diff --git a/notebooks/assessments/finalize_data_loader copy.ipynb b/notebooks/assessments/finalize_data_loader copy.ipynb index b5f5676..6022e4c 100644 --- a/notebooks/assessments/finalize_data_loader copy.ipynb +++ b/notebooks/assessments/finalize_data_loader copy.ipynb @@ -70,16 +70,16 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "48" + "263" ] }, - "execution_count": 8, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -896,7 +896,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -934,6 +934,141 @@ "## data loader" ] }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ + "from scprint.utils import getBiomartTable" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "downloading gene names from biomart\n", + "\n", + "['ensembl_gene_id', 'hgnc_symbol', 'gene_biotype', 'entrezgene_id', 'start_position', 'chromosome_name']\n" + ] + } + ], + "source": [ + "biomart = getBiomartTable(attributes=['start_position', 'chromosome_name']).set_index('ensembl_gene_id')\n", + "genedf = genedf.set_index('ensembl_gene_id')\n", + "\n", + "genedf = genedf.loc[~genedf.index.duplicated(keep='first')]\n", + "biomart = biomart.loc[~biomart.index.duplicated(keep='first')]\n", + "\n", + "genedf = genedf.join(biomart[['start_position', 'chromosome_name']], how='inner').sort_values(by=['chromosome_name', 'start_position'])" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [], + "source": [ + "pe = PositionalEncoding2D(4)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# PositionalEncodingClass where:\n", + "# PE(x,y,2i) = sin(x/10000^(4i/D))\n", + "# PE(x,y,2i+1) = cos(x/10000^(4i/D))\n", + "# PE(x,y,2j+D/2) = sin(y/10000^(4j/D))\n", + "# PE(x,y,2j+1+D/2) = cos(y/10000^(4j/D))\n", + "# \n", + "# Where:\n", + "# (x,y) is a point in 2d space\n", + "# i,j is an integer in [0, D/4), where D is the size of the ch dimension" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "ename": "NameError", + "evalue": "name 'torch' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m/home/ml4ig1/Documents code/scPRINT/notebooks/assessments/finalize_data_loader copy.ipynb Cell 38\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> 1\u001b[0m pe(torch\u001b[39m.\u001b[39mzeros((\u001b[39m1\u001b[39m,\u001b[39m10\u001b[39m,\u001b[39m10\u001b[39m,\u001b[39m4\u001b[39m)))\n", + "\u001b[0;31mNameError\u001b[0m: name 'torch' is not defined" + ] + } + ], + "source": [ + "pe(torch.zeros((1,10,10,4)))" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[ 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36\n", + " 38 40 42 44 46 48 50 52 56 60 64 68 72 76 80 84 88 92\n", + " 96 100 104 108 112 116 120 124 128 132 136 140 144 148 152 156 164 172\n", + " 180 188 196 204 212 220 228 236 244 252 260 268 276 284 292 300 308 316\n", + " 324 332 340 348 356 364 380 396]\n", + "\n" + ] + } + ], + "source": [ + "# compute rotary embeddings\n", + "import numpy as np\n", + "\n", + "def number_generator(n):\n", + " return np.cumsum(np.repeat([2, 4, 8, 16], n//3)[:n])\n", + "\n", + "numbers = number_generator(80)\n", + "print(numbers)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "rotary_emb = RotaryEmbedding(dim = 32)" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [], + "source": [ + "from rotary_embedding_torch import RotaryEmbedding" + ] + }, { "cell_type": "code", "execution_count": 106, @@ -1240,7 +1375,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 142, "metadata": {}, "outputs": [], "source": [ @@ -1258,25 +1393,4385 @@ }, { "cell_type": "code", - "execution_count": 131, + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "genedf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "genomic location" + ] + }, + { + "cell_type": "code", + "execution_count": 145, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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uidsymbolstable_idensembl_gene_idncbi_gene_idsbiotypedescriptionsynonymsorganism_idbionty_source_idupdated_atcreated_by_id
id
53102a6Xjf000WNY3LINC01772NoneENSG00000226029107984921lncRNAlong intergenic non-protein coding RNA 1772 [S...ENSG0000022602929.02023-11-22 13:16:32.368761+00:001
53103zR8psPjThixhLINC01772NoneENSG00000291388107984921lncRNAlong intergenic non-protein coding RNA 1772 [S...ENSG0000022602929.02023-11-22 13:16:32.368797+00:001
53104mRzSiS7BgReHTSPAN6NoneENSG000000000037105protein_codingtetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]T245|TSPAN-6|TM4SF629.02023-11-22 13:16:56.402584+00:001
531052wlFrfmHXEziTNMDNoneENSG0000000000564102protein_codingtenomodulin [Source:HGNC Symbol;Acc:HGNC:17757]TEM|CHM1L|BRICD4|MYODULIN|TENDIN29.02023-11-22 13:16:56.402622+00:001
53106NQ1m5CzgdgDNDPM1NoneENSG000000004198813protein_codingdolichyl-phosphate mannosyltransferase subunit...MPDS|CDGIE29.02023-11-22 13:16:56.402654+00:001
.......................................
180301z8JV8iBK7VcjRPSAP58NoneENSG00000225178NoneNoneNoneNone2NaN2023-12-05 16:38:38.056226+00:001
180302bXNCWgiDJgJkRP11-392E22.10NoneENSG00000272934NoneNoneNoneNone2NaN2023-12-05 17:00:14.850026+00:001
180303HWjP61qPcHWbSLFN12L_ENSG00000286065NoneENSG00000286065NoneNoneNoneNone2NaN2023-12-05 17:00:14.850188+00:001
180304Ok7cuO0Iu0IjCH17-476P10.1NoneENSG00000285762NoneNoneNoneNone2NaN2023-12-05 17:00:14.850334+00:001
180305PWgJ2mX9WQtLRP11-231C14.10NoneENSG00000288630NoneNoneNoneNone2NaN2023-12-06 08:15:15.190773+00:001
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70263 rows × 12 columns

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"180303 None None \n", + "180304 None None \n", + "180305 None None \n", + "\n", + " description \\\n", + "id \n", + "53102 long intergenic non-protein coding RNA 1772 [S... \n", + "53103 long intergenic non-protein coding RNA 1772 [S... \n", + "53104 tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858] \n", + "53105 tenomodulin [Source:HGNC Symbol;Acc:HGNC:17757] \n", + "53106 dolichyl-phosphate mannosyltransferase subunit... \n", + "... ... \n", + "180301 None \n", + "180302 None \n", + "180303 None \n", + "180304 None \n", + "180305 None \n", + "\n", + " synonyms organism_id bionty_source_id \\\n", + "id \n", + "53102 ENSG00000226029 2 9.0 \n", + "53103 ENSG00000226029 2 9.0 \n", + "53104 T245|TSPAN-6|TM4SF6 2 9.0 \n", + "53105 TEM|CHM1L|BRICD4|MYODULIN|TENDIN 2 9.0 \n", + "53106 MPDS|CDGIE 2 9.0 \n", + "... ... ... ... \n", + "180301 None 2 NaN \n", + "180302 None 2 NaN \n", + "180303 None 2 NaN \n", + "180304 None 2 NaN \n", + "180305 None 2 NaN \n", + "\n", + " updated_at 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"expr = i[0][np.arange(i[0].shape[0])[:,None], loc]" ] }, { diff --git a/scprint/model/model.py b/scprint/model/model.py index 173f53b..d9a4023 100644 --- a/scprint/model/model.py +++ b/scprint/model/model.py @@ -1,25 +1,23 @@ import torch.nn as nn import torch.nn.functional as F from base import BaseModel - - -class MnistModel(BaseModel): - def __init__(self, num_classes=10): - super().__init__() - self.conv1 = nn.Conv2d(1, 10, kernel_size=5) - self.conv2 = nn.Conv2d(10, 20, kernel_size=5) - self.conv2_drop = nn.Dropout2d() - self.fc1 = nn.Linear(320, 50) - self.fc2 = nn.Linear(50, num_classes) +import torch +from typing import Optional, Dict, Union +from torch import Tensor +import math +import dgl + +class scPrint(BaseModel): + def __init__(self, config): + super(scPrint, self).__init__() + self.config = config + self.encoder = Encoder(config) + self.decoder = Decoder(config) def forward(self, x): - x = F.relu(F.max_pool2d(self.conv1(x), 2)) - x = F.relu(F.max_pool2d(self.conv2_drop(self.conv2(x)), 2)) - x = x.view(-1, 320) - x = F.relu(self.fc1(x)) - x = F.dropout(x, training=self.training) - x = self.fc2(x) - return F.log_softmax(x, dim=1) + x = self.encoder(x) + x = self.decoder(x) + return x class GeneEncoder(nn.Module): @@ -63,25 +61,69 @@ class PositionalEncoding(nn.Module): Note: not used in the current version of scprint. """ - def __init__(self, d_model: int, dropout: float = 0.1, max_len: int = 5000): + def __init__(self, d_model: int, max_len: int, dropout: float = 0.1, maxval=10000.0): super().__init__() self.dropout = nn.Dropout(p=dropout) position = torch.arange(max_len).unsqueeze(1) div_term = torch.exp( - torch.arange(0, d_model, 2) * (-math.log(10000.0) / d_model) + torch.arange(0, d_model, 2) * (-math.log(maxval) / d_model) ) pe = torch.zeros(max_len, 1, d_model) pe[:, 0, 0::2] = torch.sin(position * div_term) pe[:, 0, 1::2] = torch.cos(position * div_term) self.register_buffer("pe", pe) - def forward(self, x: Tensor) -> Tensor: + def forward(self, x: Tensor, pos_x: Tensor) -> Tensor: """ Args: x: Tensor, shape [seq_len, batch_size, embedding_dim] """ - x = x + self.pe[: x.size(0)] + x = x + self.pe[pos_x] + return self.dropout(x) + + +class DPositionalEncoding(nn.Module): + """ + The PositionalEncoding module applies a positional encoding to a sequence of vectors. + This is necessary for the Transformer model, which does not have any inherent notion of + position in a sequence. The positional encoding is added to the input embeddings and + allows the model to attend to positions in the sequence. + + Args: + d_model (int): The dimension of the input vectors. + dropout (float, optional): The dropout rate to apply to the output of the positional encoding. + max_len (int, optional): The maximum length of a sequence that this module can handle. + + Note: not used in the current version of scprint. + """ + + def __init__(self, d_model: int, max_len: int, dropout: float = 0.1, maxvalue=10000.0): + super().__init__() + self.dropout = nn.Dropout(p=dropout) + + position = torch.arange(max_len).unsqueeze(1) + div_term = torch.exp( + torch.arange(0, d_model, 2) * (-math.log(maxvalue) / d_model) + ) + pe = torch.zeros(max_len, 1, d_model) + pe[:, 0, (d_model / 2) :: 2 + (d_model / 2)] = torch.sin(position * div_term) + pe[:, 0, 1 + (d_model / 2) :: 2 + (d_model / 2)] = torch.cos( + position * div_term + ) + self.register_buffer("pe", pe) + + # PE(x,y,2i) = sin(x/10000^(4i/D)) + # PE(x,y,2i+1) = cos(x/10000^(4i/D)) + # PE(x,y,2j+D/2) = sin(y/10000^(4j/D)) + # PE(x,y,2j+1+D/2) = cos(y/10000^(4j/D)) + + def forward(self, x: Tensor, pos_x: Tensor) -> Tensor: + """ + Args: + x: Tensor, shape [seq_len, batch_size, embedding_dim] + """ + x = x + self.pe[pos_x] return self.dropout(x) @@ -411,5 +453,3 @@ def __init__(self, d_model: int, nhead: int, num_layers: int): def forward(self, x: Tensor) -> Tensor: return self.transformer(x) - - diff --git a/scprint/utils/utils.py b/scprint/utils/utils.py index 275e353..2de5edb 100644 --- a/scprint/utils/utils.py +++ b/scprint/utils/utils.py @@ -38,7 +38,7 @@ def run_command(command, **kwargs): def _fetchFromServer(ensemble_server, attributes): - server = BiomartServer(ensemble_server, verbose=True) + server = BiomartServer(ensemble_server) ensmbl = server.datasets["hsapiens_gene_ensembl"] print(attributes) res = pd.read_csv( @@ -51,7 +51,7 @@ def _fetchFromServer(ensemble_server, attributes): def getBiomartTable( - ensemble_server="http://feb2023.archive.ensembl.org/biomart", + ensemble_server="http://jul2023.archive.ensembl.org/biomart", useCache=False, cache_folder="/tmp/biomart/", attributes=[],