & 1 - c \\ 1 - b & 1-c & 1 \end{bmatrix}
$$
with $0 < a, b, c \leq 1$. Without loss of generality, we assume $c \geq a$ and $c \geq b$. For $\forall x \in \mathbb{R}^3$,
\begin{align}
x^TAx\ &=\ x_1^2 + x_2^2 + x_3^2 + 2(1-a)x_1x_2 + 2(1-b)x_1x_3 + 2(1-c)x_2x_3 \\
&=\ (1-c)(x_1 + x_2 + x_3)^2 + cx_1^2 + cx_2^2 + cx_3^2 + 2(c-a)x_1x_2 + 2(c-b)x_1x_3 \\
&=\ (1 - c)(x_1 + x_2 + x_3)^2 + (c-a)(x_1 + x_2)^2 + ax_1^2 + ax_2^2 + cx_3^2 + 2(c-b)x_1x_3 \\
&=\ (1 - c)(x_1 + x_2 + x_3)^2 + (c-a)(x_1 + x_2)^2 + (c-b)(x_1 + x_3)^2 \\
&\ \ \quad \quad + (\color{red}{a + b - c})x_1^2 + ax_2^2 + bx_3^2 \\
&\geq\ 0
\end{align}
Note that $a + b - c \geq 0$ by triangle inequality. Therefore, the conjecture holds at $d = 3$.
When $d = 4$, the proof becomes harder. Using a computer, I enumerate all metric matrices whose non-diagonal elements have values from $\{\frac{1}{1000}, \frac{2}{1000}, \cdots, \frac{1000}{1000}\}$. The result shows that all these matrices are positive semi-definite. So the conjecture seems to be true for $d = 4$.
For $d = 5$, I find the following counterexample whose eigenvalues are $2.428$, $-0.089$, $0.5$, $1.161$ and $1$.
$$
M =
\begin{bmatrix}
0 & 0.5 & 0.5 & 0.5 & 1 \\
0.5 & 0 & 0.5 & 0.5 & 1 \\
0.5 & 0.5 & 0 & 1 & 0.5 \\
0.5 & 0.5 & 1 & 0 & 0.5 \\
1 & 1 & 0.5 & 0.5 & 0
\end{bmatrix},\quad
A =
\begin{bmatrix}
1 & 0.5 & 0.5 & 0.5 & 0 \\
0.5 & 1 & 0.5 & 0.5 & 0 \\
0.5 & 0.5 & 1 & 0 & 0.5 \\
0.5 & 0.5 & 0 & 1 & 0.5 \\
0 & 0 & 0.5 & 0.5 & 1
\end{bmatrix}
$$
So the conjecture does hold in general for $d \geq 5$.