I thank the referees for their useful feedback, which led to positive changes
to the manuscript. All changes made since the first submission can be found
highlighted in an attached PDF generated by latexdiff.

In addition to the changes made in response to referee comments detailed below,
there were three other changes made to the resubmitted manuscript:

 - References to a "companion paper" were changed to a "related work", since
   the two papers are not being considered as companions.

 - Soon after submission I identified a mistake in Appendix A regarding the
   matrix form of a super linear operator. This mistake did not affect any of
   the formulae or results of the rest of the manuscript, but has nevertheless
   been amended.

 - I found and repaired a spelling mistake in the paragraph after what is now
   equation 67

Report of the First Referee:
> 1) Terms such as "marginal minima" and "pseudogap" are used without clear
> definitions. These terms refers to different concepts depending on various
> fields, which can yield meaningless confusions. Provide clear definitions for
> these technical terms when they appear at the first time.

The text of the second paragraph of the introduction has been expanded to more
precisely define the terms "marginal minima" and "pseudogap". Its final
sentences now read:

  The level set associated with this threshold energy contains mostly
  \emph{marginal minima}, or minima whose Hessian matrix have a continuous
  spectral density over all sufficiently small positive eigenvalues. In most
  circumstances the spectrum is \emph{pseudogapped}, which means that the
  spectral density smoothly approaches zero as zero eigenvalue is approached
  from above.

If this level of definition is not sufficiently clear to the reviewer, or if
there are further terms I have neglected, I welcome further comment on the
matter.

> 2) In eqs (23)-(25), I could not figure out why both notations of L(x,w) and
> H(x, w) are used. If the two notations refer to the identical quantity, it
> should be unified. Otherwise, their difference should be explained.

This confusion stems from a notational ambiguity. The domain of H and the
domain of ∇H are not the same, and writing ∇H(x, ω) is not meant to imply the
existence of a function H(x, ω). I have expanded the text around equations (24)
and (25) in an attempt to clarify this point.

> 3) At the first reading, I am confused with eq. (38). The author writes
> "This is because the trace of $\partial \partial H$ is typically an order of
> $N$ smaller than trace of $\partial \partial g_i". This would be true for
> Hamiltonian of eq. (45). However, does it hold for sums of squared random
> functions such as eq. (71)? Let us consider a trivial case
> $V_i(x) = r_i \cdot x/\sqrt{N}$, where $r_i$ is a random vector from
> $N(0, I_{N\times N})$. This makes eq. (71) a quadratic form of a negative
> definite matrix, for which its trace of Hessian scale as $O(N)$.  This may be
> an exceptional case. However, statements such as the above before showing
> concrete target systems can confuse readers. I would like to ask the author
> to amend the writing.

I thank the referee for catching this mistake. Fortunately, its effect on the
manuscript was minor, because correctly accounting for cases like the referee
describes results in only a constant correction to μ. Since only the relative
value of μ is important for identifying marginal minima, the marginal
complexity calculated while neglecting it is still correct, as in the model
examined in the "related work" arXiv:2407.02092 which has such a linear term.

I have changed the text of the manuscript and several equations to correct this
mistake. This can be seen in the vicinity of equations (using the new
manuscript's numbering) 38/39, after equation 46, after equation 59, and after
equation 75. In Sections IV.C and D this leads to changes in display math that
were not captured by the latexdiff, in equations 76, 85, 86, D2, D6, D8, and
D11, all consisting of replacing μ with μ + f'(0).

Report of the Second Referee:
> (1) The first two examples (spherical spin glasses and multi-spherical spin
> glasses) exhibit the property that the complexity of marginal states splits into
> two contributions: the “unconstrained” complexity and a large deviation function
> associated with the smallest eigenvalue of the Hessian. In the text it is
> claimed that this behavior follows from the Gaussian nature of the Hessian. Is
> this statement general? If one constructs models whose Hessians are not
> invariant—for example, with an entry-dependent variance pattern—can one still
> expect this statement to hold?

This question is an astute one, and I cannot speak to whether Gaussianity alone
is a sufficient condition for the separation of the action. Positing properties
of the Hessian is not enough for reasoning about this, since the key question
is how correlations between the Hessian, gradient, and energy compare in
magnitude with their self correlations. So, one would need to construct an
ensemble of random functions whose Hessian has such a property to begin
addressing this.

Rather than venture into this probably rich research line, I have simply
clarified in the text after what is now equation 53 that this is characteristic
of isotropic and Gaussian random functions.

> (2)  It appears that Eq. (66) and its zero-temperature limit, when evaluated at
> the saddle point, provide a parametrization of the large deviation functions for
> the smallest Hessian eigenvalue, analogous to Eq. (52) for the GOE case. Is
> there any way to express this large deviation function more transparently, or in
> a form that makes the limit  ϵ→0 easier to read?

Unfortunately I have not found a way to nicely express such a thing. The
zero-temperature limit of what is now equation 67 is a much more unwieldy
expression than equation 67 itself, and is not appropriate for inclusion in a
manuscript let alone a source of intuitive insight. Though the referee's
suggestion of a reduction in the ε→0 limit does exist, it involves the
nontrivial coordination of limiting saddle-point values in the variables making
up the expression.

> (3) Maybe the author can comment on the relation between his approach and the
> methods developed in the past to track marginal minima (mostly in the sense of
> an isolated eigenvalue of the Hessian rather than pseudogapped), such as:
> 
> Marginal states in mean-field glasses
> Markus Müller, Luca Leuzzi, and Andrea Crisanti
> PHYSICAL REVIEW B 74, 134431 2006

I have added a final paragraph to the conclusion discussion the relationship
between these two papers. It reads

  The title of our paper and that of \citeauthor{Muller_2006_Marginal} suggest
  they address the same topic, but this is not the case
  \cite{Muller_2006_Marginal}. That work differs in three important and
  fundamental ways. First, it describes minima of the TAP free energy and
  involves peculiarities specific to the TAP. Second, it describes dominant
  minima which happen to be marginal, not a condition for finding subdominant
  marginal minima. Finally, it focuses on minima with a single soft direction
  (which are the typical minima of the low temperature Sherrington--Kirkpatrick
  TAP free energy), while we aim to avoid such minima in favor of ones that
  have a pseudogap (which we argue are relevant to out-of-equilibrium
  dynamics). The fact that the typical minima studied by
  \citeauthor{Muller_2006_Marginal} are not marginal in this latter sense may
  provide an intuitive explanation for the seeming discrepancy between the
  proof that the low-energy Sherrington--Kirkpatrick model cannot be sampled
  \cite{ElAlaoui_2022_Sampling} and the proof that a message passing algorithm
  can find near-ground states \cite{Montanari_2021_Optimization}: the algorithm
  finds the atypical low-lying states that are marginal in the sense considered
  here but cannot find the typical ones considered by
  \citeauthor{Muller_2006_Marginal}.

> (4) When introducing the method around Eq. (1), it should be stated that this
> works for symmetric matrices A.

The text new reflects this.

> Typos:
> 
> Eq (A8): integral should be over d2
> Page 11, last line second column: “minima can dynamics” —> a verb is missing
> here

These small mistakes have been fixed in the new manuscript.