© | Dror Bar-Natan: Knot Atlas: KnotTheory`:               This page is passe. Go here instead!

7.11 Khovanov Homology

The Khovanov Homology $\operatorname{\it KH}(L)$ of a knot or a link $L$, also known as Khovanov's categorification of the Jones polynomial of $L$, was defined by Khovanov in [Kh1] (also check my paper [BN1], where the notation is much closer to the notation used here). It is a graded homology theory; each homology group $\operatorname{\it KH}^r(L)$ is in itself a direct sum $\bigoplus_j\operatorname{\it KH}^r_j(L)$ of homogeneous components. Over a field on can form the two-variable ``Poincaré polynomial'' ${\text{\it Kh}}(L)$ (which deserves the name ``the Khovanov polynomial of $L$''),

$${\text{\it Kh}}(L)(q,t) := \sum_{r,j}t^rq^j\dim\operatorname{\it KH}^r_j(L).$$

In[1]

In[2]:= ?Kh
Kh[L][q, t] returns the Poincare polynomial of the Khovanov Homology of a knot/link L (over a field of characteristic 0) in terms of the variables q and t. Kh[L, Program -> prog] uses the program prog to perform the computation. The currently available programs are "FastKh", written in Mathematica by Dror Bar-Natan in the winter of 2005 and "JavaKh" (default), written in java (java 1.5 required!) by Jeremy Green in the summer of 2005. The java program is several thousand times faster than the Mathematica program, though java may not be available on some systems. "JavaKh" also takes the option "Modulus -> p" which changes the characteristic of the ground field to p. If p==0 JavaKh works over the rational numbers; if p==Null JavaKh works over Z (see ?ZMod for the output format).

In[3]:= Options[Kh]
{ExpansionOrder -> Automatic, Program -> "JavaKh", Modulus -> 0, JavaOptions -> ""}

Thus for example, here's the Khovanov polynomial of the knot $5_1$:

In[4]:=	kh = Kh[Knot[5, 1]][q, t]
Out[4]=	-5 -3 1 1 1 1 q + q + ------ + ------ + ------ + ----- 15 5 11 4 11 3 7 2 q t q t q t q t

The Euler characteristic of the Khovanov Homology $\operatorname{\it KH}(L)$ is (up to normalization) the Jones polynomial $J(L)$ of $L$. Precisely,

$${\text{\it Kh}}(L)(q, -1) = {\hat J}(L)(q) := (q+q^{-1})J(L)(q^2).$$

Let us verify this in the case of $5_1$:

In[5]:=	{kh /. t -> -1, Expand[(q+1/q)Jones[Knot[5, 1]][q^2]]}
Out[5]=	-15 -7 -5 -3 -15 -7 -5 -3 {-q + q + q + q , -q + q + q + q }

Khovanov's homology is a strictly stronger invariant than the Jones polynomial. Indeed, $J(5_1)=J(10_{132})$ though ${\text{\it Kh}}(5_1)\neq{\text{\it Kh}}(10_{132})$:

In[6]:=	{ Jones[Knot[5, 1]] === Jones[Knot[10, 132]], Kh[Knot[5, 1]] === Kh[Knot[10, 132]] }
Out[6]=	{True, False}

The algorithm presently used by KnotTheory` is an efficient algorithm modeled on the Kauffman bracket algorithm of Section 7.5.1, as explained in [BN3] (which follows [BN2]). Currently, two implementations of this algorithm are available:

• FastKh: My original implementation, written in Mathematica in the winter of 2005. This implementation can be explicitly invoked using the syntax Kh[L, Program -> "FastKh"][q, t] or by changing the default behaviour of Kh by evaluating SetOptions[Kh, Program -> "FastKh"].

• JavaKh: In the summer of 2005 Jeremy Green re-implemented the algorithm in java (java 1.5 required!) with much further care to the details, leading to an improvemnet factor of several thousands for large knots/links. This implementation is the default. It can also be explicitly invoked from within Mathematica using the syntax Kh[L, Program -> "JavaKh"][q, t].

  JavaKh takes an additional option, Modulus, which sets the characteristic of the ground field for the homology computations to 0 or to a prime $p$. Thus for example, the following four In lines imply that the Khovanov homology of the torus knot T(6,5) has both 3 torsion and 5 torsion, but no 7 torsion:

  In[7]:=

  T65 = TorusKnot[6, 5]; kh = Kh[T65][q, t];

  In[8]:=	Kh[T65, Modulus -> 3][q, t] - kh
  Out[8]=	43 13 43 14 q t + q t

  In[9]:=	Kh[T65, Modulus -> 5][q, t] - kh
  Out[9]=	35 10 35 11 39 11 39 12 q t + q t + q t + q t

  In[10]:=	Kh[T65, Modulus -> 7][q, t] - kh
  Out[10]=	0

  The following further example is a bit tougher. It takes my computer nearly an hour and some 256Mb of memory to find that the Khovanov homology of the 48-crossing torus knot T(8,7) has 3, 5 and 7 torsion but no 11 torsion:

  In[11]:= ?JavaOptions
  JavaOptions is an option to Kh. Kh[L, Program -> "JavaKh", JavaOptions -> jopts] calls java with options jopts. Thus for example, JavaOptions -> "-Xmx256m" sets the maximum java heap size to 256MB - useful for large computations.

  In[12]:=

  SetOptions[Kh, JavaOptions -> "-Xmx256m"];

  In[13]:=

  T87 = TorusKnot[8, 7]; kh = Kh[T87][q, t];

  In[14]:=	Factor[Kh[T87, Modulus -> 3][q, t] - kh]
  Out[14]=	79 25 q t (1 + t)

  In[15]:=	Factor[Kh[T87, Modulus -> 5][q, t] - kh]
  Out[15]=	61 11 12 10 14 12 18 13 q t (1 + t) (1 + q t + q t + q t )

  In[16]:=	Factor[Kh[T87, Modulus -> 7][q, t] - kh]
  Out[16]=	61 14 8 6 12 7 10 8 14 9 q t (1 + t) (1 + q t + q t + q t + q t )

  In[17]:=	Factor[Kh[T87, Modulus -> 11][q, t] - kh]
  Out[17]=	0

  JavaKh also works over the integers:

  In[18]:= ?ZMod
  ZMod[m] denotes the cyclic group Z/mZ. Thus if m=0 it is the infinite cyclic group Z and if m>0 it is the finite cyclic group with m elements. ZMod[m1, m2, ...] denotes the direct sum of ZMod[m1], ZMod[m2], ... .

  For example, the 22nd homology group over ${\mathbb{Z}}$ of the torus knot T(8,7) at degree 73 is the 280 element torsion group ${\mathbb{Z}}_2\oplus{\mathbb{Z}}_4\oplus{\mathbb{Z}}_5\oplus{\mathbb{Z}}_7$:

  In[19]:=	Coefficient[Kh[T87, Modulus -> Null][q, t], t^22 * q^73]
  Out[19]=	ZMod[2, 4, 5, 7]

  Finally, JavaKh may also be run outside of Mathematica, as the following example demonstrates:

  drorbn@coxeter:.../KnotTheory: cd JavaKh
  drorbn@coxeter:.../KnotTheory/JavaKh: java JavaKh
  PD[X[3, 1, 4, 6], X[1, 5, 2, 4], X[5, 3, 6, 2]]
  "+ q^1t^0 + q^3t^0 + q^5t^2 + q^9t^3 "
  

  (Type java JavaKh -help for some further help).

Figure 9: August 2002, Toronto: Mikhail Khovanov explaining his more recent paper [Kh2].