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cellflow documentation
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  • Installation
  • User API
    • Model
      • cellflow.model.CellFlow
        • cellflow.model.CellFlow.get_condition_embedding
        • cellflow.model.CellFlow.load
        • cellflow.model.CellFlow.predict
        • cellflow.model.CellFlow.prepare_data
        • cellflow.model.CellFlow.prepare_model
        • cellflow.model.CellFlow.prepare_validation_data
        • cellflow.model.CellFlow.save
        • cellflow.model.CellFlow.train
        • cellflow.model.CellFlow.adata
        • cellflow.model.CellFlow.condition_mode
        • cellflow.model.CellFlow.data_manager
        • cellflow.model.CellFlow.dataloader
        • cellflow.model.CellFlow.solver
        • cellflow.model.CellFlow.train_data
        • cellflow.model.CellFlow.trainer
        • cellflow.model.CellFlow.validation_data
        • cellflow.model.CellFlow.velocity_field
    • Solvers
      • cellflow.solvers.OTFlowMatching
        • cellflow.solvers.OTFlowMatching.get_condition_embedding
        • cellflow.solvers.OTFlowMatching.predict
        • cellflow.solvers.OTFlowMatching.step_fn
        • cellflow.solvers.OTFlowMatching.cfg_enabled
        • cellflow.solvers.OTFlowMatching.is_trained
      • cellflow.solvers.GENOT
        • cellflow.solvers.GENOT.get_condition_embedding
        • cellflow.solvers.GENOT.predict
        • cellflow.solvers.GENOT.step_fn
        • cellflow.solvers.GENOT.cfg_enabled
        • cellflow.solvers.GENOT.is_trained
    • Networks
      • cellflow.networks.ConditionalVelocityField
        • cellflow.networks.ConditionalVelocityField.act_fn
        • cellflow.networks.ConditionalVelocityField.apply
        • cellflow.networks.ConditionalVelocityField.bind
        • cellflow.networks.ConditionalVelocityField.clone
        • cellflow.networks.ConditionalVelocityField.copy
        • cellflow.networks.ConditionalVelocityField.create_train_state
        • cellflow.networks.ConditionalVelocityField.get_condition_embedding
        • cellflow.networks.ConditionalVelocityField.get_variable
        • cellflow.networks.ConditionalVelocityField.has_rng
        • cellflow.networks.ConditionalVelocityField.has_variable
        • cellflow.networks.ConditionalVelocityField.init
        • cellflow.networks.ConditionalVelocityField.init_with_output
        • cellflow.networks.ConditionalVelocityField.is_initializing
        • cellflow.networks.ConditionalVelocityField.is_mutable_collection
        • cellflow.networks.ConditionalVelocityField.lazy_init
        • cellflow.networks.ConditionalVelocityField.make_rng
        • cellflow.networks.ConditionalVelocityField.module_paths
        • cellflow.networks.ConditionalVelocityField.param
        • cellflow.networks.ConditionalVelocityField.perturb
        • cellflow.networks.ConditionalVelocityField.put_variable
        • cellflow.networks.ConditionalVelocityField.setup
        • cellflow.networks.ConditionalVelocityField.sow
        • cellflow.networks.ConditionalVelocityField.tabulate
        • cellflow.networks.ConditionalVelocityField.unbind
        • cellflow.networks.ConditionalVelocityField.variable
        • cellflow.networks.ConditionalVelocityField.__call__
        • cellflow.networks.ConditionalVelocityField.cond_output_dropout
        • cellflow.networks.ConditionalVelocityField.condition_dropout_prob
        • cellflow.networks.ConditionalVelocityField.condition_embedding_dim
        • cellflow.networks.ConditionalVelocityField.condition_mode
        • cellflow.networks.ConditionalVelocityField.condition_null
        • cellflow.networks.ConditionalVelocityField.conditioning
        • cellflow.networks.ConditionalVelocityField.decoder
        • cellflow.networks.ConditionalVelocityField.decoder_dims
        • cellflow.networks.ConditionalVelocityField.decoder_dropout
        • cellflow.networks.ConditionalVelocityField.hidden_dims
        • cellflow.networks.ConditionalVelocityField.hidden_dropout
        • cellflow.networks.ConditionalVelocityField.layer_norm_before_concatenation
        • cellflow.networks.ConditionalVelocityField.linear_projection_before_concatenation
        • cellflow.networks.ConditionalVelocityField.mask_value
        • cellflow.networks.ConditionalVelocityField.name
        • cellflow.networks.ConditionalVelocityField.output_dims
        • cellflow.networks.ConditionalVelocityField.parent
        • cellflow.networks.ConditionalVelocityField.path
        • cellflow.networks.ConditionalVelocityField.pooling
        • cellflow.networks.ConditionalVelocityField.regularization
        • cellflow.networks.ConditionalVelocityField.scope
        • cellflow.networks.ConditionalVelocityField.time_encoder
        • cellflow.networks.ConditionalVelocityField.time_encoder_dims
        • cellflow.networks.ConditionalVelocityField.time_encoder_dropout
        • cellflow.networks.ConditionalVelocityField.time_freqs
        • cellflow.networks.ConditionalVelocityField.time_max_period
        • cellflow.networks.ConditionalVelocityField.variables
        • cellflow.networks.ConditionalVelocityField.x_encoder
        • cellflow.networks.ConditionalVelocityField.output_dim
        • cellflow.networks.ConditionalVelocityField.max_combination_length
        • cellflow.networks.ConditionalVelocityField.covariates_not_pooled
        • cellflow.networks.ConditionalVelocityField.pooling_kwargs
        • cellflow.networks.ConditionalVelocityField.layers_before_pool
        • cellflow.networks.ConditionalVelocityField.layers_after_pool
        • cellflow.networks.ConditionalVelocityField.condition_encoder_kwargs
        • cellflow.networks.ConditionalVelocityField.conditioning_kwargs
      • cellflow.networks.GENOTConditionalVelocityField
        • cellflow.networks.GENOTConditionalVelocityField.act_fn
        • cellflow.networks.GENOTConditionalVelocityField.apply
        • cellflow.networks.GENOTConditionalVelocityField.bind
        • cellflow.networks.GENOTConditionalVelocityField.clone
        • cellflow.networks.GENOTConditionalVelocityField.copy
        • cellflow.networks.GENOTConditionalVelocityField.create_train_state
        • cellflow.networks.GENOTConditionalVelocityField.get_condition_embedding
        • cellflow.networks.GENOTConditionalVelocityField.get_variable
        • cellflow.networks.GENOTConditionalVelocityField.has_rng
        • cellflow.networks.GENOTConditionalVelocityField.has_variable
        • cellflow.networks.GENOTConditionalVelocityField.init
        • cellflow.networks.GENOTConditionalVelocityField.init_with_output
        • cellflow.networks.GENOTConditionalVelocityField.is_initializing
        • cellflow.networks.GENOTConditionalVelocityField.is_mutable_collection
        • cellflow.networks.GENOTConditionalVelocityField.lazy_init
        • cellflow.networks.GENOTConditionalVelocityField.make_rng
        • cellflow.networks.GENOTConditionalVelocityField.module_paths
        • cellflow.networks.GENOTConditionalVelocityField.param
        • cellflow.networks.GENOTConditionalVelocityField.perturb
        • cellflow.networks.GENOTConditionalVelocityField.put_variable
        • cellflow.networks.GENOTConditionalVelocityField.setup
        • cellflow.networks.GENOTConditionalVelocityField.sow
        • cellflow.networks.GENOTConditionalVelocityField.tabulate
        • cellflow.networks.GENOTConditionalVelocityField.unbind
        • cellflow.networks.GENOTConditionalVelocityField.variable
        • cellflow.networks.GENOTConditionalVelocityField.__call__
        • cellflow.networks.GENOTConditionalVelocityField.cond_output_dropout
        • cellflow.networks.GENOTConditionalVelocityField.condition_dropout_prob
        • cellflow.networks.GENOTConditionalVelocityField.condition_embedding_dim
        • cellflow.networks.GENOTConditionalVelocityField.condition_mode
        • cellflow.networks.GENOTConditionalVelocityField.condition_null
        • cellflow.networks.GENOTConditionalVelocityField.conditioning
        • cellflow.networks.GENOTConditionalVelocityField.decoder
        • cellflow.networks.GENOTConditionalVelocityField.decoder_dims
        • cellflow.networks.GENOTConditionalVelocityField.decoder_dropout
        • cellflow.networks.GENOTConditionalVelocityField.genot_source_dims
        • cellflow.networks.GENOTConditionalVelocityField.genot_source_dropout
        • cellflow.networks.GENOTConditionalVelocityField.hidden_dims
        • cellflow.networks.GENOTConditionalVelocityField.hidden_dropout
        • cellflow.networks.GENOTConditionalVelocityField.layer_norm_before_concatenation
        • cellflow.networks.GENOTConditionalVelocityField.linear_projection_before_concatenation
        • cellflow.networks.GENOTConditionalVelocityField.mask_value
        • cellflow.networks.GENOTConditionalVelocityField.name
        • cellflow.networks.GENOTConditionalVelocityField.output_dims
        • cellflow.networks.GENOTConditionalVelocityField.parent
        • cellflow.networks.GENOTConditionalVelocityField.path
        • cellflow.networks.GENOTConditionalVelocityField.pooling
        • cellflow.networks.GENOTConditionalVelocityField.regularization
        • cellflow.networks.GENOTConditionalVelocityField.scope
        • cellflow.networks.GENOTConditionalVelocityField.time_encoder
        • cellflow.networks.GENOTConditionalVelocityField.time_encoder_dims
        • cellflow.networks.GENOTConditionalVelocityField.time_encoder_dropout
        • cellflow.networks.GENOTConditionalVelocityField.time_freqs
        • cellflow.networks.GENOTConditionalVelocityField.time_max_period
        • cellflow.networks.GENOTConditionalVelocityField.variables
        • cellflow.networks.GENOTConditionalVelocityField.x_encoder
        • cellflow.networks.GENOTConditionalVelocityField.output_dim
        • cellflow.networks.GENOTConditionalVelocityField.max_combination_length
        • cellflow.networks.GENOTConditionalVelocityField.covariates_not_pooled
        • cellflow.networks.GENOTConditionalVelocityField.pooling_kwargs
        • cellflow.networks.GENOTConditionalVelocityField.layers_before_pool
        • cellflow.networks.GENOTConditionalVelocityField.layers_after_pool
        • cellflow.networks.GENOTConditionalVelocityField.condition_encoder_kwargs
        • cellflow.networks.GENOTConditionalVelocityField.conditioning_kwargs
      • cellflow.networks.ConditionEncoder
        • cellflow.networks.ConditionEncoder.apply
        • cellflow.networks.ConditionEncoder.bind
        • cellflow.networks.ConditionEncoder.clone
        • cellflow.networks.ConditionEncoder.copy
        • cellflow.networks.ConditionEncoder.create_train_state
        • cellflow.networks.ConditionEncoder.get_variable
        • cellflow.networks.ConditionEncoder.has_rng
        • cellflow.networks.ConditionEncoder.has_variable
        • cellflow.networks.ConditionEncoder.init
        • cellflow.networks.ConditionEncoder.init_with_output
        • cellflow.networks.ConditionEncoder.is_initializing
        • cellflow.networks.ConditionEncoder.is_mutable_collection
        • cellflow.networks.ConditionEncoder.lazy_init
        • cellflow.networks.ConditionEncoder.make_rng
        • cellflow.networks.ConditionEncoder.module_paths
        • cellflow.networks.ConditionEncoder.param
        • cellflow.networks.ConditionEncoder.perturb
        • cellflow.networks.ConditionEncoder.put_variable
        • cellflow.networks.ConditionEncoder.setup
        • cellflow.networks.ConditionEncoder.sow
        • cellflow.networks.ConditionEncoder.tabulate
        • cellflow.networks.ConditionEncoder.unbind
        • cellflow.networks.ConditionEncoder.variable
        • cellflow.networks.ConditionEncoder.__call__
        • cellflow.networks.ConditionEncoder.condition_mode
        • cellflow.networks.ConditionEncoder.decoder
        • cellflow.networks.ConditionEncoder.mask_value
        • cellflow.networks.ConditionEncoder.name
        • cellflow.networks.ConditionEncoder.output_dropout
        • cellflow.networks.ConditionEncoder.parent
        • cellflow.networks.ConditionEncoder.path
        • cellflow.networks.ConditionEncoder.pooling
        • cellflow.networks.ConditionEncoder.regularization
        • cellflow.networks.ConditionEncoder.scope
        • cellflow.networks.ConditionEncoder.takes_attention_mask
        • cellflow.networks.ConditionEncoder.variables
        • cellflow.networks.ConditionEncoder.output_dim
        • cellflow.networks.ConditionEncoder.pooling_kwargs
        • cellflow.networks.ConditionEncoder.covariates_not_pooled
        • cellflow.networks.ConditionEncoder.layers_before_pool
        • cellflow.networks.ConditionEncoder.layers_after_pool
        • cellflow.networks.ConditionEncoder.layers_decoder
      • cellflow.networks.SelfAttention
        • cellflow.networks.SelfAttention.act_fn
        • cellflow.networks.SelfAttention.apply
        • cellflow.networks.SelfAttention.bind
        • cellflow.networks.SelfAttention.clone
        • cellflow.networks.SelfAttention.copy
        • cellflow.networks.SelfAttention.get_variable
        • cellflow.networks.SelfAttention.has_rng
        • cellflow.networks.SelfAttention.has_variable
        • cellflow.networks.SelfAttention.init
        • cellflow.networks.SelfAttention.init_with_output
        • cellflow.networks.SelfAttention.is_initializing
        • cellflow.networks.SelfAttention.is_mutable_collection
        • cellflow.networks.SelfAttention.lazy_init
        • cellflow.networks.SelfAttention.make_rng
        • cellflow.networks.SelfAttention.module_paths
        • cellflow.networks.SelfAttention.param
        • cellflow.networks.SelfAttention.perturb
        • cellflow.networks.SelfAttention.put_variable
        • cellflow.networks.SelfAttention.setup
        • cellflow.networks.SelfAttention.sow
        • cellflow.networks.SelfAttention.tabulate
        • cellflow.networks.SelfAttention.unbind
        • cellflow.networks.SelfAttention.variable
        • cellflow.networks.SelfAttention.__call__
        • cellflow.networks.SelfAttention.dropout_rate
        • cellflow.networks.SelfAttention.ff_dim
        • cellflow.networks.SelfAttention.layer_norm
        • cellflow.networks.SelfAttention.name
        • cellflow.networks.SelfAttention.num_heads
        • cellflow.networks.SelfAttention.parent
        • cellflow.networks.SelfAttention.path
        • cellflow.networks.SelfAttention.qkv_dim
        • cellflow.networks.SelfAttention.scope
        • cellflow.networks.SelfAttention.takes_attention_mask
        • cellflow.networks.SelfAttention.transformer_block
        • cellflow.networks.SelfAttention.variables
      • cellflow.networks.SeedAttentionPooling
        • cellflow.networks.SeedAttentionPooling.act_fn
        • cellflow.networks.SeedAttentionPooling.apply
        • cellflow.networks.SeedAttentionPooling.bind
        • cellflow.networks.SeedAttentionPooling.clone
        • cellflow.networks.SeedAttentionPooling.copy
        • cellflow.networks.SeedAttentionPooling.get_variable
        • cellflow.networks.SeedAttentionPooling.has_rng
        • cellflow.networks.SeedAttentionPooling.has_variable
        • cellflow.networks.SeedAttentionPooling.init
        • cellflow.networks.SeedAttentionPooling.init_with_output
        • cellflow.networks.SeedAttentionPooling.is_initializing
        • cellflow.networks.SeedAttentionPooling.is_mutable_collection
        • cellflow.networks.SeedAttentionPooling.lazy_init
        • cellflow.networks.SeedAttentionPooling.make_rng
        • cellflow.networks.SeedAttentionPooling.module_paths
        • cellflow.networks.SeedAttentionPooling.param
        • cellflow.networks.SeedAttentionPooling.perturb
        • cellflow.networks.SeedAttentionPooling.put_variable
        • cellflow.networks.SeedAttentionPooling.setup
        • cellflow.networks.SeedAttentionPooling.sow
        • cellflow.networks.SeedAttentionPooling.tabulate
        • cellflow.networks.SeedAttentionPooling.unbind
        • cellflow.networks.SeedAttentionPooling.variable
        • cellflow.networks.SeedAttentionPooling.__call__
        • cellflow.networks.SeedAttentionPooling.dropout_rate
        • cellflow.networks.SeedAttentionPooling.layer_norm
        • cellflow.networks.SeedAttentionPooling.name
        • cellflow.networks.SeedAttentionPooling.num_heads
        • cellflow.networks.SeedAttentionPooling.parent
        • cellflow.networks.SeedAttentionPooling.path
        • cellflow.networks.SeedAttentionPooling.scope
        • cellflow.networks.SeedAttentionPooling.seed_dim
        • cellflow.networks.SeedAttentionPooling.takes_attention_mask
        • cellflow.networks.SeedAttentionPooling.transformer_block
        • cellflow.networks.SeedAttentionPooling.v_dim
        • cellflow.networks.SeedAttentionPooling.variables
      • cellflow.networks.TokenAttentionPooling
        • cellflow.networks.TokenAttentionPooling.act_fn
        • cellflow.networks.TokenAttentionPooling.apply
        • cellflow.networks.TokenAttentionPooling.bind
        • cellflow.networks.TokenAttentionPooling.clone
        • cellflow.networks.TokenAttentionPooling.copy
        • cellflow.networks.TokenAttentionPooling.get_variable
        • cellflow.networks.TokenAttentionPooling.has_rng
        • cellflow.networks.TokenAttentionPooling.has_variable
        • cellflow.networks.TokenAttentionPooling.init
        • cellflow.networks.TokenAttentionPooling.init_with_output
        • cellflow.networks.TokenAttentionPooling.is_initializing
        • cellflow.networks.TokenAttentionPooling.is_mutable_collection
        • cellflow.networks.TokenAttentionPooling.lazy_init
        • cellflow.networks.TokenAttentionPooling.make_rng
        • cellflow.networks.TokenAttentionPooling.module_paths
        • cellflow.networks.TokenAttentionPooling.param
        • cellflow.networks.TokenAttentionPooling.perturb
        • cellflow.networks.TokenAttentionPooling.put_variable
        • cellflow.networks.TokenAttentionPooling.setup
        • cellflow.networks.TokenAttentionPooling.sow
        • cellflow.networks.TokenAttentionPooling.tabulate
        • cellflow.networks.TokenAttentionPooling.unbind
        • cellflow.networks.TokenAttentionPooling.variable
        • cellflow.networks.TokenAttentionPooling.__call__
        • cellflow.networks.TokenAttentionPooling.dropout_rate
        • cellflow.networks.TokenAttentionPooling.ff_dim
        • cellflow.networks.TokenAttentionPooling.layer_norm
        • cellflow.networks.TokenAttentionPooling.name
        • cellflow.networks.TokenAttentionPooling.num_heads
        • cellflow.networks.TokenAttentionPooling.num_layers
        • cellflow.networks.TokenAttentionPooling.parent
        • cellflow.networks.TokenAttentionPooling.path
        • cellflow.networks.TokenAttentionPooling.qkv_dim
        • cellflow.networks.TokenAttentionPooling.scope
        • cellflow.networks.TokenAttentionPooling.takes_attention_mask
        • cellflow.networks.TokenAttentionPooling.transformer_block
        • cellflow.networks.TokenAttentionPooling.variables
      • cellflow.networks.MLPBlock
        • cellflow.networks.MLPBlock.act_fn
        • cellflow.networks.MLPBlock.apply
        • cellflow.networks.MLPBlock.bind
        • cellflow.networks.MLPBlock.clone
        • cellflow.networks.MLPBlock.copy
        • cellflow.networks.MLPBlock.get_variable
        • cellflow.networks.MLPBlock.has_rng
        • cellflow.networks.MLPBlock.has_variable
        • cellflow.networks.MLPBlock.init
        • cellflow.networks.MLPBlock.init_with_output
        • cellflow.networks.MLPBlock.is_initializing
        • cellflow.networks.MLPBlock.is_mutable_collection
        • cellflow.networks.MLPBlock.lazy_init
        • cellflow.networks.MLPBlock.make_rng
        • cellflow.networks.MLPBlock.module_paths
        • cellflow.networks.MLPBlock.param
        • cellflow.networks.MLPBlock.perturb
        • cellflow.networks.MLPBlock.put_variable
        • cellflow.networks.MLPBlock.setup
        • cellflow.networks.MLPBlock.sow
        • cellflow.networks.MLPBlock.tabulate
        • cellflow.networks.MLPBlock.unbind
        • cellflow.networks.MLPBlock.variable
        • cellflow.networks.MLPBlock.__call__
        • cellflow.networks.MLPBlock.act_last_layer
        • cellflow.networks.MLPBlock.dims
        • cellflow.networks.MLPBlock.dropout_rate
        • cellflow.networks.MLPBlock.name
        • cellflow.networks.MLPBlock.parent
        • cellflow.networks.MLPBlock.path
        • cellflow.networks.MLPBlock.scope
        • cellflow.networks.MLPBlock.takes_attention_mask
        • cellflow.networks.MLPBlock.variables
      • cellflow.networks.SelfAttentionBlock
        • cellflow.networks.SelfAttentionBlock.act_fn
        • cellflow.networks.SelfAttentionBlock.apply
        • cellflow.networks.SelfAttentionBlock.bind
        • cellflow.networks.SelfAttentionBlock.clone
        • cellflow.networks.SelfAttentionBlock.copy
        • cellflow.networks.SelfAttentionBlock.get_variable
        • cellflow.networks.SelfAttentionBlock.has_rng
        • cellflow.networks.SelfAttentionBlock.has_variable
        • cellflow.networks.SelfAttentionBlock.init
        • cellflow.networks.SelfAttentionBlock.init_with_output
        • cellflow.networks.SelfAttentionBlock.is_initializing
        • cellflow.networks.SelfAttentionBlock.is_mutable_collection
        • cellflow.networks.SelfAttentionBlock.lazy_init
        • cellflow.networks.SelfAttentionBlock.make_rng
        • cellflow.networks.SelfAttentionBlock.module_paths
        • cellflow.networks.SelfAttentionBlock.param
        • cellflow.networks.SelfAttentionBlock.perturb
        • cellflow.networks.SelfAttentionBlock.put_variable
        • cellflow.networks.SelfAttentionBlock.setup
        • cellflow.networks.SelfAttentionBlock.sow
        • cellflow.networks.SelfAttentionBlock.tabulate
        • cellflow.networks.SelfAttentionBlock.unbind
        • cellflow.networks.SelfAttentionBlock.variable
        • cellflow.networks.SelfAttentionBlock.__call__
        • cellflow.networks.SelfAttentionBlock.dropout_rate
        • cellflow.networks.SelfAttentionBlock.ff_dim
        • cellflow.networks.SelfAttentionBlock.layer_norm
        • cellflow.networks.SelfAttentionBlock.name
        • cellflow.networks.SelfAttentionBlock.parent
        • cellflow.networks.SelfAttentionBlock.path
        • cellflow.networks.SelfAttentionBlock.scope
        • cellflow.networks.SelfAttentionBlock.takes_attention_mask
        • cellflow.networks.SelfAttentionBlock.transformer_block
        • cellflow.networks.SelfAttentionBlock.variables
        • cellflow.networks.SelfAttentionBlock.num_heads
        • cellflow.networks.SelfAttentionBlock.qkv_dim
      • cellflow.networks.BaseModule
        • cellflow.networks.BaseModule.apply
        • cellflow.networks.BaseModule.bind
        • cellflow.networks.BaseModule.clone
        • cellflow.networks.BaseModule.copy
        • cellflow.networks.BaseModule.get_variable
        • cellflow.networks.BaseModule.has_rng
        • cellflow.networks.BaseModule.has_variable
        • cellflow.networks.BaseModule.init
        • cellflow.networks.BaseModule.init_with_output
        • cellflow.networks.BaseModule.is_initializing
        • cellflow.networks.BaseModule.is_mutable_collection
        • cellflow.networks.BaseModule.lazy_init
        • cellflow.networks.BaseModule.make_rng
        • cellflow.networks.BaseModule.module_paths
        • cellflow.networks.BaseModule.param
        • cellflow.networks.BaseModule.perturb
        • cellflow.networks.BaseModule.put_variable
        • cellflow.networks.BaseModule.setup
        • cellflow.networks.BaseModule.sow
        • cellflow.networks.BaseModule.tabulate
        • cellflow.networks.BaseModule.unbind
        • cellflow.networks.BaseModule.variable
        • cellflow.networks.BaseModule.__call__
        • cellflow.networks.BaseModule.name
        • cellflow.networks.BaseModule.parent
        • cellflow.networks.BaseModule.path
        • cellflow.networks.BaseModule.scope
        • cellflow.networks.BaseModule.takes_attention_mask
        • cellflow.networks.BaseModule.variables
      • cellflow.networks.FilmBlock
        • cellflow.networks.FilmBlock.act_fn
        • cellflow.networks.FilmBlock.apply
        • cellflow.networks.FilmBlock.bind
        • cellflow.networks.FilmBlock.clone
        • cellflow.networks.FilmBlock.copy
        • cellflow.networks.FilmBlock.get_variable
        • cellflow.networks.FilmBlock.has_rng
        • cellflow.networks.FilmBlock.has_variable
        • cellflow.networks.FilmBlock.init
        • cellflow.networks.FilmBlock.init_with_output
        • cellflow.networks.FilmBlock.is_initializing
        • cellflow.networks.FilmBlock.is_mutable_collection
        • cellflow.networks.FilmBlock.lazy_init
        • cellflow.networks.FilmBlock.make_rng
        • cellflow.networks.FilmBlock.module_paths
        • cellflow.networks.FilmBlock.param
        • cellflow.networks.FilmBlock.perturb
        • cellflow.networks.FilmBlock.put_variable
        • cellflow.networks.FilmBlock.setup
        • cellflow.networks.FilmBlock.sow
        • cellflow.networks.FilmBlock.tabulate
        • cellflow.networks.FilmBlock.unbind
        • cellflow.networks.FilmBlock.variable
        • cellflow.networks.FilmBlock.__call__
        • cellflow.networks.FilmBlock.name
        • cellflow.networks.FilmBlock.parent
        • cellflow.networks.FilmBlock.path
        • cellflow.networks.FilmBlock.scope
        • cellflow.networks.FilmBlock.takes_attention_mask
        • cellflow.networks.FilmBlock.variables
        • cellflow.networks.FilmBlock.input_dim
        • cellflow.networks.FilmBlock.cond_dim
      • cellflow.networks.ResNetBlock
        • cellflow.networks.ResNetBlock.act_fn
        • cellflow.networks.ResNetBlock.apply
        • cellflow.networks.ResNetBlock.bind
        • cellflow.networks.ResNetBlock.clone
        • cellflow.networks.ResNetBlock.copy
        • cellflow.networks.ResNetBlock.get_variable
        • cellflow.networks.ResNetBlock.has_rng
        • cellflow.networks.ResNetBlock.has_variable
        • cellflow.networks.ResNetBlock.init
        • cellflow.networks.ResNetBlock.init_with_output
        • cellflow.networks.ResNetBlock.is_initializing
        • cellflow.networks.ResNetBlock.is_mutable_collection
        • cellflow.networks.ResNetBlock.lazy_init
        • cellflow.networks.ResNetBlock.make_rng
        • cellflow.networks.ResNetBlock.module_paths
        • cellflow.networks.ResNetBlock.param
        • cellflow.networks.ResNetBlock.perturb
        • cellflow.networks.ResNetBlock.put_variable
        • cellflow.networks.ResNetBlock.setup
        • cellflow.networks.ResNetBlock.sow
        • cellflow.networks.ResNetBlock.tabulate
        • cellflow.networks.ResNetBlock.unbind
        • cellflow.networks.ResNetBlock.variable
        • cellflow.networks.ResNetBlock.__call__
        • cellflow.networks.ResNetBlock.dropout_rate
        • cellflow.networks.ResNetBlock.hidden_dims
        • cellflow.networks.ResNetBlock.name
        • cellflow.networks.ResNetBlock.parent
        • cellflow.networks.ResNetBlock.path
        • cellflow.networks.ResNetBlock.projection_dims
        • cellflow.networks.ResNetBlock.scope
        • cellflow.networks.ResNetBlock.variables
        • cellflow.networks.ResNetBlock.input_dim
      • cellflow.networks.SelfAttentionBlock
        • cellflow.networks.SelfAttentionBlock.act_fn
        • cellflow.networks.SelfAttentionBlock.apply
        • cellflow.networks.SelfAttentionBlock.bind
        • cellflow.networks.SelfAttentionBlock.clone
        • cellflow.networks.SelfAttentionBlock.copy
        • cellflow.networks.SelfAttentionBlock.get_variable
        • cellflow.networks.SelfAttentionBlock.has_rng
        • cellflow.networks.SelfAttentionBlock.has_variable
        • cellflow.networks.SelfAttentionBlock.init
        • cellflow.networks.SelfAttentionBlock.init_with_output
        • cellflow.networks.SelfAttentionBlock.is_initializing
        • cellflow.networks.SelfAttentionBlock.is_mutable_collection
        • cellflow.networks.SelfAttentionBlock.lazy_init
        • cellflow.networks.SelfAttentionBlock.make_rng
        • cellflow.networks.SelfAttentionBlock.module_paths
        • cellflow.networks.SelfAttentionBlock.param
        • cellflow.networks.SelfAttentionBlock.perturb
        • cellflow.networks.SelfAttentionBlock.put_variable
        • cellflow.networks.SelfAttentionBlock.setup
        • cellflow.networks.SelfAttentionBlock.sow
        • cellflow.networks.SelfAttentionBlock.tabulate
        • cellflow.networks.SelfAttentionBlock.unbind
        • cellflow.networks.SelfAttentionBlock.variable
        • cellflow.networks.SelfAttentionBlock.__call__
        • cellflow.networks.SelfAttentionBlock.dropout_rate
        • cellflow.networks.SelfAttentionBlock.ff_dim
        • cellflow.networks.SelfAttentionBlock.layer_norm
        • cellflow.networks.SelfAttentionBlock.name
        • cellflow.networks.SelfAttentionBlock.parent
        • cellflow.networks.SelfAttentionBlock.path
        • cellflow.networks.SelfAttentionBlock.scope
        • cellflow.networks.SelfAttentionBlock.takes_attention_mask
        • cellflow.networks.SelfAttentionBlock.transformer_block
        • cellflow.networks.SelfAttentionBlock.variables
        • cellflow.networks.SelfAttentionBlock.num_heads
        • cellflow.networks.SelfAttentionBlock.qkv_dim
    • Datasets
      • cellflow.datasets.ineurons
      • cellflow.datasets.pbmc_cytokines
    • Metrics
      • cellflow.metrics.compute_metrics
      • cellflow.metrics.compute_mean_metrics
      • cellflow.metrics.compute_scalar_mmd
      • cellflow.metrics.compute_r_squared
      • cellflow.metrics.compute_sinkhorn_div
      • cellflow.metrics.compute_e_distance
      • cellflow.metrics.maximum_mean_discrepancy
    • Utils
      • cellflow.utils.match_linear
    • Training
      • cellflow.training.BaseCallback
        • cellflow.training.BaseCallback.on_log_iteration
        • cellflow.training.BaseCallback.on_train_begin
        • cellflow.training.BaseCallback.on_train_end
      • cellflow.training.CallbackRunner
        • cellflow.training.CallbackRunner.on_log_iteration
        • cellflow.training.CallbackRunner.on_train_begin
        • cellflow.training.CallbackRunner.on_train_end
      • cellflow.training.ComputationCallback
        • cellflow.training.ComputationCallback.on_log_iteration
        • cellflow.training.ComputationCallback.on_train_begin
        • cellflow.training.ComputationCallback.on_train_end
      • cellflow.training.LoggingCallback
        • cellflow.training.LoggingCallback.on_log_iteration
        • cellflow.training.LoggingCallback.on_train_begin
        • cellflow.training.LoggingCallback.on_train_end
      • cellflow.training.Metrics
        • cellflow.training.Metrics.on_log_iteration
        • cellflow.training.Metrics.on_train_begin
        • cellflow.training.Metrics.on_train_end
      • cellflow.training.PCADecodedMetrics
        • cellflow.training.PCADecodedMetrics.on_log_iteration
        • cellflow.training.PCADecodedMetrics.on_train_begin
        • cellflow.training.PCADecodedMetrics.on_train_end
      • cellflow.training.VAEDecodedMetrics
        • cellflow.training.VAEDecodedMetrics.on_log_iteration
        • cellflow.training.VAEDecodedMetrics.on_train_begin
        • cellflow.training.VAEDecodedMetrics.on_train_end
      • cellflow.training.WandbLogger
        • cellflow.training.WandbLogger.on_log_iteration
        • cellflow.training.WandbLogger.on_train_begin
        • cellflow.training.WandbLogger.on_train_end
      • cellflow.training.CellFlowTrainer
        • cellflow.training.CellFlowTrainer.train
    • Plotting
      • cellflow.plotting.plot_condition_embedding
    • Preprocessing
      • cellflow.preprocessing.centered_pca
      • cellflow.preprocessing.project_pca
      • cellflow.preprocessing.reconstruct_pca
      • cellflow.preprocessing.annotate_compounds
      • cellflow.preprocessing.encode_onehot
      • cellflow.preprocessing.get_molecular_fingerprints
      • cellflow.preprocessing.compute_wknn
      • cellflow.preprocessing.transfer_labels
    • External
      • cellflow.external.CFJaxSCVI
        • cellflow.external.CFJaxSCVI.get_latent_representation
        • cellflow.external.CFJaxSCVI.get_reconstructed_expression
        • cellflow.external.CFJaxSCVI.setup_anndata
        • cellflow.external.CFJaxSCVI.to_device
        • cellflow.external.CFJaxSCVI.device
  • Developer API
    • cellflow.data.DataManager
      • cellflow.data.DataManager.get_condition_data
      • cellflow.data.DataManager.get_prediction_data
      • cellflow.data.DataManager.get_train_data
      • cellflow.data.DataManager.get_validation_data
      • cellflow.data.DataManager.adata
      • cellflow.data.DataManager.control_key
      • cellflow.data.DataManager.covar_to_idx
      • cellflow.data.DataManager.covariate_reps
      • cellflow.data.DataManager.is_categorical
      • cellflow.data.DataManager.linked_perturb_covars
      • cellflow.data.DataManager.max_combination_length
      • cellflow.data.DataManager.null_value
      • cellflow.data.DataManager.perturb_covar_keys
      • cellflow.data.DataManager.perturbation_covariate_reps
      • cellflow.data.DataManager.perturbation_covariates
      • cellflow.data.DataManager.primary_one_hot_encoder
      • cellflow.data.DataManager.sample_covariate_reps
      • cellflow.data.DataManager.sample_covariates
      • cellflow.data.DataManager.sample_rep
      • cellflow.data.DataManager.split_covariates
    • cellflow.data.TrainingData
      • cellflow.data.TrainingData.n_controls
      • cellflow.data.TrainingData.n_perturbation_covariates
      • cellflow.data.TrainingData.n_perturbations
      • cellflow.data.TrainingData.cell_data
      • cellflow.data.TrainingData.split_covariates_mask
      • cellflow.data.TrainingData.split_idx_to_covariates
      • cellflow.data.TrainingData.perturbation_covariates_mask
      • cellflow.data.TrainingData.perturbation_idx_to_covariates
      • cellflow.data.TrainingData.perturbation_idx_to_id
      • cellflow.data.TrainingData.condition_data
      • cellflow.data.TrainingData.control_to_perturbation
      • cellflow.data.TrainingData.max_combination_length
      • cellflow.data.TrainingData.null_value
      • cellflow.data.TrainingData.data_manager
    • cellflow.data.PredictionData
      • cellflow.data.PredictionData.n_controls
      • cellflow.data.PredictionData.n_perturbation_covariates
      • cellflow.data.PredictionData.n_perturbations
      • cellflow.data.PredictionData.cell_data
      • cellflow.data.PredictionData.split_covariates_mask
      • cellflow.data.PredictionData.split_idx_to_covariates
      • cellflow.data.PredictionData.perturbation_idx_to_covariates
      • cellflow.data.PredictionData.perturbation_idx_to_id
      • cellflow.data.PredictionData.condition_data
      • cellflow.data.PredictionData.control_to_perturbation
      • cellflow.data.PredictionData.max_combination_length
      • cellflow.data.PredictionData.null_value
      • cellflow.data.PredictionData.data_manager
    • cellflow.data.ValidationData
      • cellflow.data.ValidationData.n_conditions_on_log_iteration
      • cellflow.data.ValidationData.n_conditions_on_train_end
      • cellflow.data.ValidationData.n_controls
      • cellflow.data.ValidationData.n_perturbation_covariates
      • cellflow.data.ValidationData.n_perturbations
      • cellflow.data.ValidationData.cell_data
      • cellflow.data.ValidationData.split_covariates_mask
      • cellflow.data.ValidationData.split_idx_to_covariates
      • cellflow.data.ValidationData.perturbation_covariates_mask
      • cellflow.data.ValidationData.perturbation_idx_to_covariates
      • cellflow.data.ValidationData.perturbation_idx_to_id
      • cellflow.data.ValidationData.condition_data
      • cellflow.data.ValidationData.control_to_perturbation
      • cellflow.data.ValidationData.max_combination_length
      • cellflow.data.ValidationData.null_value
      • cellflow.data.ValidationData.data_manager
    • cellflow.data.ConditionData
      • cellflow.data.ConditionData.n_controls
      • cellflow.data.ConditionData.n_perturbation_covariates
      • cellflow.data.ConditionData.n_perturbations
      • cellflow.data.ConditionData.condition_data
      • cellflow.data.ConditionData.max_combination_length
      • cellflow.data.ConditionData.perturbation_idx_to_covariates
      • cellflow.data.ConditionData.perturbation_idx_to_id
      • cellflow.data.ConditionData.null_value
      • cellflow.data.ConditionData.data_manager
    • cellflow.data.BaseDataMixin
      • cellflow.data.BaseDataMixin.n_controls
      • cellflow.data.BaseDataMixin.n_perturbation_covariates
      • cellflow.data.BaseDataMixin.n_perturbations
    • cellflow.data.TrainSampler
      • cellflow.data.TrainSampler.sample
      • cellflow.data.TrainSampler.data
    • cellflow.data.ValidationSampler
      • cellflow.data.ValidationSampler.sample
      • cellflow.data.ValidationSampler.data
    • cellflow.data.PredictionSampler
      • cellflow.data.PredictionSampler.sample
      • cellflow.data.PredictionSampler.data
  • Contributing Guide
  • References
  • Notebooks
    • Predicting donor-specific cytokine effects on PBMCs
    • Predicting embryonic phenotypes of genetically modified zebrafish
    • Predicting the continuous, perturbed development of the zebrafish
    • Neuron fate prediction from combinatorial morphogen treatment
    • Predicting the effect of combinatorial drug treatments
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Solvers¶

solvers.OTFlowMatching(vf, probability_path)

(OT) flow matching [Lipman et al., 2022] extended to the conditional setting.

solvers.GENOT(vf, probability_path, ...[, ...])

GENOT [Klein et al., 2024] extended to the conditional setting.
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cellflow.solvers.OTFlowMatching
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