Wilson loops
The observables of Chern–Simons theory are the n-point correlation functions of gauge-invariant operators. The most often studied class of gauge invariant operators are Wilson loops. A Wilson loop is the holonomy around a loop in M, traced in a given representation R of G. As we will be interested in products of Wilson loops, without loss of generality we may restrict our attention to irreducible representations R.
More concretely, given an irreducible representation R and a loop K in M, one may define the Wilson loop
by

where A is the connection 1-form and we take the Cauchy principal value of the contour integral and
is the path-ordered exponential.
HOMFLY and Jones polynomials
Consider a link L in M, which is a collection of ℓ disjoint loops. A particularly interesting observable is the ℓ-point correlation function formed from the product of the Wilson loops around each disjoint loop, each traced in the fundamental representation of G. One may form a normalized correlation function by dividing this observable by the partition function Z(M), which is just the 0-point correlation function.
In the special case in which M is the 3-sphere, Witten has shown that these normalized correlation functions are proportional to known knot polynomials. For example, in G = U(N) Chern–Simons theory at level k the normalized correlation function is, up to a phase, equal to

times the HOMFLY polynomial. In particular when N = 2 the HOMFLY polynomial reduces to the Jones polynomial. In the SO(N) case, one finds a similar expression with the Kauffman polynomial.
The phase ambiguity reflects the fact that, as Witten has shown, the quantum correlation functions are not fully defined by the classical data. The linking number of a loop with itself enters into the calculation of the partition function, but this number is not invariant under small deformations and in particular, is not a topological invariant. This number can be rendered well defined if one chooses a framing for each loop, which is a choice of preferred nonzero normal vector at each point along which one deforms the loop to calculate its self-linking number. This procedure is an example of the point-splitting regularization procedure introduced by Paul Dirac and Rudolf Peierls to define apparently divergent quantities in quantum field theory in 1934.
Sir Michael Atiyah has shown that there exists a canonical choice of 2-framing,[5] which is generally used in the literature today and leads to a well-defined linking number. With the canonical framing the above phase is the exponential of 2πi/(k + N) times the linking number of L with itself.
- Problem (Extension of Jones polynomial to general 3-manifolds)
"The original Jones polynomial was defined for 1-links in the 3-sphere (the 3-ball, the 3-space R3). Can you define the Jones polynomial for 1-links in any 3-manifold?"
See section 1.1 of this paper[6] for the background and the history of this problem. Kauffman submitted a solution in the case of the product manifold of closed oriented surface and the closed interval, by introducing virtual 1-knots.[7] It is open in the other cases. Witten's path integral for Jones polynomial is written for links in any compact 3-manifold formally, but the calculus is not done even in physics level in any case other than the 3-sphere (the 3-ball, the 3-space R3). This problem is also open in physics level. In the case of Alexander polynomial, this problem is solved.