arXiv subjects

Matthew Cook

Publications and source records attributed to Matthew Cook.

At least 19 recordsLinked to original sources

arXiv2026

Forward and reverse delay-driven hippocampal replay without symmetric plasticity

Hippocampal replay is a phenomenon observed in mammals and songbirds where neural activation sequences experienced during wakeful periods are repeated during rest or sleep. This mechanism is believed to play a crucial role in episodic memory consolidation, retrieval, and planning. Interestingly, replay can occur in both forward and reverse temporal orders and across a wide range of increased speeds. The learning of activation sequences has traditionally been modeled by temporally asymmetric Hebbian plasticity rules, which explain replay as a chain of activity. The inability of such rules to strengthen backward connections has led to the widespread belief that they cannot account for bidirectional replay. Existing theoretical work therefore explains reverse replay through symmetric connections, which would be formed through symmetric plasticity rules. We propose a delay-coupled neural field model of CA3, where activity propagates as a wave in a ring, and replays occur both forwards and backwards at different speeds. Our model can learn bidirectional replay after a single noisy exposure to a stimulus with either symmetric or asymmetric plasticity. We derive a low-dimensional description of the dynamics and analyze the stability of possible replay speeds.

q-bio.NC↗

arXiv2026

Investigation of GeSn aspect ratio trapping growth up to 8% Sn

Aspect ratio trapping (ART) growth of germanium-tin (GeSn) is a promising approach to target important objectives on the quest towards commercialization of complementary metal-oxide-semiconductor (CMOS)-compatible GeSn optoelectronics devices. Its local growth on patterned substrate allows for versatile device integration into photonics integrated circuit or for stand-alone structure like focal plane array imager. Additionally, high aspect ratio from nano-sized window can terminate early threading dislocation propagation on the oxide sidewalls, leaving subsequent growth defect-free and potentially improving the device performance. Knowledge remains missing regarding GeSn ART growth kinetics, morphology and how they evolve from thin film growth, with successful growth itself yet to be demonstrated. In this work, we report GeSn ART growth up to 8% Sn. Two configurations -- self-induced Ge core/GeSn shell for Sn content between 6% and 8%, and bulk GeSn ART for Sn content below 1% -- are observed. We present a comprehensive study on GeSn ART growth kinetics through different growth rounds and designs, showing a link between pyramid shape of ART island and successful Sn incorporation, as well as the role of growth selectivity and local heating.

cond-mat.mtrl-sci↗

arXiv2026

Study of GeSn Selective Area Growth with Demonstration of SWIR Light Detection

As germanium-tin (GeSn) epitaxial growth quality continuously improves, the search for an efficient integration strategy of GeSn optoelectronics devices into complementary metal-oxide-semiconductor (CMOS) manufacturing line also accelerates. Selective area growth (SAG) on patterned substrate emerges as a promising approach for this quest, with locally controlled growth of GeSn laser/detector suitable for either co-integration with silicon-based waveguide structure or stand-alone module like focal plane array. In this work, we report successful GeSn SAG with Sn content ranging from 3.2% to 8.7% of good optical quality, with demonstration of tunable GeSn SAG photoluminescence and GeSn SAG photoconductor device, the latter with detection cutoff wavelength up to 2 um. In addition, we present a comprehensive study of GeSn SAG condition at different window sizes, from 2 um to 100 um, and shapes: circle, square, octagon, and rectangle. Presence of loading effect is revealed, where GeSn growth rate increases as pattern fill factor and window size shrink. It introduces a different growth condition compared to thin film growth, which can weaken or inhibit Sn incorporation at very small window size and induce Sn segregation in high Sn content SAG growth.

physics.app-ph↗

arXiv2026

Diagnosing Generalization Failures in Fine-Tuned LLMs: A Cross-Architectural Study on Phishing Detection

The practice of fine-tuning Large Language Models (LLMs) has achieved state-of-the-art performance on specialized tasks, yet diagnosing why these models become brittle and fail to generalize remains a critical open problem. To address this, we introduce and apply a multi-layered diagnostic framework to a cross-architectural study. We fine-tune Llama 3.1 8B, Gemma 2 9B, and Mistral models on a high-stakes phishing detection task and use SHAP analysis and mechanistic interpretability to uncover the root causes of their generalization failures. Our investigation reveals three critical findings: (1) Generalization is driven by a powerful synergy between architecture and data diversity. The Gemma 2 9B model achieves state-of-the-art performance (>91\% F1), but only when trained on a stylistically diverse ``generalist'' dataset. (2) Generalization is highly architecture-dependent. We diagnose a specific failure mode in Llama 3.1 8B, which performs well on a narrow domain but cannot integrate diverse data, leading to a significant performance drop. (3) Some architectures are inherently more generalizable. The Mistral model proves to be a consistent and resilient performer across multiple training paradigms. By pinpointing the flawed heuristics responsible for these failures, our work provides a concrete methodology for diagnosing and understanding generalization failures, underscoring that reliable AI requires deep validation of the interplay between architecture, data, and training strategy.

cs.AI↗

arXiv2025

WaveDriver: a Laser Guide Star AO System for HWO

HWO's Tier 1 Contrast Stability Technology Gap presents a key challenge for technology development in the coming years, requiring to a >100x more stable system than JWST. WaveDriver is a concept for a laser guide star spacecraft coupled to an adaptive optics (AO) system onboard HWO that would enable HWO to reach its picometer-level wavefront stability requirements while relaxing other HWO subsystem requirements. At LLNL and UCSC we are revisiting the concept initially proposed by Douglas et al. (2019). We present results from our project's first year, including (1) AO control developments, including with Linear Quadratic Gaussian control and machine learning, (2) AO wavefront sensor (WFS) trade study simulations, and (3) simulations, fabrication, and testing of a 133-port photonic lantern WFS/spectrograph. A key finding from our work is that WaveDriver could be needed to enable HWO's primary mirror segment stability and/or low order wavefront stability requirements.

astro-ph.IM↗

arXiv2025

Universality Frontier for Asynchronous Cellular Automata

In this work, we investigate the computational aspects of asynchronous cellular automata (ACAs), a modification of cellular automata in which cells update independently, following an asynchronous schedule. We introduce flip automata networks (FAN), a simple modification of automata networks that remain robust under any asynchronous update schedule. We show that asynchronous automata can efficiently simulate their synchronous counterparts with a linear memory overhead, which improves upon the previously established quadratic bound. Additionally, we address the universality gap for (a)synchronous cellular automata -- the boundary separating universal and non-universal automata, which is still not fully understood. We tighten this boundary by proving that all one-way asynchronous automata lack universal computational power. Conversely, we establish the existence of a universal 6-state first-neighbor automaton in one dimension and a 3-state von Neumann automaton in two dimensions, which represent the smallest known universal constructions to date.

cs.FL↗

arXiv2024

Learning Equivariant Maps with Variational Quantum Circuits

Geometric quantum machine learning uses the symmetries inherent in data to design tailored machine learning tasks with reduced search space dimension. The field has been well-studied recently in an effort to avoid barren plateau issues while improving the accuracy of quantum machine learning models. This work explores the related problem of learning an equivariant map given two unitary representations of a finite group, which in turn allows the symmetric embedding of the data to be learned rather than simply required. Moreover, this procedure allows the learning of covariant quantum channels, which are an essential tool in quantum information theory. We demonstrate the feasibility of this task and give examples to illustrate the procedure.

quant-ph↗

arXiv2024

Learning with SASQuaTCh: a Novel Variational Quantum Transformer Architecture with Kernel-Based Self-Attention

The recent exploding growth in size of state-of-the-art machine learning models highlights a well-known issue where exponential parameter growth, which has grown to trillions as in the case of the Generative Pre-trained Transformer (GPT), leads to training time and memory requirements which limit their advancement in the near term. The predominant models use the so-called transformer network and have a large field of applicability, including predicting text and images, classification, and even predicting solutions to the dynamics of physical systems. Here we present a variational quantum circuit architecture named Self-Attention Sequential Quantum Transformer Channel (SASQuaTCh), which builds networks of qubits that perform analogous operations of the transformer network, namely the keystone self-attention operation, and leads to an exponential improvement in parameter complexity and run-time complexity over its classical counterpart. Our approach leverages recent insights from kernel-based operator learning in the context of predicting spatiotemporal systems to represent deep layers of a vision transformer network using simple gate operations and a set of multi-dimensional quantum Fourier transforms. To validate our approach, we consider image classification tasks in simulation and with hardware, where with only 9 qubits and a handful of parameters we are able to simultaneously embed and classify a grayscale image of handwritten digits with high accuracy.

quant-ph↗

arXiv2023

Omitted Labels Induce Nontransitive Paradoxes in Causality

We explore "omitted label contexts," in which training data is limited to a subset of the possible labels. This setting is standard among specialized human experts or specific, focused studies. By studying Simpson's paradox, we observe that ``correct'' adjustments sometimes require non-exchangeable treatment and control groups. A generalization of Simpson's paradox leads us to study networks of conclusions drawn from different contexts, within which a paradox of nontransitivity arises. We prove that the space of possible nontransitive structures in these networks exactly corresponds to structures that form from aggregating ranked-choice votes.

cs.LG↗

arXiv2022

k-Means Maximum Entropy Exploration

Exploration in high-dimensional, continuous spaces with sparse rewards is an open problem in reinforcement learning. Artificial curiosity algorithms address this by creating rewards that lead to exploration. Given a reinforcement learning algorithm capable of maximizing rewards, the problem reduces to finding an optimization objective consistent with exploration. Maximum entropy exploration uses the entropy of the state visitation distribution as such an objective. However, efficiently estimating the entropy of the state visitation distribution is challenging in high-dimensional, continuous spaces. We introduce an artificial curiosity algorithm based on lower bounding an approximation to the entropy of the state visitation distribution. The bound relies on a result we prove for non-parametric density estimation in arbitrary dimensions using k-means. We show that our approach is both computationally efficient and competitive on benchmarks for exploration in high-dimensional, continuous spaces, especially on tasks where reinforcement learning algorithms are unable to find rewards.

cs.LG↗

arXiv2021

Small tile sets that compute while solving mazes

We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we call it the Maze-Walking Tile Assembly Model. The model has a number of implementation prospects, one being DNA strands that attach to a DNA origami substrate. Intuitively, the model suggests a separation of signal routing and computation: the input structure (maze) supplies a routing diagram, and the programmer's tile set provides the computational ability. We ask how simple the computational part can be. We give two tiny tile sets that are computationally universal in the Maze-Walking Tile Assembly Model. The first has four tiles and simulates Boolean circuits by directly implementing NAND, NXOR and NOT gates. Our second tile set has 6 tiles and is called the Collatz tile set as it produces patterns found in binary/ternary representations of iterations of the Collatz function. Using computer search we find that the Collatz tile set is expressive enough to encode Boolean circuits using blocks of these patterns. These two tile sets give two different methods to find simple universal tile sets, and provide motivation for using pre-assembled maze structures as circuit wiring diagrams in molecular self-assembly based computing.

cs.ET↗

arXiv2020

Microtubule Tracking in Electron Microscopy Volumes

We present a method for microtubule tracking in electron microscopy volumes. Our method first identifies a sparse set of voxels that likely belong to microtubules. Similar to prior work, we then enumerate potential edges between these voxels, which we represent in a candidate graph. Tracks of microtubules are found by selecting nodes and edges in the candidate graph by solving a constrained optimization problem incorporating biological priors on microtubule structure. For this, we present a novel integer linear programming formulation, which results in speed-ups of three orders of magnitude and an increase of 53% in accuracy compared to prior art (evaluated on three 1.2 x 4 x 4$\mu$m volumes of Drosophila neural tissue). We also propose a scheme to solve the optimization problem in a block-wise fashion, which allows distributed tracking and is necessary to process very large electron microscopy volumes. Finally, we release a benchmark dataset for microtubule tracking, here used for training, testing and validation, consisting of eight 30 x 1000 x 1000 voxel blocks (1.2 x 4 x 4$\mu$m) of densely annotated microtubules in the CREMI data set (https://github.com/nilsec/micron).

cs.CV↗

arXiv2020

Outlier Detection through Null Space Analysis of Neural Networks

Many machine learning classification systems lack competency awareness. Specifically, many systems lack the ability to identify when outliers (e.g., samples that are distinct from and not represented in the training data distribution) are being presented to the system. The ability to detect outliers is of practical significance since it can help the system behave in an reasonable way when encountering unexpected data. In prior work, outlier detection is commonly carried out in a processing pipeline that is distinct from the classification model. Thus, for a complete system that incorporates outlier detection and classification, two models must be trained, increasing the overall complexity of the approach. In this paper we use the concept of the null space to integrate an outlier detection method directly into a neural network used for classification. Our method, called Null Space Analysis (NuSA) of neural networks, works by computing and controlling the magnitude of the null space projection as data is passed through a network. Using these projections, we can then calculate a score that can differentiate between normal and abnormal data. Results are shown that indicate networks trained with NuSA retain their classification performance while also being able to detect outliers at rates similar to commonly used outlier detection algorithms.

cs.LG↗

arXiv2020

Efficient 2D neuron boundary segmentation with local topological constraints

We present a method for segmenting neuron membranes in 2D electron microscopy imagery. This segmentation task has been a bottleneck to reconstruction efforts of the brain's synaptic circuits. One common problem is the misclassification of blurry membrane fragments as cell interior, which leads to merging of two adjacent neuron sections into one via the blurry membrane region. Human annotators can easily avoid such errors by implicitly performing gap completion, taking into account the continuity of membranes. Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data. Based on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.

cs.CV↗

arXiv2020

Estimation of Z-Thickness and XY-Anisotropy of Electron Microscopy Images using Gaussian Processes

Serial section electron microscopy (ssEM) is a widely used technique for obtaining volumetric information of biological tissues at nanometer scale. However, accurate 3D reconstructions of identified cellular structures and volumetric quantifications require precise estimates of section thickness and anisotropy (or stretching) along the XY imaging plane. In fact, many image processing algorithms simply assume isotropy within the imaging plane. To ameliorate this problem, we present a method for estimating thickness and stretching of electron microscopy sections using non-parametric Bayesian regression of image statistics. We verify our thickness and stretching estimates using direct measurements obtained by atomic force microscopy (AFM) and show that our method has a lower estimation error compared to a recent indirect thickness estimation method as well as a relative Z coordinate estimation method. Furthermore, we have made the first dataset of ssSEM images with directly measured section thickness values publicly available for the evaluation of indirect thickness estimation methods.

eess.IV↗

arXiv2019

FireNet: Real-time Segmentation of Fire Perimeter from Aerial Video

In this paper, we share our approach to real-time segmentation of fire perimeter from aerial full-motion infrared video. We start by describing the problem from a humanitarian aid and disaster response perspective. Specifically, we explain the importance of the problem, how it is currently resolved, and how our machine learning approach improves it. To test our models we annotate a large-scale dataset of 400,000 frames with guidance from domain experts. Finally, we share our approach currently deployed in production with inference speed of 20 frames per second and an accuracy of 92 (F1 Score).

cs.CV↗

arXiv2019

Comparison of Possibilistic Fuzzy Local Information C-Means and Possibilistic K-Nearest Neighbors for Synthetic Aperture Sonar Image Segmentation

Synthetic aperture sonar (SAS) imagery can generate high resolution images of the seafloor. Thus, segmentation algorithms can be used to partition the images into different seafloor environments. In this paper, we compare two possibilistic segmentation approaches. Possibilistic approaches allow for the ability to detect novel or outlier environments as well as well known classes. The Possibilistic Fuzzy Local Information C-Means (PFLICM) algorithm has been previously applied to segment SAS imagery. Additionally, the Possibilistic K-Nearest Neighbors (PKNN) algorithm has been used in other domains such as landmine detection and hyperspectral imagery. In this paper, we compare the segmentation performance of a semi-supervised approach using PFLICM and a supervised method using Possibilistic K-NN. We include final segmentation results on multiple SAS images and a quantitative assessment of each algorithm.

eess.IV↗

arXiv2018

Synaptic partner prediction from point annotations in insect brains

High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identi- fied as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple post- synaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more ex- pensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3% fewer errors than the next best method.

cs.CV↗