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IBL BWB

  • Dataset
  • Setup
  • Codebase
  • Pretraining
  • TS1: Behavior
  • TS2: Dynamics
  • TS3: Anatomy
  • Submission
  • API
  • Refs
  • Leaderboard
  • GitHub
  • Dataset
  • Setup
  • Codebase
  • Pretraining
  • TS1: Behavior
  • TS2: Dynamics
  • TS3: Anatomy
  • Submission
  • API
  • Refs
  • Leaderboard
  • GitHub

Section Navigation

  • All objects

Evaluation contract

  • ibl_bwb_eval
    • TS1Task
    • TS2Task
    • TS3Task
    • task_id
    • is_task_of
    • get_ts1_supported_tasks
    • ReadoutSpec
    • TargetResolution
    • DataType
    • TS1ReadoutSpec
    • get_ts1_readout_spec
    • TS2ReadoutSpec
    • get_ts2_readout_spec
    • TS3ReadoutSpec
    • get_ts3_readout_spec
    • COSMOS_LABELS
    • check_ts3_label_order
  • ibl_bwb_eval.metrics
    • BPS
    • PoissonD2Score
    • aggregate_metrics
  • ibl_bwb_eval.multi_unit
    • multi_unit_prediction
  • ibl_bwb_eval.predictions
    • PredictionsWriter
    • version_of
  • ibl_bwb_eval.entity_ids
    • encode_entity_ids
    • decode_entity_ids

Scoring

  • ibl_bwb_eval.scoring.ts1
    • score_file
    • score_dir
    • summarize
  • ibl_bwb_eval.scoring.ts2
    • score_file
    • score_dir
    • summarize
  • ibl_bwb_eval.scoring.ts3
    • score_file
    • score_dir
    • summarize
  • ibl_bwb_eval.scoring.aggregation
    • from_ts3
    • aggregate
    • rank

Core

  • core.data
    • UnitFilteringInfo
    • BuildUnitFiltering
    • read_build_unit_filtering
    • enforce_unit_filtering
    • read_recording_ids
  • core.dataset
    • IBLBrainWideBench2026
    • VariableContextMixin
    • WholeSessionSpikeDataset
    • UnitQCPolicy
  • core.finetuning
    • FinetuningStrategy
    • FullFinetuning
    • GradualUnfreezing
    • Probe
  • core.model
    • BaseModel
  • core.trainer
    • BaseTrainer
  • core.samplers
    • DistributedSamplerWrapper
    • SessionBatchSampler
  • core.transforms
    • FilterUnits
    • UnitDropout
    • apply_unit_mask_
    • AdditiveGaussianNoise
    • AdditivePepperNoise
    • AmplitudeScaling
    • GaussianNoise
    • RandomApply
    • TemporalGaussianSmoothing
    • TemporalJittering
  • core.nn
    • Embedding
    • MultitaskReadout
    • tfixup_init_
    • self_attn
    • cross_attn
    • validate_attn_impl
    • uses_xformers
  • core.nn.loss
    • WeightedMSELoss
    • CLIPLoss
  • core.nn.metrics
    • rankme

Pretraining

  • pretrain.models
    • NDTStitch
    • NDTStitchMasker
    • NDTStitchPretrain
    • MtM
    • MtMMasker
    • MtMPretrain
    • NDT2
    • NDT2Masker
    • NDT2Pretrain
    • NEDS
    • NEDSMasker
    • NEDSPretrain
    • POYO
    • POYOSingleTaskPretrain
    • POYOPlus
    • POYOPlusMultitaskPretrain
    • POSSM
    • POSSMSingleTaskPretrain
    • POSSMMultitaskPretrain
    • RRRDecoder
    • RRRSingleTaskPretrain
    • NuCLR
    • NuCLRLoss
    • NuCLRPretrain
    • NEMO
    • NEMOPretrain
    • WVFEncoder
    • ACGEncoder
    • LinearProjector
  • pretrain.datasets
    • IBLBrainWideBenchMaskModelingSpikes
    • IBLBrainWideBenchSingleTaskBehavior
    • IBLBrainWideBenchMultiTaskBehavior

TS1: Behavior Prediction

  • ts1
    • IBLBrainWideBenchTS1
    • TS1TestMixin
    • TS1EvalTrainer
  • ts1.models.single_session
    • Linear
    • MLP
    • GRU
    • TCN
    • CEBRA
    • CEBRAEvalTrainer
    • NDTSuperv
  • ts1.models.pretrained
    • NDTStitchEvalTrainer
    • MtMEvalTrainer
    • NDT2EvalTrainer
    • NEDSEvalTrainer
    • POSSMEvalTrainer
    • POYOEvalTrainer
    • POYOPlusEvalTrainer
    • RRREvalTrainer

TS2: Neural Activity Prediction

  • ts2
    • IBLBrainWideBenchTS2
    • TS2TestMixin
    • TS2EvalTrainer
  • ts2.models.single_session
    • AutoencoderMLP
    • LFADS
    • LFADSEvalTrainer
    • NDT
    • NDTEvalTrainer
    • StatBaseline
    • PopCoupling
    • RRRReadout
    • RRRReadoutWithISI
    • TrailingMean
    • Shrinkage
    • RidgeAR
    • StatBaselineTrainer
  • ts2.models.pretrained
    • MtMEvalTrainer
    • NDTStitchEvalTrainer

TS3: Brain Region Prediction

  • ts3
    • IBLBrainWideBenchTS3
    • Extractor
    • compute_isi_histogram
  • ts3.models.inductive
    • NuCLRExtractor
    • NEMOExtractor
    • ISIExtractor
  • ts3.models.transductive
    • TransductiveExtractor
    • POYOPlusExtractor
    • POSSMExtractor
    • NDTStitchExtractor
    • MtMExtractor
    • NDTStitchCalibrateTrainer
    • MtMCalibrateTrainer
    • POSSMCalibrateTrainer
    • POYOPlusCalibrateTrainer
  • ts3.models.supervised
    • LOLCAT
    • MultiHeadGlobalAttention
    • LOLCATTrainer
    • LossFeedbackSampler
  • ts3.probes
    • Probe
    • LinearProbe
    • MLPProbe
  • API Reference
  • pretrain.datasets

pretrain.datasets#

What a pretraining run reads, shared by the models that fit the same objective.

IBLBrainWideBenchMaskModelingSpikes

Binned spikes alone, for objectives that mask them and reconstruct them.

IBLBrainWideBenchSingleTaskBehavior

Spikes aligned to one behavioral target.

IBLBrainWideBenchMultiTaskBehavior

Spikes aligned to several behavioral targets at once.

previous

LinearProjector

next

IBLBrainWideBenchMaskModelingSpikes

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