Federico Vaggi FedericoV
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| @numba.jit(target='cpu', nopython=True) | |
| def _compute_overlaps(u, v): | |
| a = 0 | |
| b = 0 | |
| c = 0 | |
| m = u.shape[0] | |
| for idx in range(m): | |
| a += u[idx] & v[idx] | |
| b += u[idx] & ~v[idx] | |
| c += ~u[idx] & v[idx] |
FedericoV
/ gist:0e7d6d8c8794a99a7a42
Created
May 28, 2015 08:06
Cosine Similarity that handles NaN with Numba
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| import numba | |
| @numba.jit(target='cpu', nopython=True) | |
| def fast_cosine(u, v): | |
| m = u.shape[0] | |
| udotv = 0 | |
| u_norm = 0 | |
| v_norm = 0 | |
| for i in range(m): | |
| if (np.isnan(u[i])) or (np.isnan(v[i])): |
FedericoV
/ gist:ac04d3b0cc028e5e8018
Created
March 16, 2015 15:44
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| Ab Ratio_12h 448 | |
| Ratio_18h 431 | |
| Ratio_24h 1088 | |
| Ratio_6h 141 | |
| FUS Ratio_12h 272 | |
| Ratio_18h 1656 | |
| Ratio_24h 1867 | |
| Ratio_6h 489 | |
| GFP Ratio_12h 40 | |
| Ratio_18h 1042 |
FedericoV
/ gist:6c6cf9dee3557e0fe9de
Created
February 26, 2015 19:30
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| self.rotation = rotation_matrix(np.array([0, 0, 1]), | |
| self.model.stem_rotation) | |
| self.axis = self.__get_axis() | |
| self.rotation = np.dot(self.rotation, | |
| rotation_matrix(self.axis, | |
| self.model.tree_rotation)) |
FedericoV
/ gist:2eac0090d5cfeb6b33be
Created
February 25, 2015 14:22
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| self.rotation = rotation_matrix(np.array([0,0,1]), self.model.stem_rotation) | |
| self.axis = self.__get_axis() | |
| self.rotation = np.dot(rotation_matrix(self.axis, self.model.tree_rotation), self.rotation) |
FedericoV
/ gist:50b5a2cea3e0802351cc
Created
February 5, 2015 15:34
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| Jaccard | |
| Unclustered Communities: 2984 | |
| Total Clustered Genes: 4555 | |
| Number of Communities: 205 | |
| --------------------------- | |
| Simpson | |
| Unclustered Communities: 162 | |
| Total Clustered Genes: 6328 |
FedericoV
/ gist:7d08ef6e173f030bb611
Created
February 4, 2015 10:36
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| @numba.jit(target='cpu', nopython=True) | |
| def fast_simpson(i, j): | |
| a = 0 | |
| b = 0 | |
| c = 0 | |
| M = i.shape[0] | |
| for idx in range(M): | |
| a += (i[idx] == 1) and (j[idx] == 1) |
FedericoV
/ Numba_ODEINT_benchmark.ipynb
Created
September 9, 2014 09:47
Showing numba at speeding up a complicated ODE
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| total 16G | |
| drwx------ 4 keu_vaggi kore 60K 12 giu 11:19 . | |
| drwxrwxr-x 49 root kore 4,0K 6 giu 09:33 .. | |
| -rw------- 1 keu_vaggi kore 17K 11 giu 10:36 .bash_history | |
| -rw-r--r-- 1 keu_vaggi kore 18 10 mag 2012 .bash_logout | |
| -rw-r--r-- 1 keu_vaggi kore 176 10 mag 2012 .bash_profile | |
| -rw-r--r-- 1 keu_vaggi kore 155 30 ago 2013 .bashrc | |
| -rw-r--r-- 1 keu_vaggi kore 179 28 mar 17:28 batch.sh | |
| -rw------- 1 keu_vaggi kore 150M 12 giu 11:06 core.12240 | |
| -rw------- 1 keu_vaggi kore 1,3G 12 giu 11:07 core.12241 |
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| bash: module: line 1: syntax error: unexpected end of file | |
| bash: error importing function definition for `module' | |
| bash: module: line 1: syntax error: unexpected end of file | |
| bash: error importing function definition for `module' | |
| bash: module: line 1: syntax error: unexpected end of file | |
| bash: error importing function definition for `module' | |
| bash: module: line 1: syntax error: unexpected end of file | |
| bash: error importing function definition for `module' | |
| /fem0/keu_albanese/local/lib/python2.7/site-packages/scipy/integrate/quadpack.py:315: RuntimeWarning: overflow encountered in square | |
| return _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit) |