Mercurial > repos > goeckslab > multimodal_learner

annotate multimodal_learner.xml @ 4:de753cf07008 draft

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 528178a2b2ca39924fd596859fe658aeaf984e6d
author goeckslab
date Thu, 22 Jan 2026 22:41:21 +0000
parents 25bb80df7c0c
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25bb80df7c0c planemo upload for repository https://github.com/goeckslab/gleam.git commit f0daa5846b336584c708d88f6d7f1b5ee8dc3093
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1 <tool id="multimodal_learner" name="Multimodal Learner" version="0.1.2" profile="22.01">
0
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2 <description>Train and evaluate an AutoGluon Multimodal model (tabular + image + text)</description>
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3
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4 <requirements>
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5 <container type='docker'>quay.io/goeckslab/multimodal-learner:1.4.0</container>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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6 </requirements>
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7
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8 <required_files>
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9 <include path="multimodal_learner.py"/>
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10 <include path="utils.py"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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11 <include path="split_logic.py"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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12 <include path="training_pipeline.py"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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13 <include path="test_pipeline.py"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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14 <include path="metrics_logic.py"/>
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15 <include path="plot_logic.py"/>
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16 <include path="report_utils.py"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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17 <include path="feature_help_modal.py"/>
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18 </required_files>
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19
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20 <stdio>
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21 <exit_code range="137" level="fatal_oom" description="Out of Memory"/>
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22 <exit_code range="1:" level="fatal" description="Tool failed — see Tool Standard Error"/>
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23 </stdio>
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25 <command detect_errors="exit_code"><![CDATA[
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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26 #import re
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27
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28 #set $image_zip_paths = []
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29 #if $use_images_conditional.use_images == "yes"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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30 #for $zip_file in $use_images_conditional.images_zip_repeat
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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31 #set $image_zip_paths = $image_zip_paths + [$zip_file.images_zip]
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32 #end for
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33 #end if
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34 #if len($image_zip_paths) > 0
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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35 #set $images_zip_cli = " ".join(["'%s'" % z for z in $image_zip_paths])
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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36 #else
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37 #set $images_zip_cli = None
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38 #end if
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39
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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40 set -e;
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41 ln -sf '$input_csv' 'train_input.csv';
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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42 #if $test_dataset_conditional.has_test_dataset == "yes"
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43 ln -sf '$test_dataset_conditional.input_test' 'test_input.csv';
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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44 #end if
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45
4
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46 #set $TORCH_HOME = "./torch_cache"
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47 #set $HF_HOME = "./hf_cache"
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48 #set $HUGGINGFACE_HUB_CACHE = "./hf_cache/hub"
de753cf07008 planemo upload for repository https://github.com/goeckslab/gleam.git commit 528178a2b2ca39924fd596859fe658aeaf984e6d
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49 export TORCH_HOME="$TORCH_HOME" &&
de753cf07008 planemo upload for repository https://github.com/goeckslab/gleam.git commit 528178a2b2ca39924fd596859fe658aeaf984e6d
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50 export HF_HOME="$HF_HOME" &&
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51 export HUGGINGFACE_HUB_CACHE="$HUGGINGFACE_HUB_CACHE" &&
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52 mkdir -p "$TORCH_HOME" "$HUGGINGFACE_HUB_CACHE" &&
de753cf07008 planemo upload for repository https://github.com/goeckslab/gleam.git commit 528178a2b2ca39924fd596859fe658aeaf984e6d
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53
3
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54 python '$__tool_directory__/multimodal_learner.py'
0
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55 --input_csv_train 'train_input.csv'
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56 #if $test_dataset_conditional.has_test_dataset == "yes"
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57 --input_csv_test 'test_input.csv'
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58 #end if
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59 --target_column '$target_column'
3
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60 #if $sample_id_selector.use_sample_id == "yes"
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61 --sample_id_column '$sample_id_selector.sample_id_column'
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62 #end if
0
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63
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64 #if $use_images_conditional.use_images == "yes"
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65 #if $images_zip_cli
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66 --images_zip $images_zip_cli
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67 #end if
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68 --missing_image_strategy '$use_images_conditional.missing_image_strategy'
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69 #if $use_images_conditional.backbone_image
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70 --backbone_image '$use_images_conditional.backbone_image'
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71 #end if
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72 #end if
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73
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74 #if $backbone_text not in ("", None)
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75 --backbone_text '$backbone_text'
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76 #end if
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77
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78 --preset '$preset'
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79 --eval_metric '$eval_metric'
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80
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81 --random_seed '$random_seed'
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82 #if $time_limit
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83 --time_limit $time_limit
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84 #end if
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85 #if $deterministic == "true"
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86 --deterministic
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87 #end if
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88
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89 #if $customize_defaults_conditional.customize_defaults == "yes"
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90 #if $customize_defaults_conditional.validation_size not in ("", None)
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91 --validation_size $customize_defaults_conditional.validation_size
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92 #end if
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93 #if $customize_defaults_conditional.split_probabilities and str($customize_defaults_conditional.split_probabilities).strip()
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94 --split_probabilities #echo " ".join([str(float(x)) for x in str($customize_defaults_conditional.split_probabilities).replace(",", " ").split() if x.strip()]) #
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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95 #end if
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96 #if $customize_defaults_conditional.cross_validation == "true"
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97 --cross_validation true
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98 --num_folds $customize_defaults_conditional.num_folds
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99 #end if
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100 #if $customize_defaults_conditional.epochs
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101 --epochs $customize_defaults_conditional.epochs
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102 #end if
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103 #if $customize_defaults_conditional.learning_rate
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104 --learning_rate $customize_defaults_conditional.learning_rate
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105 #end if
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106 #if $customize_defaults_conditional.batch_size
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107 --batch_size $customize_defaults_conditional.batch_size
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108 #end if
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109 #if $customize_defaults_conditional.threshold
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110 --threshold $customize_defaults_conditional.threshold
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111 #end if
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112 #if $customize_defaults_conditional.hyperparameters
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113 --hyperparameters '$customize_defaults_conditional.hyperparameters'
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114 #end if
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115 #end if
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116
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117 --output_json '$output_json'
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118 --output_html '$output_html'
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119 --output_config '$output_config'
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120 ]]></command>
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121
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122 <inputs>
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123 <param name="input_csv" type="data" format="csv,tsv" label="Training dataset (CSV/TSV)" help="Must contain the target column and optional image paths"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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124 <param name="target_column" type="data_column" data_ref="input_csv" numerical="false" use_header_names="true" label="Target / Label column"/>
3
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125 <conditional name="sample_id_selector">
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126 <param name="use_sample_id" type="select" label="Use a sample ID column for leakage-aware splitting?" help="Select yes to choose a column that groups related records (e.g., patient_id or slide_id).">
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127 <option value="no" selected="true">No column selected</option>
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128 <option value="yes">Yes</option>
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129 </param>
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130 <when value="yes">
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131 <param name="sample_id_column" type="data_column" data_ref="input_csv" use_header_names="true" label="Sample ID column" help="All rows with the same ID stay in the same split or fold to reduce leakage. Used for internal train/val/test splits and group-aware CV folds." />
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132 </when>
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133 <when value="no"/>
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134 </conditional>
0
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135
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136 <conditional name="test_dataset_conditional">
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137 <param name="has_test_dataset" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Provide separate test dataset?"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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138 <when value="yes">
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139 <param name="input_test" type="data" format="csv,tsv" optional="true" label="Test dataset (CSV/TSV)"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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140 </when>
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141 <when value="no"/>
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142 </conditional>
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143
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144 <param name="backbone_text" type="select" label="Text backbone" optional="true">
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145 <option value="microsoft/deberta-v3-base" selected="true">microsoft/deberta-v3-base</option>
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146 <option value="microsoft/deberta-v3-small">microsoft/deberta-v3-small</option>
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147 <option value="google/electra-base-discriminator">google/electra-base-discriminator</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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148 <option value="google/electra-small-discriminator">google/electra-small-discriminator</option>
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149 <option value="roberta-base">roberta-base</option>
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150 <option value="bert-base-uncased">bert-base-uncased</option>
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151 <option value="distilroberta-base">distilroberta-base</option>
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152 <option value="albert-base-v2">albert-base-v2</option>
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153 </param>
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154
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155 <conditional name="use_images_conditional">
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156 <param name="use_images" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use image modality?"/>
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157 <when value="yes">
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158 <repeat name="images_zip_repeat" title="Image archive(s)" min="1">
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159 <param name="images_zip" type="data" format="zip" label="ZIP file containing images"/>
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160 </repeat>
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161 <param name="backbone_image" type="select" label="Image backbone" optional="true">
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162 <option value='swin_base_patch4_window7_224' selected='true'>swin_base_patch4_window7_224</option>
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163 <option value='swin_large_patch4_window12_384.in22k_ft_in1k'>swin_large_patch4_window12_384.in22k_ft_in1k</option>
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164 <option value='swin_small_patch4_window7_224'>swin_small_patch4_window7_224</option>
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165 <option value='swin_tiny_patch4_window7_224'>swin_tiny_patch4_window7_224</option>
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166 <option value='caformer_b36.in21k_ft_in1k'>caformer_b36.in21k_ft_in1k</option>
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167 <option value='caformer_m36.in21k_ft_in1k'>caformer_m36.in21k_ft_in1k</option>
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168 <option value='caformer_s36.in21k_ft_in1k'>caformer_s36.in21k_ft_in1k</option>
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169 <option value='caformer_s18.in1k'>caformer_s18.in1k</option>
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170 <option value='caformer_b36.sail_in22k_ft_in1k'>caformer_b36.sail_in22k_ft_in1k</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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171 <option value='caformer_m36.sail_in22k_ft_in1k'>caformer_m36.sail_in22k_ft_in1k</option>
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172 <option value='caformer_s36.sail_in22k_ft_in1k'>caformer_s36.sail_in22k_ft_in1k</option>
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173 <option value='vit_base_patch16_224'>vit_base_patch16_224</option>
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174 <option value='vit_large_patch14_224'>vit_large_patch14_224</option>
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175 <option value='convnext_base'>convnext_base</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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176 <option value='eva02_base_patch14_448.mim_in22k_ft_in22k_in1k'>eva02_base_patch14_448.mim_in22k_ft_in22k_in1k</option>
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177 <option value='resnet50'>resnet50</option>
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178 </param>
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179 <param name="missing_image_strategy" type="boolean" truevalue="true" falsevalue="false" checked="false"
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180 label="Drop rows with missing images?" help="True = drop, False = replace with placeholder (default)"/>
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181 </when>
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182 <when value="no"/>
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183 </conditional>
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184
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185 <param name="preset" type="select" label="Quality preset">
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186 <option value="medium_quality" selected="true">Medium quality (fast)</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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187 <option value="high_quality">High quality</option>
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188 <option value="best_quality">Best quality (slowest)</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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189 </param>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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190
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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191 <param name="eval_metric" type="select" label="Primary evaluation metric">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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192 <option value="auto" selected="true">Auto (let AutoGluon choose)</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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193 <option value="roc_auc">ROC AUC</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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194 <option value="accuracy">Accuracy</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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195 <option value="balanced_accuracy">Balanced Accuracy</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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196 <option value="f1">F1</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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197 <option value="f1_macro">F1 Macro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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198 <option value="f1_micro">F1 Micro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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199 <option value="f1_weighted">F1 Weighted</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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200 <option value="precision">Precision</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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201 <option value="precision_macro">Precision Macro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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202 <option value="precision_micro">Precision Micro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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203 <option value="precision_weighted">Precision Weighted</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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204 <option value="recall">Recall</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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205 <option value="recall_macro">Recall Macro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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206 <option value="recall_micro">Recall Micro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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207 <option value="recall_weighted">Recall Weighted</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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208 <option value="average_precision">Average Precision</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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209 <option value="roc_auc_ovo_macro">ROC AUC OVO Macro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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210 <option value="roc_auc_ovo_weighted">ROC AUC OVO Weighted</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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211 <option value="roc_auc_ovr_macro">ROC AUC OVR Macro</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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212 <option value="roc_auc_ovr_weighted">ROC AUC OVR Weighted</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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213 <option value="log_loss">Log Loss</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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214 <option value="mse">MSE</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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215 <option value="rmse">RMSE</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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216 <option value="mae">MAE</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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217 <option value="msle">MSLE</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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218 <option value="r2">R2</option>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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219 </param>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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220
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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221 <param name="random_seed" type="integer" value="42" label="Random seed"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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222
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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223 <param name="time_limit" type="integer" optional="true" min="60" label="Time limit (seconds)" help="Total training time budget. Recommended: 3600+ for real runs"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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224 <param name="deterministic" type="boolean" truevalue="true" falsevalue="false" checked="false"
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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225 label="Enable deterministic mode" help="Use deterministic algorithms and CuDNN settings to reduce run-to-run variance (may slow training)"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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226
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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227 <conditional name="customize_defaults_conditional">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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228 <param name="customize_defaults" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Advanced: customize training settings?"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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229 <when value="yes">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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230 <param name="validation_size" type="float" value="0.2" label="Validation fraction (when test set provided)"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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231 <param name="split_probabilities" type="text" value="0.7 0.1 0.2" label="Train / Val / Test split (space-separated) when no test set"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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232 <param name="cross_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable k-fold cross-validation"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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233 <param name="num_folds" type="integer" value="5" label="Number of CV folds"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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234 <param name="epochs" type="integer" optional="true" label="Max epochs"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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235 <param name="learning_rate" type="float" optional="true" label="Learning rate"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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236 <param name="batch_size" type="integer" optional="true" label="Batch size"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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237 <param name="threshold" type="float" optional="true" min="0" max="1" label="Binary classification threshold"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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238 <param name="hyperparameters" type="text" optional="true" label="Extra AutoGluon hyperparameters (JSON or YAML string)"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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239 </when>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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240 <when value="no"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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241 </conditional>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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242 </inputs>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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243
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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244 <outputs>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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245 <data name="output_html" format="html" label="Multimodal Learner analysis report on data ${input_csv.name}"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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246 <data name="output_config" format="yaml" label="Multimodal Learner training config on data ${input_csv.name}"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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247 <data name="output_json" format="json" label="Multimodal Learner metric results on data ${input_csv.name}"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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248 </outputs>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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249
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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250 <tests>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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251 <!-- Basic run with images + external test set -->
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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252 <test expect_num_outputs="3">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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253 <param name="input_csv" value="train.csv"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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254 <param name="target_column" value="7"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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255 <param name="test_dataset_conditional|has_test_dataset" value="yes"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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256 <param name="test_dataset_conditional|input_test" value="test.csv"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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257 <param name="use_images_conditional|use_images" value="yes"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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258 <param name="use_images_conditional|images_zip_repeat_0|images_zip" value="images.zip"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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259 <param name="use_images_conditional|backbone_image" value="resnet50"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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260 <param name="backbone_text" value="google/electra-base-discriminator"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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261 <output name="output_html">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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262 <assert_contents>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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263 <has_text text="Model Performance Summary"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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264 </assert_contents>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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265 </output>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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266 </test>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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267
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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268 <!-- Custom threshold -->
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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269 <test expect_num_outputs="3">
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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270 <param name="input_csv" value="train.csv"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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271 <param name="target_column" value="7"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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272 <param name="test_dataset_conditional|has_test_dataset" value="yes"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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273 <param name="test_dataset_conditional|input_test" value="test.csv"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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274 <param name="use_images_conditional|use_images" value="yes"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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275 <param name="use_images_conditional|images_zip_repeat_0|images_zip" value="images.zip"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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276 <param name="customize_defaults_conditional|customize_defaults" value="yes"/>
375c36923da1 planemo upload for repository https://github.com/goeckslab/gleam.git commit 1c6c1ad7a1b2bd3645aa0eafa2167784820b52e0
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277 <param name="customize_defaults_conditional|threshold" value="0.4"/>
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278 <output name="output_json">
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279 <assert_contents>
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280 <has_text text="&quot;threshold&quot;: 0.4"/>
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281 </assert_contents>
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282 </output>
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283 </test>
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284
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285 <!-- No external test set; internal split -->
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286 <test expect_num_outputs="3">
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287 <param name="input_csv" value="train.csv"/>
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288 <param name="target_column" value="7"/>
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289 <param name="test_dataset_conditional|has_test_dataset" value="no"/>
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290 <param name="use_images_conditional|use_images" value="yes"/>
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291 <param name="use_images_conditional|images_zip_repeat_0|images_zip" value="images.zip"/>
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292 <output name="output_json">
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293 <assert_contents>
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294 <has_text text="&quot;val&quot;"/>
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295 </assert_contents>
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296 </output>
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297 </test>
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298
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299 <!-- Text/tabular only (ignore images) -->
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300 <test expect_num_outputs="3">
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301 <param name="input_csv" value="train.csv"/>
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302 <param name="target_column" value="7"/>
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303 <param name="test_dataset_conditional|has_test_dataset" value="yes"/>
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304 <param name="test_dataset_conditional|input_test" value="test.csv"/>
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305 <param name="use_images_conditional|use_images" value="no"/>
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306 <output name="output_html">
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307 <assert_contents>
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308 <has_text text="Train and Validation Performance Summary"/>
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309 </assert_contents>
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310 </output>
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311 </test>
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312 </tests>
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313
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314 <help><![CDATA[
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315 **AutoGluon Multimodal Learner**
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316
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317 Trains a powerful multimodal model combining tabular features, images, and text using AutoGluon-Multimodal.
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318
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319 - Handles missing images intelligently
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320 - Supports cross-validation
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321 - Produces detailed HTML reports and transparent metrics
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322 - Fully reproducible
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323
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324 Ideal for medical imaging + clinical data, product images + descriptions, etc.
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325 ]]></help>
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326
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327 <citations>
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328 <citation type="bibtex">
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329 @article{AutoGluon2023,
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330 author = {Erickson, Nick and Mueller, Jonas and Wang, Yizhou and others},
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331 title = {AutoGluon-Tabular: Robust and Accurate AutoML for Structured Data},
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332 journal = {arXiv preprint arXiv:2003.06505},
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333 year = {2023}
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334 }
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335 </citation>
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336 </citations>
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337 </tool>