arXiv subjects

Kristofer E. Bouchard

Publications and source records attributed to Kristofer E. Bouchard.

16 recordsLinked to original sources

arXiv2026

Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation

Multimodal models that jointly reason over protein sequences, structures, and function annotations within a unified representation hold immense potential for integrating multimodal data and generating new proteins with designed functional properties. To utilize transformer architectures, such models require a tokenizer that converts protein structure from continuous atomic coordinates into discrete representations suitable for scalable multimodal training. The quality of such models are fundamentally upper bounded by the fidelity and expressiveness of the underlying tokenized structure. However, existing tokenizers prioritize reconstruction over generative abilities. To address these gaps, we introduce Yeti, a simple and compact protein structure tokenizer based on lookup free quantization and trained end to end with a flow matching objective for multimodal learning. Compared to existing models, Yeti generally achieves the best codebook utilization and token diversity, and second best reconstruction accuracy (with 10x fewer parameters than ESM3) on diverse datasets. To validate Yeti's generative capability, we trained a compact multimodal model jointly over its structure tokens and amino acid sequence entirely from scratch, with no pretrained initialization. The resulting multimodal model generates plausible structures under unconditional cogeneration of protein sequence and structures, achieving comparable results to 10x larger models. Together, these results demonstrate that Yeti is a compact and expressive protein structure tokenizer suitable for training multimodal models that cogenerates highly plausible sequences and structures.

q-bio.BM↗

arXiv2025

Sparse and Low-bias Estimation of High Dimensional Vector Autoregressive Models

Vector autoregressive (VAR) models are widely used for causal discovery and forecasting in multivariate time series analysis. In the high-dimensional setting, which is increasingly common in fields such as neuroscience and econometrics, model parameters are inferred by L1-regularized maximum likelihood (RML). A well-known feature of RML inference is that in general the technique produces a trade-off between sparsity and bias that depends on the choice of the regularization hyperparameter. In the context of multivariate time series analysis, sparse estimates are favorable for causal discovery and low-bias estimates are favorable for forecasting. However, owing to a paucity of research on hyperparameter selection methods, practitioners must rely on ad-hoc methods such as cross-validation (or manual tuning). The particular balance that such approaches achieve between the two goals -- causal discovery and forecasting -- is poorly understood. Our paper investigates this behavior and proposes a method (UoI-VAR) that achieves a better balance between sparsity and bias when the underlying causal influences are in fact sparse. We demonstrate through simulation that RML with a hyperparameter selected by cross-validation tends to overfit, producing relatively dense estimates. We further demonstrate that UoI-VAR much more effectively approximates the correct sparsity pattern with only a minor compromise in model fit, particularly so for larger data dimensions, and that the estimates produced by UoI-VAR exhibit less bias. We conclude that our method achieves improved performance especially well-suited to applications involving simultaneous causal discovery and forecasting in high-dimensional settings.

stat.ME↗

arXiv2024

Identifying Feedforward and Feedback Controllable Subspaces of Neural Population Dynamics

There is overwhelming evidence that cognition, perception, and action rely on feedback control. However, if and how neural population dynamics are amenable to different control strategies is poorly understood, in large part because machine learning methods to directly assess controllability in neural population dynamics are lacking. To address this gap, we developed a novel dimensionality reduction method, Feedback Controllability Components Analysis (FCCA), that identifies subspaces of linear dynamical systems that are most feedback controllable based on a new measure of feedback controllability. We further show that PCA identifies subspaces of linear dynamical systems that maximize a measure of feedforward controllability. As such, FCCA and PCA are data-driven methods to identify subspaces of neural population data (approximated as linear dynamical systems) that are most feedback and feedforward controllable respectively, and are thus natural contrasts for hypothesis testing. We developed new theory that proves that non-normality of underlying dynamics determines the divergence between FCCA and PCA solutions, and confirmed this in numerical simulations. Applying FCCA to diverse neural population recordings, we find that feedback controllable dynamics are geometrically distinct from PCA subspaces and are better predictors of animal behavior. Our methods provide a novel approach towards analyzing neural population dynamics from a control theoretic perspective, and indicate that feedback controllable subspaces are important for behavior.

q-bio.NC↗

arXiv2024

Methods for Linking Data to Online Resources and Ontologies with Applications to Neurophysiology

Across many domains, large swaths of digital assets are being stored across distributed data repositories, e.g., the DANDI Archive [8]. The distribution and diversity of these repositories impede researchers from formally defining terminology within experiments, integrating information across datasets, and easily querying, reusing, and analyzing data that follow the FAIR principles [15]. As such, it has become increasingly important to have a standardized method to attach contextual metadata to datasets. Neuroscience is an exemplary use case of this issue due to the complex multimodal nature of experiments. Here, we present the HDMF External Resources Data (HERD) standard and related tools, enabling researchers to annotate new and existing datasets by mapping external references to the data without requiring modification of the original dataset. We integrated HERD closely with Neurodata Without Borders (NWB) [2], a widely used data standard for sharing and storing neurophysiology data. By integrating with NWB, our tools provide neuroscientists with the capability to more easily create and manage neurophysiology data in compliance with controlled sets of terms, enhancing rigor and accuracy of data and facilitating data reuse.

cs.DB↗

arXiv2024

The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies

The Artificial Intelligence Ontology (AIO) is a systematization of artificial intelligence (AI) concepts, methodologies, and their interrelations. Developed via manual curation, with the additional assistance of large language models (LLMs), AIO aims to address the rapidly evolving landscape of AI by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for AIO includes AI researchers, developers, and educators seeking standardized terminology and concepts within the AI domain. The ontology is structured around six top-level branches: Networks, Layers, Functions, LLMs, Preprocessing, and Bias, each designed to support the modular composition of AI methods and facilitate a deeper understanding of deep learning architectures and ethical considerations in AI. AIO's development utilized the Ontology Development Kit (ODK) for its creation and maintenance, with its content being dynamically updated through AI-driven curation support. This approach not only ensures the ontology's relevance amidst the fast-paced advancements in AI but also significantly enhances its utility for researchers, developers, and educators by simplifying the integration of new AI concepts and methodologies. The ontology's utility is demonstrated through the annotation of AI methods data in a catalog of AI research publications and the integration into the BioPortal ontology resource, highlighting its potential for cross-disciplinary research. The AIO ontology is open source and is available on GitHub (https://github.com/berkeleybop/artificial-intelligence-ontology) and BioPortal (https://bioportal.bioontology.org/ontologies/AIO).

cs.LG↗

arXiv2023

AutoCT: Automated CT registration, segmentation, and quantification

The processing and analysis of computed tomography (CT) imaging is important for both basic scientific development and clinical applications. In AutoCT, we provide a comprehensive pipeline that integrates an end-to-end automatic preprocessing, registration, segmentation, and quantitative analysis of 3D CT scans. The engineered pipeline enables atlas-based CT segmentation and quantification leveraging diffeomorphic transformations through efficient forward and inverse mappings. The extracted localized features from the deformation field allow for downstream statistical learning that may facilitate medical diagnostics. On a lightweight and portable software platform, AutoCT provides a new toolkit for the CT imaging community to underpin the deployment of artificial intelligence-driven applications.

eess.IV↗

arXiv2023

FAIR for AI: An interdisciplinary and international community building perspective

A foundational set of findable, accessible, interoperable, and reusable (FAIR) principles were proposed in 2016 as prerequisites for proper data management and stewardship, with the goal of enabling the reusability of scholarly data. The principles were also meant to apply to other digital assets, at a high level, and over time, the FAIR guiding principles have been re-interpreted or extended to include the software, tools, algorithms, and workflows that produce data. FAIR principles are now being adapted in the context of AI models and datasets. Here, we present the perspectives, vision, and experiences of researchers from different countries, disciplines, and backgrounds who are leading the definition and adoption of FAIR principles in their communities of practice, and discuss outcomes that may result from pursuing and incentivizing FAIR AI research. The material for this report builds on the FAIR for AI Workshop held at Argonne National Laboratory on June 7, 2022.

cs.CY↗

arXiv2021

Hangul Fonts Dataset: a Hierarchical and Compositional Dataset for Investigating Learned Representations

Hierarchy and compositionality are common latent properties in many natural and scientific datasets. Determining when a deep network's hidden activations represent hierarchy and compositionality is important both for understanding deep representation learning and for applying deep networks in domains where interpretability is crucial. However, current benchmark machine learning datasets either have little hierarchical or compositional structure, or the structure is not known. This gap impedes precise analysis of a network's representations and thus hinders development of new methods that can learn such properties. To address this gap, we developed a new benchmark dataset with known hierarchical and compositional structure. The Hangul Fonts Dataset (HFD) is comprised of 35 fonts from the Korean writing system (Hangul), each with 11,172 blocks (syllables) composed from the product of initial consonant, medial vowel, and final consonant glyphs. All blocks can be grouped into a few geometric types which induces a hierarchy across blocks. In addition, each block is composed of individual glyphs with rotations, translations, scalings, and naturalistic style variation across fonts. We find that both shallow and deep unsupervised methods only show modest evidence of hierarchy and compositionality in their representations of the HFD compared to supervised deep networks. Supervised deep network representations contain structure related to the geometrical hierarchy of the characters, but the compositional structure of the data is not evident. Thus, HFD enables the identification of shortcomings in existing methods, a critical first step toward developing new machine learning algorithms to extract hierarchical and compositional structure in the context of naturalistic variability.

cs.CV↗

arXiv2020

Critical Point-Finding Methods Reveal Gradient-Flat Regions of Deep Network Losses

Despite the fact that the loss functions of deep neural networks are highly non-convex, gradient-based optimization algorithms converge to approximately the same performance from many random initial points. One thread of work has focused on explaining this phenomenon by characterizing the local curvature near critical points of the loss function, where the gradients are near zero, and demonstrating that neural network losses enjoy a no-bad-local-minima property and an abundance of saddle points. We report here that the methods used to find these putative critical points suffer from a bad local minima problem of their own: they often converge to or pass through regions where the gradient norm has a stationary point. We call these gradient-flat regions, since they arise when the gradient is approximately in the kernel of the Hessian, such that the loss is locally approximately linear, or flat, in the direction of the gradient. We describe how the presence of these regions necessitates care in both interpreting past results that claimed to find critical points of neural network losses and in designing second-order methods for optimizing neural networks.

cs.LG↗

arXiv2019

Unsupervised Discovery of Temporal Structure in Noisy Data with Dynamical Components Analysis

Linear dimensionality reduction methods are commonly used to extract low-dimensional structure from high-dimensional data. However, popular methods disregard temporal structure, rendering them prone to extracting noise rather than meaningful dynamics when applied to time series data. At the same time, many successful unsupervised learning methods for temporal, sequential and spatial data extract features which are predictive of their surrounding context. Combining these approaches, we introduce Dynamical Components Analysis (DCA), a linear dimensionality reduction method which discovers a subspace of high-dimensional time series data with maximal predictive information, defined as the mutual information between the past and future. We test DCA on synthetic examples and demonstrate its superior ability to extract dynamical structure compared to commonly used linear methods. We also apply DCA to several real-world datasets, showing that the dimensions extracted by DCA are more useful than those extracted by other methods for predicting future states and decoding auxiliary variables. Overall, DCA robustly extracts dynamical structure in noisy, high-dimensional data while retaining the computational efficiency and geometric interpretability of linear dimensionality reduction methods.

cs.IT↗

arXiv2019

Numerically Recovering the Critical Points of a Deep Linear Autoencoder

Numerically locating the critical points of non-convex surfaces is a long-standing problem central to many fields. Recently, the loss surfaces of deep neural networks have been explored to gain insight into outstanding questions in optimization, generalization, and network architecture design. However, the degree to which recently-proposed methods for numerically recovering critical points actually do so has not been thoroughly evaluated. In this paper, we examine this issue in a case for which the ground truth is known: the deep linear autoencoder. We investigate two sub-problems associated with numerical critical point identification: first, because of large parameter counts, it is infeasible to find all of the critical points for contemporary neural networks, necessitating sampling approaches whose characteristics are poorly understood; second, the numerical tolerance for accurately identifying a critical point is unknown, and conservative tolerances are difficult to satisfy. We first identify connections between recently-proposed methods and well-understood methods in other fields, including chemical physics, economics, and algebraic geometry. We find that several methods work well at recovering certain information about loss surfaces, but fail to take an unbiased sample of critical points. Furthermore, numerical tolerance must be very strict to ensure that numerically-identified critical points have similar properties to true analytical critical points. We also identify a recently-published Newton method for optimization that outperforms previous methods as a critical point-finding algorithm. We expect our results will guide future attempts to numerically study critical points in large nonlinear neural networks.

cs.LG↗

arXiv2018

Spiking Linear Dynamical Systems on Neuromorphic Hardware for Low-Power Brain-Machine Interfaces

Neuromorphic architectures achieve low-power operation by using many simple spiking neurons in lieu of traditional hardware. Here, we develop methods for precise linear computations in spiking neural networks and use these methods to map the evolution of a linear dynamical system (LDS) onto an existing neuromorphic chip: IBM's TrueNorth. We analytically characterize, and numerically validate, the discrepancy between the spiking LDS state sequence and that of its non-spiking counterpart. These analytical results shed light on the multiway tradeoff between time, space, energy, and accuracy in neuromorphic computation. To demonstrate the utility of our work, we implemented a neuromorphic Kalman filter (KF) and used it for offline decoding of human vocal pitch from neural data. The neuromorphic KF could be used for low-power filtering in domains beyond neuroscience, such as navigation or robotics.

cs.NE↗

arXiv2018

Deep learning as a tool for neural data analysis: speech classification and cross-frequency coupling in human sensorimotor cortex

A fundamental challenge in neuroscience is to understand what structure in the world is represented in spatially distributed patterns of neural activity from multiple single-trial measurements. This is often accomplished by learning a simple, linear transformations between neural features and features of the sensory stimuli or motor task. While successful in some early sensory processing areas, linear mappings are unlikely to be ideal tools for elucidating nonlinear, hierarchical representations of higher-order brain areas during complex tasks, such as the production of speech by humans. Here, we apply deep networks to predict produced speech syllables from cortical surface electric potentials recorded from human sensorimotor cortex. We found that deep networks had higher decoding prediction accuracy compared to baseline models, and also exhibited greater improvements in accuracy with increasing dataset size. We further demonstrate that deep network's confusions revealed hierarchical latent structure in the neural data, which recapitulated the underlying articulatory nature of speech motor control. Finally, we used deep networks to compare task-relevant information in different neural frequency bands, and found that the high-gamma band contains the vast majority of information relevant for the speech prediction task, with little-to-no additional contribution from lower-frequencies. Together, these results demonstrate the utility of deep networks as a data analysis tool for neuroscience.

cs.NE↗

arXiv2017

Union of Intersections (UoI) for Interpretable Data Driven Discovery and Prediction

The increasing size and complexity of scientific data could dramatically enhance discovery and prediction for basic scientific applications. Realizing this potential, however, requires novel statistical analysis methods that are both interpretable and predictive. We introduce Union of Intersections (UoI), a flexible, modular, and scalable framework for enhanced model selection and estimation. Methods based on UoI perform model selection and model estimation through intersection and union operations, respectively. We show that UoI-based methods achieve low-variance and nearly unbiased estimation of a small number of interpretable features, while maintaining high-quality prediction accuracy. We perform extensive numerical investigation to evaluate a UoI algorithm ($UoI_{Lasso}$) on synthetic and real data. In doing so, we demonstrate the extraction of interpretable functional networks from human electrophysiology recordings as well as accurate prediction of phenotypes from genotype-phenotype data with reduced features. We also show (with the $UoI_{L1Logistic}$ and $UoI_{CUR}$ variants of the basic framework) improved prediction parsimony for classification and matrix factorization on several benchmark biomedical data sets. These results suggest that methods based on the UoI framework could improve interpretation and prediction in data-driven discovery across scientific fields.

stat.ML↗

arXiv2015

Bootstrapped Adaptive Threshold Selection for Statistical Model Selection and Estimation

A central goal of neuroscience is to understand how activity in the nervous system is related to features of the external world, or to features of the nervous system itself. A common approach is to model neural responses as a weighted combination of external features, or vice versa. The structure of the model weights can provide insight into neural representations. Often, neural input-output relationships are sparse, with only a few inputs contributing to the output. In part to account for such sparsity, structured regularizers are incorporated into model fitting optimization. However, by imposing priors, structured regularizers can make it difficult to interpret learned model parameters. Here, we investigate a simple, minimally structured model estimation method for accurate, unbiased estimation of sparse models based on Bootstrapped Adaptive Threshold Selection followed by ordinary least-squares refitting (BoATS). Through extensive numerical investigations, we show that this method often performs favorably compared to L1 and L2 regularizers. In particular, for a variety of model distributions and noise levels, BoATS more accurately recovers the parameters of sparse models, leading to more parsimonious explanations of outputs. Finally, we apply this method to the task of decoding human speech production from ECoG recordings.

stat.ML↗

arXiv2015

An adapting auditory-motor feedback loop can contribute to generating vocal repetition

Consecutive repetition of actions is common in behavioral sequences. Although integration of sensory feedback with internal motor programs is important for sequence generation, if and how feedback contributes to repetitive actions is poorly understood. Here we study how auditory feedback contributes to generating repetitive syllable sequences in songbirds. We propose that auditory signals provide positive feedback to ongoing motor commands, but this influence decays as feedback weakens from response adaptation during syllable repetitions. Computational models show that this mechanism explains repeat distributions observed in Bengalese finch song. We experimentally confirmed two predictions of this mechanism in Bengalese finches: removal of auditory feedback by deafening reduces syllable repetitions; and neural responses to auditory playback of repeated syllable sequences gradually adapt in sensory-motor nucleus HVC. Together, our results implicate a positive auditory-feedback loop with adaptation in generating repetitive vocalizations, and suggest sensory adaptation is important for feedback control of motor sequences.

q-bio.NC↗