Kristin Branson

B. A. Schreiber, J. Denholm, F. Jaeckle et al.

We present an innovative method for rapidly segmenting hematoxylin and eosin (H&E)-stained tissue in whole-slide images (WSIs) that eliminates a wide range of undesirable artefacts such as pen marks and scanning artefacts. Our method involves taking a single-channel representation of a lowmagnification RGB overview of the WSI in which the pixel values are bimodally distributed such that H&E-stained tissue is easily distinguished from both background and a wide variety of artefacts. We demonstrate our method on 30 WSIs prepared from a wide range of institutions and WSI digital scanners, each containing substantial artefacts, and compare it to segmentations provided by Otsu thresholding and Histolab tissue segmentation and pen filtering tools. We found that our method segmented the tissue and fully removed all artefacts in 29 out of 30 WSIs, whereas Otsu thresholding failed to remove any artefacts, and the Histolab pen filtering tools only partially removed the pen marks. The beauty of our approach lies in its simplicity: manipulating RGB colour space and using Otsu thresholding allows for the segmentation of H&E-stained tissue and the rapid removal of artefacts without the need for machine learning or parameter tuning.

Jennifer J. Sun, Markus Marks, Andrew Ulmer et al.

We introduce MABe22, a large-scale, multi-agent video and trajectory benchmark to assess the quality of learned behavior representations. This dataset is collected from a variety of biology experiments, and includes triplets of interacting mice (4.7 million frames video+pose tracking data, 10 million frames pose only), symbiotic beetle-ant interactions (10 million frames video data), and groups of interacting flies (4.4 million frames of pose tracking data). Accompanying these data, we introduce a panel of real-life downstream analysis tasks to assess the quality of learned representations by evaluating how well they preserve information about the experimental conditions (e.g. strain, time of day, optogenetic stimulation) and animal behavior. We test multiple state-of-the-art self-supervised video and trajectory representation learning methods to demonstrate the use of our benchmark, revealing that methods developed using human action datasets do not fully translate to animal datasets. We hope that our benchmark and dataset encourage a broader exploration of behavior representation learning methods across species and settings.

Daniel Jiwoong Im, Iljung Kwak, Kristin Branson

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.

Daniel Jiwoong Im, Rutuja Patil, Kristin Branson

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.

Iljung S. Kwak, Jian-Zhong Guo, Adam Hantman et al.

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.

Daniel Jiwoong Im, Sridhama Prakhya, Jinyao Yan et al.

The Importance Weighted Auto Encoder (IWAE) objective has been shown to improve the training of generative models over the standard Variational Auto Encoder (VAE) objective. Here, we derive importance weighted extensions to AVB and AAE. These latent variable models use implicitly defined inference networks whose approximate posterior density q_φ(z|x) cannot be directly evaluated, an essential ingredient for importance weighting. We show improved training and inference in latent variable models with our adversarially trained importance weighting method, and derive new theoretical connections between adversarial generative model training criteria and marginal likelihood based methods. We apply these methods to the important problem of inferring spiking neural activity from calcium imaging data, a challenging posterior inference problem in neuroscience, and show that posterior samples from the adversarial methods outperform factorized posteriors used in VAEs.

Daniel Jiwoong Im, Nakul Verma, Kristin Branson

The t-distributed Stochastic Neighbor Embedding (t-SNE) is a powerful and popular method for visualizing high-dimensional data. It minimizes the Kullback-Leibler (KL) divergence between the original and embedded data distributions. In this work, we propose extending this method to other f-divergences. We analytically and empirically evaluate the types of latent structure-manifold, cluster, and hierarchical-that are well-captured using both the original KL-divergence as well as the proposed f-divergence generalization, and find that different divergences perform better for different types of structure. A common concern with $t$-SNE criterion is that it is optimized using gradient descent, and can become stuck in poor local minima. We propose optimizing the f-divergence based loss criteria by minimizing a variational bound. This typically performs better than optimizing the primal form, and our experiments show that it can improve upon the embedding results obtained from the original $t$-SNE criterion as well.

Daniel Jiwoong Im, He Ma, Graham Taylor et al.

Generative adversarial networks (GANs) have been extremely effective in approximating complex distributions of high-dimensional, input data samples, and substantial progress has been made in understanding and improving GAN performance in terms of both theory and application. However, we currently lack quantitative methods for model assessment. Because of this, while many GAN variants are being proposed, we have relatively little understanding of their relative abilities. In this paper, we evaluate the performance of various types of GANs using divergence and distance functions typically used only for training. We observe consistency across the various proposed metrics and, interestingly, the test-time metrics do not favour networks that use the same training-time criterion. We also compare the proposed metrics to human perceptual scores.

Mayank Kabra, Kristin Branson

We give a covering number bound for deep learning networks that is independent of the size of the network. The key for the simple analysis is that for linear classifiers, rotating the data doesn't affect the covering number. Thus, we can ignore the rotation part of each layer's linear transformation, and get the covering number bound by concentrating on the scaling part.

Daniel Jiwoong Im, Michael Tao, Kristin Branson

The success of deep neural networks hinges on our ability to accurately and efficiently optimize high-dimensional, non-convex functions. In this paper, we empirically investigate the loss functions of state-of-the-art networks, and how commonly-used stochastic gradient descent variants optimize these loss functions. To do this, we visualize the loss function by projecting them down to low-dimensional spaces chosen based on the convergence points of different optimization algorithms. Our observations suggest that optimization algorithms encounter and choose different descent directions at many saddle points to find different final weights. Based on consistency we observe across re-runs of the same stochastic optimization algorithm, we hypothesize that each optimization algorithm makes characteristic choices at these saddle points.

Eyrun Eyjolfsdottir, Kristin Branson, Yisong Yue et al.

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.

Nakul Verma, Kristin Branson

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.