Nir Shavit

Micah Adler, Nir Shavit

Superposition, the ability of neural networks to represent more features than neurons, is increasingly seen as key to the efficiency of large models. This paper investigates the theoretical foundations of computing in superposition, establishing complexity bounds for explicit, provably correct algorithms. We present the first lower bounds for a neural network computing in superposition, showing that for a broad class of problems, including permutations and pairwise logical operations, computing $m'$ features in superposition requires at least $Ω(\sqrt{m' \log m'})$ neurons and $Ω(m' \log m')$ parameters. This implies an explicit limit on how much one can sparsify or distill a model while preserving its expressibility, and complements empirical scaling laws by implying the first subexponential bound on capacity: a network with $n$ neurons can compute at most $O(n^2 / \log n)$ features. Conversely, we provide a nearly tight constructive upper bound: logical operations like pairwise AND can be computed using $O(\sqrt{m'} \log m')$ neurons and $O(m' \log^2 m')$ parameters. There is thus an exponential gap between the complexity of computing in superposition (the subject of this work) versus merely representing features, which can require as little as $O(\log m')$ neurons based on the Johnson-Lindenstrauss Lemma. Our work analytically establishes that the number of parameters is a good estimator of the number of features a neural network computes.

Tri Nguyen, Mukul Narwani, Mark Larson et al.

The wiring and connectivity of neurons form a structural basis for the function of the nervous system. Advances in volume electron microscopy (EM) and image segmentation have enabled mapping of circuit diagrams (connectomics) within local regions of the mouse brain. However, applying volume EM over the whole brain is not currently feasible due to technological challenges. As a result, comprehensive maps of long-range connections between brain regions are lacking. Recently, we demonstrated that X-ray holographic nanotomography (XNH) can provide high-resolution images of brain tissue at a much larger scale than EM. In particular, XNH is wellsuited to resolve large, myelinated axon tracts (white matter) that make up the bulk of long-range connections (projections) and are critical for inter-region communication. Thus, XNH provides an imaging solution for brain-wide projectomics. However, because XNH data is typically collected at lower resolutions and larger fields-of-view than EM, accurate segmentation of XNH images remains an important challenge that we present here. In this task, we provide volumetric XNH images of cortical white matter axons from the mouse brain along with ground truth annotations for axon trajectories. Manual voxel-wise annotation of ground truth is a time-consuming bottleneck for training segmentation networks. On the other hand, skeleton-based ground truth is much faster to annotate, and sufficient to determine connectivity. Therefore, we encourage participants to develop methods to leverage skeleton-based training. To this end, we provide two types of ground-truth annotations: a small volume of voxel-wise annotations and a larger volume with skeleton-based annotations. Entries will be evaluated on how accurately the submitted segmentations agree with the ground-truth skeleton annotations.

Yicong Li, Yaron Meirovitch, Aaron T. Kuan et al.

Comprehensive, synapse-resolution imaging of the brain will be crucial for understanding neuronal computations and function. In connectomics, this has been the sole purview of volume electron microscopy (EM), which entails an excruciatingly difficult process because it requires cutting tissue into many thin, fragile slices that then need to be imaged, aligned, and reconstructed. Unlike EM, hard X-ray imaging is compatible with thick tissues, eliminating the need for thin sectioning, and delivering fast acquisition, intrinsic alignment, and isotropic resolution. Unfortunately, current state-of-the-art X-ray microscopy provides much lower resolution, to the extent that segmenting membranes is very challenging. We propose an uncertainty-aware 3D reconstruction model that translates X-ray images to EM-like images with enhanced membrane segmentation quality, showing its potential for developing simpler, faster, and more accurate X-ray based connectomics pipelines.

Armand Nicolicioiu, Eugenia Iofinova, Andrej Jovanovic et al.

The availability of powerful open-source large language models (LLMs) opens exciting use-cases, such as using personal data to fine-tune these models to imitate a user's unique writing style. Two key requirements for such assistants are personalization - in the sense that the assistant should recognizably reflect the user's own writing style - and privacy - users may justifiably be wary of uploading extremely personal data, such as their email archive, to a third-party service. In this paper, we present a new design and evaluation for such an automated assistant, for the specific use case of email generation, which we call Panza. Panza's personalization features are based on a combination of fine-tuning using a variant of the Reverse Instructions technique together with Retrieval-Augmented Generation (RAG). We demonstrate that this combination allows us to fine-tune an LLM to reflect a user's writing style using limited data, while executing on extremely limited resources, e.g. on a free Google Colab instance. Our key methodological contribution is the first detailed study of evaluation metrics for this personalized writing task, and of how different choices of system components--the use of RAG and of different fine-tuning approaches-impact the system's performance. Additionally, we demonstrate that very little data - under 100 email samples - are sufficient to create models that convincingly imitate humans. This finding showcases a previously-unknown attack vector in language models - that access to a small number of writing samples can allow a bad actor to cheaply create generative models that imitate a target's writing style. We are releasing the full Panza code as well as three new email datasets licensed for research use at https://github.com/IST-DASLab/PanzaMail.

Tony T. Wang, Igor Zablotchi, Nir Shavit et al.

We study the data-scaling of transfer learning from foundation models in the low-downstream-data regime. We observe an intriguing phenomenon which we call cliff-learning. Cliff-learning refers to regions of data-scaling laws where performance improves at a faster than power law rate (i.e. regions of concavity on a log-log scaling plot). We conduct an in-depth investigation of foundation-model cliff-learning and study toy models of the phenomenon. We observe that the degree of cliff-learning reflects the degree of compatibility between the priors of a learning algorithm and the task being learned.

Micah Adler, Dan Alistarh, Nir Shavit

We introduce combinatorial interpretability, a methodology for understanding neural computation by analyzing the combinatorial structures in the sign-based categorization of a network's weights and biases. We demonstrate its power through feature channel coding, a theory that explains how neural networks compute Boolean expressions and potentially underlies other categories of neural network computation. According to this theory, features are computed via feature channels: unique cross-neuron encodings shared among the inputs the feature operates on. Because different feature channels share neurons, the neurons are polysemantic and the channels interfere with one another, making the computation appear inscrutable. We show how to decipher these computations by analyzing a network's feature channel coding, offering complete mechanistic interpretations of several small neural networks that were trained with gradient descent. Crucially, this is achieved via static combinatorial analysis of the weight matrices, without examining activations or training new autoencoding networks. Feature channel coding reframes the superposition hypothesis, shifting the focus from neuron activation directionality in high-dimensional space to the combinatorial structure of codes. It also allows us for the first time to exactly quantify and explain the relationship between a network's parameter size and its computational capacity (i.e. the set of features it can compute with low error), a relationship that is implicitly at the core of many modern scaling laws. Though our initial studies of feature channel coding are restricted to Boolean functions, we believe they provide a rich, controlled, and informative research space, and that the path we propose for combinatorial interpretation of neural computation can provide a basis for understanding both artificial and biological neural circuits.

Tony T. Wang, John Hughes, Henry Sleight et al.

Defending large language models against jailbreaks so that they never engage in a broadly-defined set of forbidden behaviors is an open problem. In this paper, we investigate the difficulty of jailbreak-defense when we only want to forbid a narrowly-defined set of behaviors. As a case study, we focus on preventing an LLM from helping a user make a bomb. We find that popular defenses such as safety training, adversarial training, and input/output classifiers are unable to fully solve this problem. In pursuit of a better solution, we develop a transcript-classifier defense which outperforms the baseline defenses we test. However, our classifier defense still fails in some circumstances, which highlights the difficulty of jailbreak-defense even in a narrow domain.

Shashata Sawmya, Linghao Kong, Ilia Markov et al.

Disentangling polysemantic neurons is at the core of many current approaches to interpretability of large language models. Here we attempt to study how disentanglement can be used to understand performance, particularly under weight sparsity, a leading post-training optimization technique. We suggest a novel measure for estimating neuronal entanglement: the Wasserstein distance of a neuron's output distribution to a Gaussian. Moreover, we show the existence of a small number of highly entangled "Wasserstein Neurons" in each linear layer of an LLM, characterized by their highly non-Gaussian output distributions, their role in mapping similar inputs to dissimilar outputs, and their significant impact on model accuracy. To study these phenomena, we propose a new experimental framework for disentangling polysemantic neurons. Our framework separates each layer's inputs to create a mixture of experts where each neuron's output is computed by a mixture of neurons of lower Wasserstein distance, each better at maintaining accuracy when sparsified without retraining. We provide strong evidence that this is because the mixture of sparse experts is effectively disentangling the input-output relationship of individual neurons, in particular the difficult Wasserstein neurons.

Tony T. Wang, Miles Wang, Kaivalya Hariharan et al.

LLMs often face competing pressures (for example helpfulness vs. harmlessness). To understand how models resolve such conflicts, we study Llama-2-chat models on the forbidden fact task. Specifically, we instruct Llama-2 to truthfully complete a factual recall statement while forbidding it from saying the correct answer. This often makes the model give incorrect answers. We decompose Llama-2 into 1000+ components, and rank each one with respect to how useful it is for forbidding the correct answer. We find that in aggregate, around 35 components are enough to reliably implement the full suppression behavior. However, these components are fairly heterogeneous and many operate using faulty heuristics. We discover that one of these heuristics can be exploited via a manually designed adversarial attack which we call The California Attack. Our results highlight some roadblocks standing in the way of being able to successfully interpret advanced ML systems. Project website available at https://forbiddenfacts.github.io .

Yaron Meirovitch, Fuming Yang, Jeff Lichtman et al.

Most pruning methods remove parameters ranked by impact on loss (e.g., magnitude or gradient). We propose Budgeted Broadcast (BB), which gives each unit a local traffic budget (the product of its long-term on-rate $a_i$ and fan-out $k_i$). A constrained-entropy analysis shows that maximizing coding entropy under a global traffic budget yields a selectivity-audience balance, $\log\frac{1-a_i}{a_i}=βk_i$. BB enforces this balance with simple local actuators that prune either fan-in (to lower activity) or fan-out (to reduce broadcast). In practice, BB increases coding entropy and decorrelation and improves accuracy at matched sparsity across Transformers for ASR, ResNets for face identification, and 3D U-Nets for synapse prediction, sometimes exceeding dense baselines. On electron microscopy images, it attains state-of-the-art F1 and PR-AUC under our evaluation protocol. BB is easy to integrate and suggests a path toward learning more diverse and efficient representations.

Avichal Goel, Yoon Kim, Nir Shavit et al.

Finetuning (pretrained) language models is a standard approach for updating their internal parametric knowledge and specializing them to new tasks and domains. However, the corresponding model weight changes ("weight diffs") are not generally interpretable. While inspecting the finetuning dataset can give a sense of how the model might have changed, these datasets are often not publicly available or are too large to work with directly. Towards the goal of comprehensively understanding weight diffs in natural language, we introduce Diff Interpretation Tuning (DIT), a method that trains models to describe their own finetuning-induced modifications. Our approach uses synthetic, labeled weight diffs to train a DIT-adapter, which can be applied to a compatible finetuned model to make it describe how it has changed. We demonstrate in two proof-of-concept settings (reporting hidden behaviors and summarizing finetuned knowledge) that our method enables models to describe their finetuning-induced modifications using accurate natural language descriptions.

Linghao Kong, Inimai Subramanian, Yonadav Shavit et al.

This work demonstrates how increasing the number of neurons in a network without increasing its number of non-zero parameters improves performance. We show that this gain corresponds with a decrease in interference between multiple features that would otherwise share the same neurons. To reduce such entanglement at a fixed non-zero parameter count, we introduce Fixed Parameter Expansion (FPE): replace a neuron with multiple children and partition the parent's weights disjointly across them, so that each child inherits a non-overlapping subset of connections. On symbolic tasks, specifically Boolean code problems, clause-aligned FPE systematically reduces polysemanticity metrics and yields higher task accuracy. Notably, random splits of neuron weights approximate these gains, indicating that reduced collisions, not precise assignment, are a primary driver. Consistent with the superposition hypothesis, the benefits of FPE grow with increasing interference: when polysemantic load is high, accuracy improvements are the largest. Transferring these insights to real models (classifiers over CLIP embeddings and deeper multilayer networks) we find that widening networks while maintaining a constant non-zero parameter count consistently increases accuracy. These results identify an interpretability-grounded mechanism to leverage width against superposition, improving performance without increasing the number of non-zero parameters. Such a direction is well matched to modern accelerators, where memory movement of non-zero parameters, rather than raw compute, is the dominant bottleneck.

Linghao Kong, Angelina Ning, Micah Adler et al.

A recently discovered class of entangled neurons, known as Wasserstein neurons, is disproportionately critical in large language models despite constituting only a very small fraction of the network: their targeted removal collapses the model, consistent with their unique role in differentiating similar inputs. Interestingly, in Wasserstein neurons immediately preceding smooth activation functions, such differentiation manifests in the negative pre-activation space, especially in early layers. Pairs of similar inputs are driven to highly distinct negative values, and these pairs involve syntactic tokens such as determiners and prepositions. We show that this negative region is functional rather than simply favorable for optimization. A minimal, sign-specific intervention that zeroes only the negative pre-activations of a small subset of entangled neurons significantly weakens overall model function and disrupts grammatical behavior, while both random and perplexity-matched controls leave grammatical performance largely unchanged. Part of speech analysis localizes the excess surprisal to syntactic scaffolding tokens, and layer-specific interventions reveal that small local degradations accumulate across depth. Over training checkpoints, the same ablation impairs grammatical behavior as Wasserstein neurons emerge and stabilize. Together, these results identify negative differentiation in a sparse subset of entangled neurons as a crucial mechanism that language models rely on for syntax.

Shashata Sawmya, Micah Adler, Nir Shavit

This paper studies the emergence of interpretable categorical features within large language models (LLMs), analyzing their behavior across training checkpoints (time), transformer layers (space), and varying model sizes (scale). Using sparse autoencoders for mechanistic interpretability, we identify when and where specific semantic concepts emerge within neural activations. Results indicate clear temporal and scale-specific thresholds for feature emergence across multiple domains. Notably, spatial analysis reveals unexpected semantic reactivation, with early-layer features re-emerging at later layers, challenging standard assumptions about representational dynamics in transformer models.

Thomas L. Athey, Shashata Sawmya, Nir Shavit

As both computer vision models and biomedical datasets grow in size, there is an increasing need for efficient inference algorithms. We utilize cascade detectors to efficiently identify sparse objects in multiresolution images. Given an object's prevalence and a set of detectors at different resolutions with known accuracies, we derive the accuracy, and expected number of classifier calls by a cascade detector. These results generalize across number of dimensions and number of cascade levels. Finally, we compare one- and two-level detectors in fluorescent cell detection, organelle segmentation, and tissue segmentation across various microscopy modalities. We show that the multi-level detector achieves comparable performance in 30-75% less time. Our work is compatible with a variety of computer vision models and data domains.

Lu Mi, Tianxing He, Core Francisco Park et al.

Latent-space interpolation is commonly used to demonstrate the generalization ability of deep latent variable models. Various algorithms have been proposed to calculate the best trajectory between two encodings in the latent space. In this work, we show how data labeled with semantically continuous attributes can be utilized to conduct a quantitative evaluation of latent-space interpolation algorithms, for variational autoencoders. Our framework can be used to complement the standard qualitative comparison, and also enables evaluation for domains (such as graph) in which the visualization is difficult. Interestingly, our experiments reveal that the superiority of interpolation algorithms could be domain-dependent. While normalised interpolation works best for the image domain, spherical linear interpolation achieves the best performance in the graph domain. Next, we propose a simple-yet-effective method to restrict the latent space via a bottleneck structure in the encoder. We find that all interpolation algorithms evaluated in this work can benefit from this restriction. Finally, we conduct interpolation-aware training with the labeled attributes, and show that this explicit supervision can improve the interpolation performance.

Lu Mi, Hang Zhao, Charlie Nash et al.

High Definition (HD) maps are maps with precise definitions of road lanes with rich semantics of the traffic rules. They are critical for several key stages in an autonomous driving system, including motion forecasting and planning. However, there are only a small amount of real-world road topologies and geometries, which significantly limits our ability to test out the self-driving stack to generalize onto new unseen scenarios. To address this issue, we introduce a new challenging task to generate HD maps. In this work, we explore several autoregressive models using different data representations, including sequence, plain graph, and hierarchical graph. We propose HDMapGen, a hierarchical graph generation model capable of producing high-quality and diverse HD maps through a coarse-to-fine approach. Experiments on the Argoverse dataset and an in-house dataset show that HDMapGen significantly outperforms baseline methods. Additionally, we demonstrate that HDMapGen achieves high scalability and efficiency.

Jonathan S. Rosenfeld, Jonathan Frankle, Michael Carbin et al.

We show that the error of iteratively magnitude-pruned networks empirically follows a scaling law with interpretable coefficients that depend on the architecture and task. We functionally approximate the error of the pruned networks, showing it is predictable in terms of an invariant tying width, depth, and pruning level, such that networks of vastly different pruned densities are interchangeable. We demonstrate the accuracy of this approximation over orders of magnitude in depth, width, dataset size, and density. We show that the functional form holds (generalizes) for large scale data (e.g., ImageNet) and architectures (e.g., ResNets). As neural networks become ever larger and costlier to train, our findings suggest a framework for reasoning conceptually and analytically about a standard method for unstructured pruning.

Rati Gelashvili, Nir Shavit, Aleksandar Zlateski

Fast convolutions via transforms, either Winograd or FFT, had emerged as a preferred way of performing the computation of convolutional layers, as it greatly reduces the number of required operations. Recent work shows that, for many layer structures, a well--designed implementation of fast convolutions can greatly utilize modern CPUs, significantly reducing the compute time. However, the generous amount of shared L3 cache present on modern CPUs is often neglected, and the algorithms are optimized solely for the private L2 cache. In this paper we propose an efficient `L3 Fusion` algorithm that is specifically designed for CPUs with significant amount of shared L3 cache. Using the hierarchical roofline model, we show that in many cases, especially for layers with fewer channels, the `L3 fused` approach can greatly outperform standard 3 stage one provided by big vendors such as Intel. We validate our theoretical findings, by benchmarking our `L3 fused` implementation against publicly available state of the art.

Lu Mi, Hao Wang, Yonglong Tian et al.

Uncertainty estimation is an essential step in the evaluation of the robustness for deep learning models in computer vision, especially when applied in risk-sensitive areas. However, most state-of-the-art deep learning models either fail to obtain uncertainty estimation or need significant modification (e.g., formulating a proper Bayesian treatment) to obtain it. Most previous methods are not able to take an arbitrary model off the shelf and generate uncertainty estimation without retraining or redesigning it. To address this gap, we perform a systematic exploration into training-free uncertainty estimation for dense regression, an unrecognized yet important problem, and provide a theoretical construction justifying such estimations. We propose three simple and scalable methods to analyze the variance of outputs from a trained network under tolerable perturbations: infer-transformation, infer-noise, and infer-dropout. They operate solely during the inference, without the need to re-train, re-design, or fine-tune the models, as typically required by state-of-the-art uncertainty estimation methods. Surprisingly, even without involving such perturbations in training, our methods produce comparable or even better uncertainty estimation when compared to training-required state-of-the-art methods.

Jonathan S. Rosenfeld, Amir Rosenfeld, Yonatan Belinkov et al.

The dependency of the generalization error of neural networks on model and dataset size is of critical importance both in practice and for understanding the theory of neural networks. Nevertheless, the functional form of this dependency remains elusive. In this work, we present a functional form which approximates well the generalization error in practice. Capitalizing on the successful concept of model scaling (e.g., width, depth), we are able to simultaneously construct such a form and specify the exact models which can attain it across model/data scales. Our construction follows insights obtained from observations conducted over a range of model/data scales, in various model types and datasets, in vision and language tasks. We show that the form both fits the observations well across scales, and provides accurate predictions from small- to large-scale models and data.

Yaron Meirovitch, Lu Mi, Hayk Saribekyan et al.

Pixel-accurate tracking of objects is a key element in many computer vision applications, often solved by iterated individual object tracking or instance segmentation followed by object matching. Here we introduce cross-classification clustering (3C), a technique that simultaneously tracks complex, interrelated objects in an image stack. The key idea in cross-classification is to efficiently turn a clustering problem into a classification problem by running a logarithmic number of independent classifications per image, letting the cross-labeling of these classifications uniquely classify each pixel to the object labels. We apply the 3C mechanism to achieve state-of-the-art accuracy in connectomics -- the nanoscale mapping of neural tissue from electron microscopy volumes. Our reconstruction system increases scalability by an order of magnitude over existing single-object tracking methods (such as flood-filling networks). This scalability is important for the deployment of connectomics pipelines, since currently the best performing techniques require computing infrastructures that are beyond the reach of most laboratories. Our algorithm may offer benefits in other domains that require pixel-accurate tracking of multiple objects, such as segmentation of videos and medical imagery.

David Rolnick, Yaron Meirovitch, Toufiq Parag et al.

Deep learning algorithms for connectomics rely upon localized classification, rather than overall morphology. This leads to a high incidence of erroneously merged objects. Humans, by contrast, can easily detect such errors by acquiring intuition for the correct morphology of objects. Biological neurons have complicated and variable shapes, which are challenging to learn, and merge errors take a multitude of different forms. We present an algorithm, MergeNet, that shows 3D ConvNets can, in fact, detect merge errors from high-level neuronal morphology. MergeNet follows unsupervised training and operates across datasets. We demonstrate the performance of MergeNet both on a variety of connectomics data and on a dataset created from merged MNIST images.

David Rolnick, Andreas Veit, Serge Belongie et al.

Deep neural networks trained on large supervised datasets have led to impressive results in image classification and other tasks. However, well-annotated datasets can be time-consuming and expensive to collect, lending increased interest to larger but noisy datasets that are more easily obtained. In this paper, we show that deep neural networks are capable of generalizing from training data for which true labels are massively outnumbered by incorrect labels. We demonstrate remarkably high test performance after training on corrupted data from MNIST, CIFAR, and ImageNet. For example, on MNIST we obtain test accuracy above 90 percent even after each clean training example has been diluted with 100 randomly-labeled examples. Such behavior holds across multiple patterns of label noise, even when erroneous labels are biased towards confusing classes. We show that training in this regime requires a significant but manageable increase in dataset size that is related to the factor by which correct labels have been diluted. Finally, we provide an analysis of our results that shows how increasing noise decreases the effective batch size.

Shibani Santurkar, David Budden, Nir Shavit

Traditional image and video compression algorithms rely on hand-crafted encoder/decoder pairs (codecs) that lack adaptability and are agnostic to the data being compressed. Here we describe the concept of generative compression, the compression of data using generative models, and suggest that it is a direction worth pursuing to produce more accurate and visually pleasing reconstructions at much deeper compression levels for both image and video data. We also demonstrate that generative compression is orders-of-magnitude more resilient to bit error rates (e.g. from noisy wireless channels) than traditional variable-length coding schemes.

Shibani Santurkar, David Budden, Alexander Matveev et al.

Connectomics is an emerging field in neuroscience that aims to reconstruct the 3-dimensional morphology of neurons from electron microscopy (EM) images. Recent studies have successfully demonstrated the use of convolutional neural networks (ConvNets) for segmenting cell membranes to individuate neurons. However, there has been comparatively little success in high-throughput identification of the intercellular synaptic connections required for deriving connectivity graphs. In this study, we take a compositional approach to segmenting synapses, modeling them explicitly as an intercellular cleft co-located with an asymmetric vesicle density along a cell membrane. Instead of requiring a deep network to learn all natural combinations of this compositionality, we train lighter networks to model the simpler marginal distributions of membranes, clefts and vesicles from just 100 electron microscopy samples. These feature maps are then combined with simple rules-based heuristics derived from prior biological knowledge. Our approach to synapse detection is both more accurate than previous state-of-the-art (7% higher recall and 5% higher F1-score) and yields a 20-fold speed-up compared to the previous fastest implementations. We demonstrate by reconstructing the first complete, directed connectome from the largest available anisotropic microscopy dataset (245 GB) of mouse somatosensory cortex (S1) in just 9.7 hours on a single shared-memory CPU system. We believe that this work marks an important step toward the goal of a microscope-pace streaming connectomics pipeline.

Yaron Meirovitch, Alexander Matveev, Hayk Saribekyan et al.

The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide relatively good accuracy but are unacceptably slow, and would require years to extract connectivity graphs from even a single cubic millimeter of neural tissue. Here we present a viable real-time solution, a multi-pass pipeline optimized for shared-memory multicore systems, capable of processing data at near the terabyte-per-hour pace of multi-beam electron microscopes. The pipeline makes an initial fast-pass over the data, and then makes a second slow-pass to iteratively correct errors in the output of the fast-pass. We demonstrate the accuracy of a sparse slow-pass reconstruction algorithm and suggest new methods for detecting morphological errors. Our fast-pass approach provided many algorithmic challenges, including the design and implementation of novel shallow convolutional neural nets and the parallelization of watershed and object-merging techniques. We use it to reconstruct, from image stack to skeletons, the full dataset of Kasthuri et al. (463 GB capturing 120,000 cubic microns) in a matter of hours on a single multicore machine rather than the weeks it has taken in the past on much larger distributed systems.

David Budden, Alexander Matveev, Shibani Santurkar et al.

Deep convolutional neural networks (ConvNets) of 3-dimensional kernels allow joint modeling of spatiotemporal features. These networks have improved performance of video and volumetric image analysis, but have been limited in size due to the low memory ceiling of GPU hardware. Existing CPU implementations overcome this constraint but are impractically slow. Here we extend and optimize the faster Winograd-class of convolutional algorithms to the $N$-dimensional case and specifically for CPU hardware. First, we remove the need to manually hand-craft algorithms by exploiting the relaxed constraints and cheap sparse access of CPU memory. Second, we maximize CPU utilization and multicore scalability by transforming data matrices to be cache-aware, integer multiples of AVX vector widths. Treating 2-dimensional ConvNets as a special (and the least beneficial) case of our approach, we demonstrate a 5 to 25-fold improvement in throughput compared to previous state-of-the-art.