arXiv subjects

Kristofer Bouchard

Publications and source records attributed to Kristofer Bouchard.

11 recordsLinked to original sources

arXiv2025

Robust electron counting for direct electron detectors with the Back-Propagation Counting method

Electron microscopy (EM) is a foundational tool for directly assessing the structure of materials. Recent advances in direct electron detectors have improved signal-to noise ratios via single-electron counting. However, accurately counting electrons at high fluence remains challenging. We developed a new method of electron counting for direct electron detectors, Back-Propagation Counting (BPC). BPC uses machine learning techniques designed for mathematical operations on large tensors but does not require large training datasets. In synthetic data, we show BPC is able to count multiple electron strikes per pixel and is robust to increasing occupancy. In experimental data, frames counted with BPC are shown to reconstruct diffraction peaks corresponding to individual nanoparticles with relatively higher intensity and produce images with improved contrast when compared to a standard counting method. Together, these results show that BPC excels in experiments where pixels see a high flux of electron irradiation such as in situ TEM movies and diffraction.

physics.ins-det↗

arXiv2024

Towards Reverse-Engineering the Brain: Brain-Derived Neuromorphic Computing Approach with Photonic, Electronic, and Ionic Dynamicity in 3D integrated circuits

The human brain has immense learning capabilities at extreme energy efficiencies and scale that no artificial system has been able to match. For decades, reverse engineering the brain has been one of the top priorities of science and technology research. Despite numerous efforts, conventional electronics-based methods have failed to match the scalability, energy efficiency, and self-supervised learning capabilities of the human brain. On the other hand, very recent progress in the development of new generations of photonic and electronic memristive materials, device technologies, and 3D electronic-photonic integrated circuits (3D EPIC ) promise to realize new brain-derived neuromorphic systems with comparable connectivity, density, energy-efficiency, and scalability. When combined with bio-realistic learning algorithms and architectures, it may be possible to realize an 'artificial brain' prototype with general self-learning capabilities. This paper argues the possibility of reverse-engineering the brain through architecting a prototype of a brain-derived neuromorphic computing system consisting of artificial electronic, ionic, photonic materials, devices, and circuits with dynamicity resembling the bio-plausible molecular, neuro/synaptic, neuro-circuit, and multi-structural hierarchical macro-circuits of the brain based on well-tested computational models. We further argue the importance of bio-plausible local learning algorithms applicable to the neuromorphic computing system that capture the flexible and adaptive unsupervised and self-supervised learning mechanisms central to human intelligence. Most importantly, we emphasize that the unique capabilities in brain-derived neuromorphic computing prototype systems will enable us to understand links between specific neuronal and network-level properties with system-level functioning and behavior.

cs.ET↗

arXiv2022

Perspectives for self-driving labs in synthetic biology

Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior. However, the level of investment required for the creation of biological SDLs is only warranted if directed towards solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.

q-bio.OT↗

arXiv2022

Compressed Predictive Information Coding

Unsupervised learning plays an important role in many fields, such as artificial intelligence, machine learning, and neuroscience. Compared to static data, methods for extracting low-dimensional structure for dynamic data are lagging. We developed a novel information-theoretic framework, Compressed Predictive Information Coding (CPIC), to extract useful representations from dynamic data. CPIC selectively projects the past (input) into a linear subspace that is predictive about the compressed data projected from the future (output). The key insight of our framework is to learn representations by minimizing the compression complexity and maximizing the predictive information in latent space. We derive variational bounds of the CPIC loss which induces the latent space to capture information that is maximally predictive. Our variational bounds are tractable by leveraging bounds of mutual information. We find that introducing stochasticity in the encoder robustly contributes to better representation. Furthermore, variational approaches perform better in mutual information estimation compared with estimates under a Gaussian assumption. We demonstrate that CPIC is able to recover the latent space of noisy dynamical systems with low signal-to-noise ratios, and extracts features predictive of exogenous variables in neuroscience data.

cs.LG↗

arXiv2021

Learning from learning machines: a new generation of AI technology to meet the needs of science

We outline emerging opportunities and challenges to enhance the utility of AI for scientific discovery. The distinct goals of AI for industry versus the goals of AI for science create tension between identifying patterns in data versus discovering patterns in the world from data. If we address the fundamental challenges associated with "bridging the gap" between domain-driven scientific models and data-driven AI learning machines, then we expect that these AI models can transform hypothesis generation, scientific discovery, and the scientific process itself.

cs.LG↗

arXiv2021

Stochastic Collapsed Variational Inference for Structured Gaussian Process Regression Network

This paper presents an efficient variational inference framework for deriving a family of structured gaussian process regression network (SGPRN) models. The key idea is to incorporate auxiliary inducing variables in latent functions and jointly treats both the distributions of the inducing variables and hyper-parameters as variational parameters. Then we propose structured variable distributions and marginalize latent variables, which enables the decomposability of a tractable variational lower bound and leads to stochastic optimization. Our inference approach is able to model data in which outputs do not share a common input set with a computational complexity independent of the size of the inputs and outputs and thus easily handle datasets with missing values. We illustrate the performance of our method on synthetic data and real datasets and show that our model generally provides better imputation results on missing data than the state-of-the-art. We also provide a visualization approach for time-varying correlation across outputs in electrocoticography data and those estimates provide insight to understand the neural population dynamics.

cs.LG↗

arXiv2021

Bayesian Inference in High-Dimensional Time-Serieswith the Orthogonal Stochastic Linear Mixing Model

Many modern time-series datasets contain large numbers of output response variables sampled for prolonged periods of time. For example, in neuroscience, the activities of 100s-1000's of neurons are recorded during behaviors and in response to sensory stimuli. Multi-output Gaussian process models leverage the nonparametric nature of Gaussian processes to capture structure across multiple outputs. However, this class of models typically assumes that the correlations between the output response variables are invariant in the input space. Stochastic linear mixing models (SLMM) assume the mixture coefficients depend on input, making them more flexible and effective to capture complex output dependence. However, currently, the inference for SLMMs is intractable for large datasets, making them inapplicable to several modern time-series problems. In this paper, we propose a new regression framework, the orthogonal stochastic linear mixing model (OSLMM) that introduces an orthogonal constraint amongst the mixing coefficients. This constraint reduces the computational burden of inference while retaining the capability to handle complex output dependence. We provide Markov chain Monte Carlo inference procedures for both SLMM and OSLMM and demonstrate superior model scalability and reduced prediction error of OSLMM compared with state-of-the-art methods on several real-world applications. In neurophysiology recordings, we use the inferred latent functions for compact visualization of population responses to auditory stimuli, and demonstrate superior results compared to a competing method (GPFA). Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale time-series datasets.

cs.LG↗

arXiv2021

Numerical Characterization of Support Recovery in Sparse Regression with Correlated Design

Sparse regression is frequently employed in diverse scientific settings as a feature selection method. A pervasive aspect of scientific data that hampers both feature selection and estimation is the presence of strong correlations between predictive features. These fundamental issues are often not appreciated by practitioners, and jeapordize conclusions drawn from estimated models. On the other hand, theoretical results on sparsity-inducing regularized regression such as the Lasso have largely addressed conditions for selection consistency via asymptotics, and disregard the problem of model selection, whereby regularization parameters are chosen. In this numerical study, we address these issues through exhaustive characterization of the performance of several regression estimators, coupled with a range of model selection strategies. These estimators and selection criteria were examined across correlated regression problems with varying degrees of signal to noise, distribution of the non-zero model coefficients, and model sparsity. Our results reveal a fundamental tradeoff between false positive and false negative control in all regression estimators and model selection criteria examined. Additionally, we are able to numerically explore a transition point modulated by the signal-to-noise ratio and spectral properties of the design covariance matrix at which the selection accuracy of all considered algorithms degrades. Overall, we find that SCAD coupled with BIC or empirical Bayes model selection performs the best feature selection across the regression problems considered.

stat.ME↗

arXiv2019

Provably convergent acceleration in factored gradient descent with applications in matrix sensing

We present theoretical results on the convergence of \emph{non-convex} accelerated gradient descent in matrix factorization models with $\ell_2$-norm loss. The purpose of this work is to study the effects of acceleration in non-convex settings, where provable convergence with acceleration should not be considered a \emph{de facto} property. The technique is applied to matrix sensing problems, for the estimation of a rank $r$ optimal solution $X^\star \in \mathbb{R}^{n \times n}$. Our contributions can be summarized as follows. $i)$ We show that acceleration in factored gradient descent converges at a linear rate; this fact is novel for non-convex matrix factorization settings, under common assumptions. $ii)$ Our proof technique requires the acceleration parameter to be carefully selected, based on the properties of the problem, such as the condition number of $X^\star$ and the condition number of objective function. $iii)$ Currently, our proof leads to the same dependence on the condition number(s) in the contraction parameter, similar to recent results on non-accelerated algorithms. $iv)$ Acceleration is observed in practice, both in synthetic examples and in two real applications: neuronal multi-unit activities recovery from single electrode recordings, and quantum state tomography on quantum computing simulators.

cs.LG↗

arXiv2018

Optimizing the Union of Intersections LASSO ($UoI_{LASSO}$) and Vector Autoregressive ($UoI_{VAR}$) Algorithms for Improved Statistical Estimation at Scale

The analysis of scientific data of increasing size and complexity requires statistical machine learning methods that are both interpretable and predictive. Union of Intersections (UoI), a recently developed framework, is a two-step approach that separates model selection and model estimation. A linear regression algorithm based on UoI, $UoI_{LASSO}$, simultaneously achieves low false positives and low false negative feature selection as well as low bias and low variance estimates. Together, these qualities make the results both predictive and interpretable. In this paper, we optimize the $UoI_{LASSO}$ algorithm for single-node execution on NERSC's Cori Knights Landing, a Xeon Phi based supercomputer. We then scale $UoI_{LASSO}$ to execute on cores ranging from 68-278,528 cores on a range of dataset sizes demonstrating the weak and strong scaling of the implementation. We also implement a variant of $UoI_{LASSO}$, $UoI_{VAR}$ for vector autoregressive models, to analyze high dimensional time-series data. We perform single node optimization and multi-node scaling experiments for $UoI_{VAR}$ to demonstrate the effectiveness of the algorithm for weak and strong scaling. Our implementations enable to use estimate the largest VAR model (1000 nodes) we are aware of, and apply it to large neurophysiology data 192 nodes).

cs.LG↗

arXiv2015

Modeling neural activity at the ensemble level

Here we demonstrate that the activity of neural ensembles can be quantitatively modeled. We first show that an ensemble dynamical model (EDM) accurately approximates the distribution of voltages and average firing rate per neuron of a population of simulated integrate-and-fire neurons. EDMs are high-dimensional nonlinear dynamical models. To faciliate the estimation of their parameters we present a dimensionality reduction method and study its performance with simulated data. We then introduce and evaluate a maximum-likelihood method to estimate connectivity parameters in networks of EDMS. Finally, we show that this model an methods accurately approximate the high-gamma power evoked by pure tones in the auditory cortex of rodents. Overall, this article demonstrates that quantitatively modeling brain activity at the ensemble level is indeed possible, and opens the way to understanding the computations performed by neural ensembles, which could revolutionarize our understanding of brain function.

q-bio.NC↗