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What is a topological feature, that a (some) tqft (e.g. in 3 or 4 dim) sees but homology/cohomology/homotopy groups dont? Or: what is an example where using classical theories is hard, but using a tqft is comparatively easy?

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All the answers so far have focused on 3 dimensions, but the answer is much more striking in 4 dimensions. Freedman's theorem tells you that classical homology invariants give you complete information about topological, simply-connected 4-manifolds. These classical invariants cannot, however, distinguish between distinct smooth structures on the same topological 4-manifold, and essentially our only technique for distinguishing smooth 4-manifolds is Donaldson's invariant or the Seiberg-Witten invariant or their relatives. These do not quite form a TQFT, but are related to TQFTs.

Edit: On request, a little about how the 4-manifold invariants are related to a TQFT. This is all nicely explained in the beginning of Kronheimer and Mrowka's book Monopoles and 3-manifolds.

There are actually three different theories, denoted $\widehat{\mathit{HM}}$ ("HM-from"), $\check{\mathit{HM}}$ ("HM-to", unfortunately typeset badly here), and $\overline{\mathit{HM}}$. All are close to satisfying axioms for a TQFT assigning a vector space to a 3-manifold and maps to a 4-manifold, at least for connected manifolds. (The vector spaces are infinite dimensional, but finite in each graded piece.) Unfortunately, however you slice it, in each case the invariant associated to a closed 4-manifold in the usual TQFT way (when defined) is zero.

Instead, you use the fact that there is an exact triangle $$ \cdots \longrightarrow \widehat{\mathit{HM}} \longrightarrow \overline{\mathit{HM}} \longrightarrow \check{\mathit{HM}}\longrightarrow \cdots $$ (with right mapping to left), and the map $\overline{\mathit{HM}}(W)$ is $0$ for $b_2^+(W) \ge 1$.

If you have a 4-manifold $W$ with $b_2^+(W) \ge 2$, you factor it as two cobordisms $W = W_1 \cup_Y W_2$ for some 3-manifold $Y$, with $b_2^+(W_i) \ge 1$. Then the properties above let you map from $\check{\mathit{HM}}(S^3)$, to $\check{\mathit{HM}}(Y)$, backwards in the exact triangle to $\widehat{\mathit{HM}}(Y)$, and then forwards to $\widehat{\mathit{HM}}(S^3)$. The resulting map (from $\check{\mathit{HM}}(S^3)$ to $\widehat{\mathit{HM}}(S^3)$) gives the interesting Seiberg-Witten invariants of $W$.

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@Kelly It's not a standard TQFT, if only because the invariants (both Donaldson and SW) are only defined for 4-manifolds with $b_2^+ \ge 2$. I also don't know what vector spaces to associate to a general 3-manifold for the Donaldson invariants. The theory would be call "instanton Floer homology", but, as I understand it, there are severe technical issues with reducibles in general. If you know how to define such a TQFT related to Donaldson theory, I'm very interested to hear about it. –  Dylan Thurston Apr 5 '11 at 11:23
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@Kelly: there's a terminological issue, I think. Regarded as a QFT, Chern-Simons theory (for example) is considered by Witten to be a TQFT just because the action does not involve the metric. However, it does involve a hard-to-interpret path integral. Mathematicians usually prefer the Atiyah-Segal axioms for TQFT, and that's what Dylan is referring to. –  Tim Perutz Apr 5 '11 at 15:04
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There are more things in heaven and earth, Dylan, Than are dreamt of in the Atiyah-Segal axioms. :-) –  Kelly Davis Apr 5 '11 at 19:48
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@Kelly has just posted an article following up on this last comment: arxiv.org/abs/1106.2358 –  Scott Morrison Jun 14 '11 at 17:07
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@Kelly: the main theorem of your article (Theorem 4.1) seems to have been proven by Freedman et. al.: front.math.ucdavis.edu/0503.5054 (Theorem 4.2) –  Ian Agol Jul 1 '11 at 15:50
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The only topological information in 3-manifolds besides homology and homotopy is Reidemeister torsion (see this question). TQFT sees Ray-Singer torsion, which is the same thing. Indeed, it was this discovery by Schwartz (and independently, unpublished, by Singer) which sparked the subject and which motivated Witten's work on a TQFT for the Jones polynomial.

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..and peripheral structure if the manifold has boundary. The TQFT underlying the Witten-Reshitkhin-Turaev invariant keeps track of peripheral structure also. You might try: Frohman, Charles; Kania-Bartoszyńska, Joanna A quantum obstruction to embedding. Math. Proc. Cambridge Philos. Soc. 131 (2001), no. 2, 279–293 and Frohman, Charles; Gelca, Răzvan; Lofaro, Walter The A-polynomial from the noncommutative viewpoint. Trans. Amer. Math. Soc. 354 (2002), no. 2, 735–747 for examples of using TQFT to construct invariants that detect peripheral structure. –  Charlie Frohman Apr 4 '11 at 16:43
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Stepping away from $3$-manifolds, the highest impact of the ideas of TQFT came in combinatorial algebraic geometry. The Gromov-Witten potential allowed the solution of classical problems in enumerative geometry...that were not going to be solved by purely homotopy theoretic means. –  Charlie Frohman Apr 4 '11 at 16:49
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There seems to be some historical revisionism going on here. It is true that Schwarz (and independently also Singer, albeit unpublished) discovered a three-dimensional abelian Chern-Simons (aka BF) theory which computes the analytic Ray-Singer torsion of a 3-manifold. To further claim that this sparked the subject, though, seems to fly in the face of the evidence, not to mention the well-documented historical accounts by Atiyah, say. Whereas or not the work of Witten was motivated by Schwarz's BF theory is debatable, but that it was Witten's paper that sparked the subject is not. –  José Figueroa-O'Farrill Apr 4 '11 at 22:49
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@Jose: Fair enough- I exaggerated in order to emphasize a point. Undoubtedly, it was indeed Witten's paper which sparked the subject. I struck the passage out. –  Daniel Moskovich Apr 4 '11 at 23:21
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Rasmussen's $s$ invariant detects non-sliceness of some knots that no other method applies to.

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The Tait flyping conjecture was proven by Menasco and Thistlethwaite using knot polynomial invariants (which are a version of TQFT invariants).

There is a lower bound on the braid index of a knot in terms of the Jones polynomial. I don't think that there is an efficient algorithm to compute the braid index of knots in general using geometric techniques, so sometimes this works better. There are related estimates of tunnel number and Heegaard genus in terms of TQFT invariants, but these are not sharp in many cases. However, computing TQFT invariants is straightforward, but exponential, so I'm not sure these estimates are necessarily "easier". Estimates of Heegaard genus for Seifert spaces were given Boileau and Zieschang using algebraic techniques, and this has been done by Helen Wong using TQFT invariants.

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The other Tait conjectures (alternating diagrams are minimal) was proved before the flyping conjecture, also using the Jones polynomial. The proof was easier. –  Dylan Thurston Apr 7 '11 at 13:44
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At a very concrete level, Turaev-Viro invariants of a compact 3-manifold (with or without boundary) can be easily computed by a computer from a triangulation and very often (although not always) distinguish non-homeomorphic manifolds.

To calculate a Turaev-Viro invariant you need to fix a level $r=3,4,\ldots$: for $r=5, 7$ you already obtain a quite powerful (and mysterious) invariant, which works on any kind of compact 3-manifold. For instance, it helped to distinguish immediately most of the non-homeomorphic manifolds in these lists.

So, distinguishing many triangulated 3-manifolds is maybe "an example where using classical theories is hard, but using a tqft is comparatively easy". The "classical theory" here would involve recognizing prime summands, decomposing along tori, finding a hyperbolic structure, etc. etc.

Note however that the cost of calculating Turaev-Viro invariants increases exponentially with $r$ and the number of tetrahedra, so I don't know if they can be effectively used to distinguish -- say -- two manifolds having 20 tetrahedra.

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