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Kristin Branson

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Machine Learning Artificial Intelligence Computer Vision Neural and Evolutionary Computing

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preprint2026arXiv

Neurodata Without Boredom: Benchmarking Agentic AI for Data Reuse

Neuroscience data are highly fragmented across labs, formats, and experimental paradigms, and reuse often requires substantial manual effort. A persistent roadblock to data reuse and integration is the need to decipher bespoke and diverse data formatting choices. Common data formats have been proposed in response, but the field continues to struggle with a fundamental tension: formats flexible enough to accommodate diverse experiments are rarely descriptive enough to be self-explanatory, and sufficiently descriptive formats demand detailed documentation and curation effort that few labs can sustain. Agentic AI is a natural candidate to solve this problem: LLMs read code and text faster and with sustained attention to the low-level details humans tend to skim over. To measure how well agentic AI performs on this task, we selected eight recent papers studying large-scale mouse neural population recordings that shared both data and code, spanning diverse recording modalities, behavioral paradigms, and dataset formats (e.g., NWB, specialized APIs, and general-purpose Python or MATLAB files). We provided agents with the data, code, and paper, and prompted them to load, understand, and reformat the data for a common downstream task: training a decoder from neural activity to task or behavioral variables. General-purpose coding agents commonly used by scientists performed well on each sub-task, but rarely strung together a fully error-free end-to-end solution. We characterize the types of mistakes agents made and the dataset properties that elicited them, and propose data-sharing best practices for the agentic-AI era. We further find that agents-as-judges are unreliable at catching errors, especially without ground-truth references, so interactive, human-in-the-loop coding remains necessary.

preprint2020arXiv

Detecting the Starting Frame of Actions in Video

In this work, we address the problem of precisely localizing key frames of an action, for example, the precise time that a pitcher releases a baseball, or the precise time that a crowd begins to applaud. Key frame localization is a largely overlooked and important action-recognition problem, for example in the field of neuroscience, in which we would like to understand the neural activity that produces the start of a bout of an action. To address this problem, we introduce a novel structured loss function that properly weights the types of errors that matter in such applications: it more heavily penalizes extra and missed action start detections over small misalignments. Our structured loss is based on the best matching between predicted and labeled action starts. We train recurrent neural networks (RNNs) to minimize differentiable approximations of this loss. To evaluate these methods, we introduce the Mouse Reach Dataset, a large, annotated video dataset of mice performing a sequence of actions. The dataset was collected and labeled by experts for the purpose of neuroscience research. On this dataset, we demonstrate that our method outperforms related approaches and baseline methods using an unstructured loss.

preprint2020arXiv

Evaluation metrics for behaviour modeling

A primary difficulty with unsupervised discovery of structure in large data sets is a lack of quantitative evaluation criteria. In this work, we propose and investigate several metrics for evaluating and comparing generative models of behavior learned using imitation learning. Compared to the commonly-used model log-likelihood, these criteria look at longer temporal relationships in behavior, are relevant if behavior has some properties that are inherently unpredictable, and highlight biases in the overall distribution of behaviors produced by the model. Pointwise metrics compare real to model-predicted trajectories given true past information. Distribution metrics compare statistics of the model simulating behavior in open loop, and are inspired by how experimental biologists evaluate the effects of manipulations on animal behavior. We show that the proposed metrics correspond with biologists' intuitions about behavior, and allow us to evaluate models, understand their biases, and enable us to propose new research directions.

preprint2019arXiv

Are skip connections necessary for biologically plausible learning rules?

Backpropagation is the workhorse of deep learning, however, several other biologically-motivated learning rules have been introduced, such as random feedback alignment and difference target propagation. None of these methods have produced a competitive performance against backpropagation. In this paper, we show that biologically-motivated learning rules with skip connections between intermediate layers can perform as well as backpropagation on the MNIST dataset and are robust to various sets of hyper-parameters.

preprint2016arXiv

Learning recurrent representations for hierarchical behavior modeling

We propose a framework for detecting action patterns from motion sequences and modeling the sensory-motor relationship of animals, using a generative recurrent neural network. The network has a discriminative part (classifying actions) and a generative part (predicting motion), whose recurrent cells are laterally connected, allowing higher levels of the network to represent high level phenomena. We test our framework on two types of data, fruit fly behavior and online handwriting. Our results show that 1) taking advantage of unlabeled sequences, by predicting future motion, significantly improves action detection performance when training labels are scarce, 2) the network learns to represent high level phenomena such as writer identity and fly gender, without supervision, and 3) simulated motion trajectories, generated by treating motion prediction as input to the network, look realistic and may be used to qualitatively evaluate whether the model has learnt generative control rules.

preprint2015arXiv

Sample complexity of learning Mahalanobis distance metrics

Metric learning seeks a transformation of the feature space that enhances prediction quality for the given task at hand. In this work we provide PAC-style sample complexity rates for supervised metric learning. We give matching lower- and upper-bounds showing that the sample complexity scales with the representation dimension when no assumptions are made about the underlying data distribution. However, by leveraging the structure of the data distribution, we show that one can achieve rates that are fine-tuned to a specific notion of intrinsic complexity for a given dataset. Our analysis reveals that augmenting the metric learning optimization criterion with a simple norm-based regularization can help adapt to a dataset's intrinsic complexity, yielding better generalization. Experiments on benchmark datasets validate our analysis and show that regularizing the metric can help discern the signal even when the data contains high amounts of noise.