mlsanityData to 14 Oct 2026

ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish

arXiv 2503.02618 ↗First posted 4 Mar 2025q-bio.NC cs.CV cs.LGcited by 10

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Abstract (arXiv)

Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of over 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into forecasting methods.

Key facts. Cited by 10 papers in the map (data through 14 Oct 2026). Builds on 16 of its 64 references that are in the map. First posted on arXiv 4 Mar 2025.

Builds on

16 of 64 references.

References · 16

  1. 2015U-Net: Convolutional Networks for Biomedical Image Segmentationcited by 19,713
  2. 2017FiLM: Visual Reasoning with a General Conditioning Layercited by 2,333
  3. 2022A Time Series is Worth 64 Words: Long-term Forecasting with Transformerscited by 2,039
  4. 2016Identity Mappings in Deep Residual Networkscited by 1,965
  5. 2017Decoupled Weight Decay Regularizationcited by 1,831
  6. 2018Group Normalizationcited by 1,524
  7. 2022Are Transformers Effective for Time Series Forecasting?cited by 1,424
  8. 2023Long-term Forecasting with TiDE: Time-series Dense Encodercited by 332
  9. 2020WeatherBench: A benchmark dataset for data-driven weather forecastingcited by 275
  10. 2023TSMixer: An All-MLP Architecture for Time Series Forecastingcited by 240
  11. 2023WeatherBench 2: A benchmark for the next generation of data-driven global weather modelscited by 236
  12. 2023Deep Learning for Day Forecasts from Sparse Observationscited by 72
4 more
  1. 2021Neural Latents Benchmark '21: Evaluating latent variable models of neural population activitycited by 60
  2. 2023The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videoscited by 11
  3. 2025Forecasting Whole-Brain Neuronal Activity from Volumetric Videocited by 5
  4. 2013Low-dimensional functionality of complex network dynamics: Neuro-sensory integration in the Caenorhabditis elegans connectomecited by 1

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 4; 2026: 6.

10 papers.

  1. 2026Structured Scaling of AI Discovery Across Diverse Scientific Domainscited by 21
  2. 2025POCO: Scalable Neural Forecasting through Population Conditioningcited by 7
  3. 2026Aster: Autonomous Scientific Discovery over 20x Faster Than Existing Methodscited by 5
  4. 2025Neuroprobe: Evaluating Intracranial Brain Responses to Naturalistic Stimulicited by 3
  5. 2025Benchmarking Probabilistic Time Series Forecasting Models on Neural Activitycited by 1
  6. 2025NLP4Neuro: Sequence-to-sequence learning for neural population decodingcited by 0
  7. 2026Discovering Mechanistic Models of Neural Activity: System Identification in an in Silico Zebrafishcited by 0
  8. 2026Graph neural networks uncover structure and functions underlying the activity of simulated neural assembliescited by 0
  9. 2026Probabilistic Prediction of Neural Dynamics via Autoregressive Flow Matchingcited by 0
  10. 2026Integrative neurocybernetic modeling in the era of large-scale neurosciencecited by 0