arXiv subjects

Richard Gao

Publications and source records attributed to Richard Gao.

11 recordsLinked to original sources

arXiv2026

CoCoT-EEG: Contrastive-Pretrained Multiscale Convolutional Transformer for EEG Decoding

Self-supervised pretrained foundation models (FM) have shown early promise for non-invasive electroencephalogram (EEG) decoding applications. Many recent large-scale models converged on the approach of tokenizing raw EEG followed by masked reconstruction pretraining. However, this recipe has been shown to be suboptimal for data, like EEG, with high noise amplitude and information confined to limited dimensions such as narrow frequency bands. Building on this insight, we develop a novel contrastive-pretrained EEG model with multiscale temporal convolution input layers and Transformer encoder blocks (CoCoT). CoCoT matches or beats state-of-the-art reconstruction-pretrained EEG models on extensive benchmark decoding tasks with heterogeneous electrode configurations. Furthermore, CoCoT trained from scratch outperforms previous single-task decoding models and even rivals pretrained models, showcasing the architecture's flexibility and data efficiency. Through systematic ablations, including model architecture and pretraining objective, we demonstrate the viability of contrastive learning for building EEG FMs while suggesting key architectural design considerations, prompting further investigations in alternative large-scale pretraining strategies.

cs.LG↗

arXiv2026

stable-worldmodel: A Platform for Reproducible World Modeling Research and Evaluation

World models are central to building agents that can reason, plan, and generalize beyond their training data. However, research on world models is currently fragmented, with disparate codebases, data pipelines, and evaluation protocols hindering reproducibility and fair comparison. Current practice is further limited by three key bottlenecks: fragile one-off codebases, slow video data loading, and the lack of standardized generalization benchmarks. We present stable-worldmodel (swm), an open-source platform for standardized and reproducible world modeling research and evaluation. It delivers (1) a high-performance Lance-based data layer with native support and conversion tools for MP4, HDF5, and LeRobot datasets, (2) clean, well-tested implementations of modern world model baselines and planning solvers, and (3) a broad suite of environments and tasks extended with controllable visual, geometric, and physical factors of variation for systematic in-silico evaluation of dynamics understanding, control performance, representation quality, and out-of-distribution generalization. By unifying the full pipeline under a single, scalable framework, \texttt{swm} dramatically reduces research overhead and accelerates trustworthy progress toward reliable world models.

cs.LG↗

arXiv2024

sbi reloaded: a toolkit for simulation-based inference workflows

Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challenge. Simulation-based inference (SBI) addresses this by enabling Bayesian inference for simulators, identifying parameters that match observed data and align with prior knowledge. Unlike traditional Bayesian inference, SBI only needs access to simulations from the model and does not require evaluations of the likelihood function. In addition, SBI algorithms do not require gradients through the simulator, allow for massive parallelization of simulations, and can perform inference for different observations without further simulations or training, thereby amortizing inference. Over the past years, we have developed, maintained, and extended sbi, a PyTorch-based package that implements Bayesian SBI algorithms based on neural networks. The sbi toolkit implements a wide range of inference methods, neural network architectures, sampling methods, and diagnostic tools. In addition, it provides well-tested default settings, but also offers flexibility to fully customize every step of the simulation-based inference workflow. Taken together, the sbi toolkit enables scientists and engineers to apply state-of-the-art SBI methods to black-box simulators, opening up new possibilities for aligning simulations with empirically observed data.

cs.LG↗

arXiv2024

Neural timescales from a computational perspective

Neural activity fluctuates over a wide range of timescales within and across brain areas. Experimental observations suggest that diverse neural timescales reflect information in dynamic environments. However, how timescales are defined and measured from brain recordings vary across the literature. Moreover, these observations do not specify the mechanisms underlying timescale variations, nor whether specific timescales are necessary for neural computation and brain function. Here, we synthesize three directions where computational approaches can distill the broad set of empirical observations into quantitative and testable theories: We review (i) how different data analysis methods quantify timescales across distinct behavioral states and recording modalities, (ii) how biophysical models provide mechanistic explanations for the emergence of diverse timescales, and (iii) how task-performing networks and machine learning models uncover the functional relevance of neural timescales. This integrative computational perspective thus complements experimental investigations, providing a holistic view on how neural timescales reflect the relationship between brain structure, dynamics, and behavior.

q-bio.NC↗

arXiv2024

Latent Diffusion for Neural Spiking Data

Modern datasets in neuroscience enable unprecedented inquiries into the relationship between complex behaviors and the activity of many simultaneously recorded neurons. While latent variable models can successfully extract low-dimensional embeddings from such recordings, using them to generate realistic spiking data, especially in a behavior-dependent manner, still poses a challenge. Here, we present Latent Diffusion for Neural Spiking data (LDNS), a diffusion-based generative model with a low-dimensional latent space: LDNS employs an autoencoder with structured state-space (S4) layers to project discrete high-dimensional spiking data into continuous time-aligned latents. On these inferred latents, we train expressive (conditional) diffusion models, enabling us to sample neural activity with realistic single-neuron and population spiking statistics. We validate LDNS on synthetic data, accurately recovering latent structure, firing rates, and spiking statistics. Next, we demonstrate its flexibility by generating variable-length data that mimics human cortical activity during attempted speech. We show how to equip LDNS with an expressive observation model that accounts for single-neuron dynamics not mediated by the latent state, further increasing the realism of generated samples. Finally, conditional LDNS trained on motor cortical activity during diverse reaching behaviors can generate realistic spiking data given reach direction or unseen reach trajectories. In summary, LDNS simultaneously enables inference of low-dimensional latents and realistic conditional generation of neural spiking datasets, opening up further possibilities for simulating experimentally testable hypotheses.

q-bio.NC↗

arXiv2024

A Practical Guide to Sample-based Statistical Distances for Evaluating Generative Models in Science

Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the samples these models generate? This work aims to provide an accessible entry point to understanding popular sample-based statistical distances, requiring only foundational knowledge in mathematics and statistics. We focus on four commonly used notions of statistical distances representing different methodologies: Using low-dimensional projections (Sliced-Wasserstein; SW), obtaining a distance using classifiers (Classifier Two-Sample Tests; C2ST), using embeddings through kernels (Maximum Mean Discrepancy; MMD), or neural networks (Fr\'echet Inception Distance; FID). We highlight the intuition behind each distance and explain their merits, scalability, complexity, and pitfalls. To demonstrate how these distances are used in practice, we evaluate generative models from different scientific domains, namely a model of decision-making and a model generating medical images. We showcase that distinct distances can give different results on similar data. Through this guide, we aim to help researchers to use, interpret, and evaluate statistical distances for generative models in science.

cs.LG↗

arXiv2024

Sourcerer: Sample-based Maximum Entropy Source Distribution Estimation

Scientific modeling applications often require estimating a distribution of parameters consistent with a dataset of observations - an inference task also known as source distribution estimation. This problem can be ill-posed, however, since many different source distributions might produce the same distribution of data-consistent simulations. To make a principled choice among many equally valid sources, we propose an approach which targets the maximum entropy distribution, i.e., prioritizes retaining as much uncertainty as possible. Our method is purely sample-based - leveraging the Sliced-Wasserstein distance to measure the discrepancy between the dataset and simulations - and thus suitable for simulators with intractable likelihoods. We benchmark our method on several tasks, and show that it can recover source distributions with substantially higher entropy than recent source estimation methods, without sacrificing the fidelity of the simulations. Finally, to demonstrate the utility of our approach, we infer source distributions for parameters of the Hodgkin-Huxley model from experimental datasets with thousands of single-neuron measurements. In summary, we propose a principled method for inferring source distributions of scientific simulator parameters while retaining as much uncertainty as possible.

cs.LG↗

arXiv2023

Generalized Bayesian Inference for Scientific Simulators via Amortized Cost Estimation

Simulation-based inference (SBI) enables amortized Bayesian inference for simulators with implicit likelihoods. But when we are primarily interested in the quality of predictive simulations, or when the model cannot exactly reproduce the observed data (i.e., is misspecified), targeting the Bayesian posterior may be overly restrictive. Generalized Bayesian Inference (GBI) aims to robustify inference for (misspecified) simulator models, replacing the likelihood-function with a cost function that evaluates the goodness of parameters relative to data. However, GBI methods generally require running multiple simulations to estimate the cost function at each parameter value during inference, making the approach computationally infeasible for even moderately complex simulators. Here, we propose amortized cost estimation (ACE) for GBI to address this challenge: We train a neural network to approximate the cost function, which we define as the expected distance between simulations produced by a parameter and observed data. The trained network can then be used with MCMC to infer GBI posteriors for any observation without running additional simulations. We show that, on several benchmark tasks, ACE accurately predicts cost and provides predictive simulations that are closer to synthetic observations than other SBI methods, especially for misspecified simulators. Finally, we apply ACE to infer parameters of the Hodgkin-Huxley model given real intracellular recordings from the Allen Cell Types Database. ACE identifies better data-matching parameters while being an order of magnitude more simulation-efficient than a standard SBI method. In summary, ACE combines the strengths of SBI methods and GBI to perform robust and simulation-amortized inference for scientific simulators.

stat.ML↗

arXiv2021

SoK: Vehicle Orientation Representations for Deep Rotation Estimation

In recent years, there is an influx of deep learning models for 3D vehicle object detection. However, little attention was paid to orientation prediction. Existing research work proposed various vehicle orientation representation methods for deep learning, however a holistic, systematic review has not been conducted. Through our experiments, we categorize and compare the accuracy performance of various existing orientation representations using the KITTI 3D object detection dataset, and propose a new form of orientation representation: Tricosine. Among these, the 2D Cartesian-based representation, or Single Bin, achieves the highest accuracy, with additional channeled inputs (positional encoding and depth map) not boosting prediction performance. Our code is published on GitHub: https://github.com/umd-fire-coml/KITTI-orientation-learning

cs.CV↗

arXiv2021

Systematic benchmarking of HTTPS third party copy on 100Gbps links using XRootD

The High Luminosity Large Hadron Collider provides a data challenge. The amount of data recorded from the experiments and transported to hundreds of sites will see a thirty fold increase in annual data volume. A systematic approach to contrast the performance of different Third Party Copy(TPC) transfer protocols arises. Two contenders, XRootD-HTTPS and the GridFTP are evaluated in their performance for transferring files from one server to an-other over 100Gbps interfaces. The benchmarking is done by scheduling pods on the Pacific Research Platform Kubernetes cluster to ensure reproducible and repeatable results. This opens a future pathway for network testing of any TPC transfer protocol.

cs.DC↗

arXiv2017

Statistical profiling to predict the biosecurity risk presented by non-compliant international passengers

Biosecurity risk material (BRM) presents a clear and significant threat to national and international environmental and economic assets. Intercepting BRM carried by non-compliant international passengers is a key priority of border biosecurity services. Global travel rates are constantly increasing, which complicates this important responsibility, and necessitates judicious intervention. Selection of passengers for intervention is generally performed manually, and the quality of the selection depends on the experience and judgement of the officer making the selection. In this article we report on a case study to assess the predictive ability of statistical profiling methods that predict non-compliance with biosecurity regulations using data obtained from regulatory documents as inputs. We then evaluate the performance arising from using risk predictions to select higher risk passengers for screening. We find that both prediction performance and screening higher risk passengers from regulatory documents are superior to manual and random screening, and recommend that authorities further investigate statistical profiling for efficient intervention of biosecurity risk material on incoming passengers.

stat.AP↗