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Viren Jain

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6 papers

2 author rows

ICLR Conference 2025 Conference Paper

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

Jan-Matthis Lueckmann
Alexander Immer
Alex Bo-Yuan Chen
Peter H. Li
Mariela D. Petkova
Nirmala A. Iyer
Luuk Willem Hesselink
Aparna Dev

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.

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NeurIPS Conference 2016 Conference Paper

Combinatorial Energy Learning for Image Segmentation

Jeremy Maitin-Shepard
Viren Jain
Michal Januszewski
Peter Li
Pieter Abbeel

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

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ICLR Conference 2014 Conference Paper

Learned versus Hand-Designed Feature Representations for 3d Agglomeration

John A. Bogovic
Gary B. Huang
Viren Jain

For image recognition and labeling tasks, recent results suggest that machine learning methods that rely on manually specified feature representations may be outperformed by methods that automatically derive feature representations based on the data. Yet for problems that involve analysis of 3d objects, such as mesh segmentation, shape retrieval, or neuron fragment agglomeration, there remains a strong reliance on hand-designed feature descriptors. In this paper, we evaluate a large set of hand-designed 3d feature descriptors alongside features learned from the raw data using both end-to-end and unsupervised learning techniques, in the context of agglomeration of 3d neuron fragments. By combining unsupervised learning techniques with a novel dynamic pooling scheme, we show how pure learning-based methods are for the first time competitive with hand-designed 3d shape descriptors. We investigate data augmentation strategies for dramatically increasing the size of the training set, and show how combining both learned and hand-designed features leads to the highest accuracy.

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NeurIPS Conference 2011 Conference Paper

Learning to Agglomerate Superpixel Hierarchies

Viren Jain
Srinivas Turaga
K Briggman
Moritz Helmstaedter
Winfried Denk
H. Seung

An agglomerative clustering algorithm merges the most similar pair of clusters at every iteration. The function that evaluates similarity is traditionally hand- designed, but there has been recent interest in supervised or semisupervised settings in which ground-truth clustered data is available for training. Here we show how to train a similarity function by regarding it as the action-value function of a reinforcement learning problem. We apply this general method to segment images by clustering superpixels, an application that we call Learning to Agglomerate Superpixel Hierarchies (LASH). When applied to a challenging dataset of brain images from serial electron microscopy, LASH dramatically improved segmentation accuracy when clustering supervoxels generated by state of the boundary detection algorithms. The naive strategy of directly training only supervoxel similarities and applying single linkage clustering produced less improvement.

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NeurIPS Conference 2008 Conference Paper

Natural Image Denoising with Convolutional Networks

Viren Jain
Sebastian Seung

We present an approach to low-level vision that combines two main ideas: the use of convolutional networks as an image processing architecture and an unsupervised learning procedure that synthesizes training samples from specific noise models. We demonstrate this approach on the challenging problem of natural image denoising. Using a test set with a hundred natural images, we find that convolutional networks provide comparable and in some cases superior performance to state of the art wavelet and Markov random field (MRF) methods. Moreover, we find that a convolutional network offers similar performance in the blind denoising setting as compared to other techniques in the non-blind setting. We also show how convolutional networks are mathematically related to MRF approaches by presenting a mean field theory for an MRF specially designed for image denoising. Although these approaches are related, convolutional networks avoid computational difficulties in MRF approaches that arise from probabilistic learning and inference. This makes it possible to learn image processing architectures that have a high degree of representational power (we train models with over 15, 000 parameters), but whose computational expense is significantly less than that associated with inference in MRF approaches with even hundreds of parameters.

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NeurIPS Conference 2005 Conference Paper

Representing Part-Whole Relationships in Recurrent Neural Networks

Viren Jain
Valentin Zhigulin
H. Seung

There is little consensus about the computational function of top-down synaptic connections in the visual system. Here we explore the hypothesis that top-down connections, like bottom-up connections, reflect partwhole relationships. We analyze a recurrent network with bidirectional synaptic interactions between a layer of neurons representing parts and a layer of neurons representing wholes. Within each layer, there is lateral inhibition. When the network detects a whole, it can rigorously enforce part-whole relationships by ignoring parts that do not belong. The network can complete the whole by filling in missing parts. The network can refuse to recognize a whole, if the activated parts do not conform to a stored part-whole relationship. Parameter regimes in which these behaviors happen are identified using the theory of permitted and forbidden sets [3, 4]. The network behaviors are illustrated by recreating Rumelhart and McClelland's "interactive activation" model [7]. In neural network models of visual object recognition [2, 6, 8], patterns of synaptic connectivity often reflect part-whole relationships between the features that are represented by neurons. For example, the connections of Figure 1 reflect the fact that feature B both contains simpler features A1, A2, and A3, and is contained in more complex features C1, C2, and C3. Such connectivity allows neurons to follow the rule that existence of the part is evidence for existence of the whole. By combining synaptic input from multiple sources of evidence for a feature, a neuron can "decide" whether that feature is present. 1 The synapses shown in Figure 1 are purely bottom-up, directed from simple to complex features. However, there are also top-down connections in the visual system, and there is little consensus about their function. One possibility is that top-down connections also reflect part-whole relationships. They allow feature detectors to make decisions using the rule that existence of the whole is evidence for existence of its parts. In this paper, we analyze the dynamics of a recurrent network in which part-whole relationships are stored as bidirectional synaptic interactions, rather than the unidirectional interactions of Figure 1. The network has a number of interesting computational capabilities. When the network detects a whole, it can rigorously enforce part-whole relationships Synaptic connectivity may reflect other relationships besides part-whole. For example, invariances can be implemented by connecting detectors of several instances of the same feature to the same target, which is consequently an invariant detector of the feature. 1

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