Traditional approaches to studying decision-making in neuroscience focus on simplified behavioral tasks where animals perform repetitive, stereotyped actions to receive explicit rewards. While informative, these methods constrain our understanding of decision-making to short timescale behaviors driven by explicit goals. In natural environments, animals exhibit more complex, long-term behaviors driven by intrinsic motivations that are often unobservable. Recent works in time-varying inverse reinforcement learning (IRL) aim to capture shifting motivations in long-term, freely moving behaviors. However, a crucial challenge remains: animals make decisions based on their history, not just their current state. To address this, we introduce SWIRL (SWitching IRL), a novel framework that extends traditional IRL by incorporating time-varying, history-dependent reward functions. SWIRL models long behavioral sequences as transitions between short-term decision-making processes, each governed by a unique reward function. SWIRL incorporates biologically plausible history dependency to capture how past decisions and environmental contexts shape behavior, offering a more accurate description of animal decision-making. We apply SWIRL to simulated and real-world animal behavior datasets and show that it outperforms models lacking history dependency, both quantitatively and qualitatively. This work presents the first IRL model to incorporate history-dependent policies and rewards to advance our understanding of complex, naturalistic decision-making in animals.

Understanding and constructing brain communications that capture dynamic communications across multiple regions is fundamental to modern system neuroscience, yet current methods struggle to find time-varying region-level communications or scale to large neural datasets with long recording durations. We present a novel framework using Markovian Gaussian Processes to learn brain communications with time-varying temporal delays from multi-region neural recordings, named Adaptive Delay Model (ADM). Our method combines Gaussian Processes with State Space Models and employs parallel scan inference algorithms, enabling efficient scaling to large datasets while identifying concurrent communication patterns that evolve over time. This time-varying approach captures how brain region interactions shift dynamically during cognitive processes. Validated on synthetic and multi-region neural recordings datasets, our approach discovers both the directionality and temporal dynamics of neural communication. This work advances our understanding of distributed neural computation and provides a scalable tool for analyzing dynamic brain networks.

Fairness in artificial intelligence has garnered increasing attention due to concerns about discriminatory AI-based decision-making, prompting the development of numerous mitigation approaches. However, most existing methods assume that demographic information is readily available, which may not align with real-world scenarios where such information is often incomplete. To this end, this paper tackles the pervasive yet overlooked challenge of developing fair machine learning algorithms with limited demographics. Specifically, we explore leveraging limited demographic information to accurately infer missing demographics while simultaneously evaluating and optimizing model fairness. We argue that this approach better aligns with common real-world socially sensitive scenarios involving limited demographics. Extensive experiments on three benchmark datasets highlight the effectiveness of the proposed method, surpassing state-of-the-art with significant gains in fairness while maintaining comparable utility.

Latent heat flux (LE) is pivotal in the regional water-energy nexus, exemplifying complex interplays between atmosphere and land surface. Thermal infrared (TIR) land surface temperature (LST) offers direct and vital information for estimating LE through the single-source energy balance method. Nevertheless, variations in the viewing angles of remote sensing sensors can introduce angular effects in the retrieval of LST, potentially causing significant incompatibility issues in estimating LE. To alleviate this uncertainty, we adopt a viable approach by using two composited LSTs derived from the integration of soil and vegetation component temperatures from Sentinel-3 SLSTR, combined with fraction vegetation coverage (FVC) obtained from both the GEOV2 FVC product and MODIS LAI-derived estimates. This composited LST was subsequently used as one of the inputs of a single-source energy balance system (SEBS) model driven by measured meteorological and ERA5 reanalysis data in Heihe River Basin in China during 2016-2022, respectively. The results demonstrate that two types of composited LST reduced the root mean square error (RMSE) of estimated LE by 4.8 W/m2and 8.8 W/m2, respectively, by using measured meteorological data; and using ERA5 meteorological data, the RMSE was reduced by 6.8 W/m2and 11.0 W/m2, respectively. Regardless of the meteorological data and FVC used, the RMSE for all stations assessed in the study decreased. This indicates that by partially mitigating the angular effects of TIR LST, improvements in TIR-based surface LE estimation can be achieved over regional scales.

Current timestamp-supervised temporal action segmentation (TS-TAS) methods typically follow a two-phase pipeline: initializing the model with timestamp labels and refining it with pseudo-labels. However, limited by the sparsity of timestamp annotations, current methods' performance is sub-optimal. Specifically, initializing the model with only timestamp annotations may cause overfitting to labeled frames. Additionally, sparse timestamp annotations cannot capture the diverse action representations throughout the whole instance, especially those near the ambiguous action boundaries, leading to pseudo-label noise. Inspired by the cluster assumption of semi-supervised learning (SSL) that points within the same manifold likely share the same label, we here model TS-TAS as an SSL problem. Specifically, we propose a Temporal Embedding Consistency (TEC) strategy to mitigate the excessive focus on annotated frames. The TEC strategy encourages frames with similar representations within the video to have similar classification probability distributions, thereby propagating labeled frames' information to implicit ones. Besides, we design a TS-Mix strategy to further leverage unlabeled data to mitigate the influence of pseudo-label noise in a consistency regularization manner. The TS-Mix strategy includes intra-mix, which adds linear interpolation of two adjacent timestamps to every frame between them, and inter-mix, which mixes frames from two different untrimmed videos frame-by-frame. Then the mixed video is trained with the correspondingly mixed pseudo-labels. Comprehensive experimental results on different benchmarks show that we achieve new state-of-the-art performances. Furthermore, the proposed method can seamlessly enhance existing methods, significantly improving their performances.

Electroencephalography (EEG) plays a crucial role in neuroscience research and clinical practice, but it remains limited by nonuniform data, noise, and difficulty in labeling. To address these challenges, we develop a pretraining framework named DMAE-EEG, a denoising masked autoencoder for mining generalizable spatiotemporal representation from massive unlabeled EEG. First, we propose a novel brain region topological heterogeneity (BRTH) division method to partition the nonuniform data into fixed patches based on neuroscientific priors. Second, we design a denoised pseudo-label generator (DPLG), which utilizes a denoising reconstruction pretext task to enable the learning of generalizable representations from massive unlabeled EEG, suppressing the influence of noise and artifacts. Furthermore, we utilize an asymmetric autoencoder with self-attention as the backbone in the proposed DMAE-EEG, which captures long-range spatiotemporal dependencies and interactions from unlabeled EEG data across 14 public datasets. The proposed DMAE-EEG is validated on both generative (signal quality enhancement) and discriminative tasks (motion intention recognition). In the quality enhancement, DMAE-EEG outperforms existing statistical methods with normalized mean squared error (nMSE) reduction of 27.78%-50.00% under corruption levels of 25%, 50%, and 75%, respectively. In motion intention recognition, DMAE-EEG achieves a relative improvement of 2.71%-6.14% in intrasession classification balanced accuracy across 2-6 class motor execution and imagery tasks, outperforming state-of-the-art methods. Overall, the results suggest that the pretraining framework DMAE-EEG can capture generalizable spatiotemporal representations from massive unlabeled EEG and enhance the knowledge transferability across sessions, subjects, and tasks in various downstream scenarios, advancing EEG-aided diagnosis and brain-computer communication and control, and other clinical practice.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional connectivity. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional connectivity can change over time. To model dynamically changing functional connectivity, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional connectivities are shaped and confined by the underlying anatomical connectome. Here, we propose two novel prior-informed state-switching GLMs, called Gaussian HMM-GLM (Gaussian prior) and one-hot HMM-GLM (Gumbel-Softmax one-hot prior). We show that the learned prior should capture the state-invariant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood, and enhance the interpretability of interaction patterns and hidden states when applied to real neural data. The code is available at \url{https://github.com/JerrySoybean/onehot-hmmglm}.

Studying the complex interactions between different brain regions is crucial in neuroscience. Various statistical methods have explored the latent communication across multiple brain regions. Two main categories are the Gaussian Process (GP) and Linear Dynamical System (LDS), each with unique strengths. The GP-based approach effectively discovers latent variables with frequency bands and communication directions. Conversely, the LDS-based approach is computationally efficient but lacks powerful expressiveness in latent representation. In this study, we merge both methodologies by creating an LDS mirroring a multi-output GP, termed Multi-Region Markovian Gaussian Process (MRM-GP). Our work establishes a connection between an LDS and a multi-output GP that explicitly models frequencies and phase delays within the latent space of neural recordings. Consequently, the model achieves a linear inference cost over time points and provides an interpretable low-dimensional representation, revealing communication directions across brain regions and separating oscillatory communications into different frequency bands.

The partially observable generalized linear model (POGLM) is a powerful tool for understanding neural connectivities under the assumption of existing hidden neurons. With spike trains only recorded from visible neurons, existing works use variational inference to learn POGLM meanwhile presenting the difficulty of learning this latent variable model. There are two main issues: (1) the sampled Poisson hidden spike count hinders the use of the pathwise gradient estimator in VI; and (2) the existing design of the variational model is neither expressive nor time-efficient, which further affects the performance. For (1), we propose a new differentiable POGLM, which enables the pathwise gradient estimator, better than the score function gradient estimator used in existing works. For (2), we propose the forward-backward message-passing sampling scheme for the variational model. Comprehensive experiments show that our differentiable POGLMs with our forward-backward message passing produce a better performance on one synthetic and two real-world datasets. Furthermore, our new method yields more interpretable parameters, underscoring its significance in neuroscience.

Enabling bipedal walking robots to learn how to maneuver over highly uneven, dynamically changing terrains is challenging due to the complexity of robot dynamics and interacted environments. Recent advancements in learning from demonstrations have shown promising results for robot learning in complex environments. While imitation learning of expert policies has been well-explored, the study of learning expert reward functions is largely under-explored in legged locomotion. This paper brings state-of-the-art Inverse Reinforcement Learning (IRL) techniques to solving bipedal locomotion problems over complex terrains. We propose algorithms for learning expert reward functions, and we subsequently analyze the learned functions. Through nonlinear function approximation, we uncover meaningful insights into the expert’s locomotion strategies. Furthermore, we empirically demonstrate that training a bipedal locomotion policy with the inferred reward functions enhances its walking performance on unseen terrains, highlighting the adaptability offered by reward learning.

Evapotranspiration (ET) plays an important role in water resources, crop management and other fields. Thermal infrared (TIR) land surface temperature (LST) provides essential information for estimating ET by using single-source energy balance method. Nevertheless, variations in the viewing angles of remote sensing sensors can introduce angular effects in the retrieval of LST, potentially causing significant incompatibility issues in estimating ET. To alleviate this uncertainty, we adopt a viable approach by using two composited LSTs derived from the integration of soil and vegetation component temperatures based on Sentinel-3 SLSTR and two kinds of fraction vegetation coverage data. This composited LST was subsequently applied in a single-source energy balance system (SEBS) model driven by measured and ERA5 reanalysis meteorological data in Heihe River Basin in China, respectively. The results demonstrate that our improved approach with two kinds of composited LST reduced the root mean square error (RMSE) of estimated ET by 4.84 W/m2 and 8.81 W/m2 using measured meteorological data driven model; and using ERA5 meteorological data driven model, the RMSE was reduced by 6.78 W/m2 and 10.97 W/m2, with a reduction observed at each site.

Understanding the neural basis of behavior is a fundamental goal in neuroscience. Current research in large-scale neuro-behavioral data analysis often relies on decoding models, which quantify behavioral information in neural data but lack details on behavior encoding. This raises an intriguing scientific question: "how can we enable in-depth exploration of neural representations in behavioral tasks, revealing interpretable neural dynamics associated with behaviors". However, addressing this issue is challenging due to the varied behavioral encoding across different brain regions and mixed selectivity at the population level. To tackle this limitation, our approach, named ("BeNeDiff"), first identifies a fine-grained and disentangled neural subspace using a behavior-informed latent variable model. It then employs state-of-the-art generative diffusion models to synthesize behavior videos that interpret the neural dynamics of each latent factor. We validate the method on multi-session datasets containing widefield calcium imaging recordings across the dorsal cortex. Through guiding the diffusion model to activate individual latent factors, we verify that the neural dynamics of latent factors in the disentangled neural subspace provide interpretable quantifications of the behaviors of interest. At the same time, the neural subspace in BeNeDiff demonstrates high disentanglement and neural reconstruction quality.

We study the problem of Inverse Reinforcement Learning (IRL) with an average-reward criterion. The goal is to recover an unknown policy and a reward function when the agent only has samples of states and actions from an experienced agent. Previous IRL methods assume that the expert is trained in a discounted environment, and the discount factor is known. This work alleviates this assumption by proposing an average-reward framework with efficient learning algorithms. We develop novel stochastic first-order methods to solve the IRL problem under the average-reward setting, which requires solving an Average-reward Markov Decision Process (AMDP) as a subproblem. To solve the subproblem, we develop a Stochastic Policy Mirror Descent (SPMD) method under general state and action spaces that needs $\mathcal{O}(1/\varepsilon)$ steps of gradient computation. Equipped with SPMD, we propose the Inverse Policy Mirror Descent (IPMD) method for solving the IRL problem with a $\mathcal{O}(1/\varepsilon^2)$ complexity. To the best of our knowledge, the aforementioned complexity results are new in IRL with the average reward criterion. Finally, we corroborate our analysis with numerical experiments using the MuJoCo benchmark and additional control tasks.

Ship detection receives increasing concerns as an essential ocean mission. Recently, deep learning (DL) has greatly improved ship detection accuracy from traditional methods. However, most of exist methods only utilize single source data, there are still some challenges that influence the ship detection performance. Therefore, we propose a highlight foreground and local scale features network (HFL-Net) for cross-domain ship detection to solve the problems of complex inshore background interferences and multi-scale ship feature differences. It is evaluated on two datasets with three other state-of-the-art methods and the experimental results confirm the superiority ofHFL-Net.

Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting in an increased need for computer vision algorithms that extract useful information from video data. Here we introduce a new video analysis tool that combines the output of supervised pose estimation algorithms (e.g. DeepLabCut) with unsupervised dimensionality reduction methods to produce interpretable, low-dimensional representations of behavioral videos that extract more information than pose estimates alone. We demonstrate this tool by extracting interpretable behavioral features from videos of three different head-fixed mouse preparations, as well as a freely moving mouse in an open field arena, and show how these interpretable features can facilitate downstream behavioral and neural analyses. We also show how the behavioral features produced by our model improve the precision and interpretation of these downstream analyses compared to using the outputs of either fully supervised or fully unsupervised methods alone.

Noninvasive behavioral tracking of animals is crucial for many scientific investigations. Recent transfer learning approaches for behavioral tracking have considerably advanced the state of the art. Typically these methods treat each video frame and each object to be tracked independently. In this work, we improve on these methods (particularly in the regime of few training labels) by leveraging the rich spatiotemporal structures pervasive in behavioral video --- specifically, the spatial statistics imposed by physical constraints (e.g., paw to elbow distance), and the temporal statistics imposed by smoothness from frame to frame. We propose a probabilistic graphical model built on top of deep neural networks, Deep Graph Pose (DGP), to leverage these useful spatial and temporal constraints, and develop an efficient structured variational approach to perform inference in this model. The resulting semi-supervised model exploits both labeled and unlabeled frames to achieve significantly more accurate and robust tracking while requiring users to label fewer training frames. In turn, these tracking improvements enhance performance on downstream applications, including robust unsupervised segmentation of behavioral syllables,'' and estimation of interpretabledisentangled'' low-dimensional representations of the full behavioral video. Open source code is available at \href{\CodeLink}{https://github.com/paninski-lab/deepgraphpose}.

In many problem settings, parameter vectors are not merely sparse but dependent in such a way that non-zero coefficients tend to cluster together. We refer to this form of dependency as “region sparsity.” Classical sparse regression methods, such as the lasso and automatic relevance determination (ARD), which model parameters as independent a priori, and therefore do not exploit such dependencies. Here we introduce a hierarchical model for smooth, region-sparse weight vectors and tensors in a linear regression setting. Our approach represents a hierarchical extension of the relevance determination framework, where we add a transformed Gaussian process to model the dependencies between the prior variances of regression weights. We combine this with a structured model of the prior variances of Fourier coefficients, which eliminates unnecessary high frequencies. The resulting prior encourages weights to be region-sparse in two different bases simultaneously. We develop Laplace approximation and Monte Carlo Markov Chain (MCMC) sampling to provide efficient inference for the posterior. Furthermore, a two-stage convex relaxation of the Laplace approximation approach is also provided to relax the inevitable non-convexity during the optimization. We finally show substantial improvements over comparable methods for both simulated and real datasets from brain imaging.

A major difficulty in studying the neural mechanisms underlying olfactory perception is the lack of obvious structure in the relationship between odorants and the neural activity patterns they elicit. Here we use odor-evoked responses in piriform cortex to identify a latent manifold specifying latent distance relationships between olfactory stimuli. Our approach is based on the Gaussian process latent variable model, and seeks to map odorants to points in a low-dimensional embedding space, where distances between points in the embedding space relate to the similarity of population responses they elicit. The model is specified by an explicit continuous mapping from a latent embedding space to the space of high-dimensional neural population firing rates via nonlinear tuning curves, each parametrized by a Gaussian process. Population responses are then generated by the addition of correlated, odor-dependent Gaussian noise. We fit this model to large-scale calcium fluorescence imaging measurements of population activity in layers 2 and 3 of mouse piriform cortex following the presentation of a diverse set of odorants. The model identifies a low-dimensional embedding of each odor, and a smooth tuning curve over the latent embedding space that accurately captures each neuron's response to different odorants. The model captures both signal and noise correlations across more than 500 neurons. We validate the model using a cross-validation analysis known as co-smoothing to show that the model can accurately predict the responses of a population of held-out neurons to test odorants.

A large body of recent work focuses on methods for extracting low-dimensional latent structure from multi-neuron spike train data. Most such methods employ either linear latent dynamics or linear mappings from latent space to log spike rates. Here we propose a doubly nonlinear latent variable model that can identify low-dimensional structure underlying apparently high-dimensional spike train data. We introduce the Poisson Gaussian-Process Latent Variable Model (P-GPLVM), which consists of Poisson spiking observations and two underlying Gaussian processes—one governing a temporal latent variable and another governing a set of nonlinear tuning curves. The use of nonlinear tuning curves enables discovery of low-dimensional latent structure even when spike responses exhibit high linear dimensionality (e.g., as found in hippocampal place cell codes). To learn the model from data, we introduce the decoupled Laplace approximation, a fast approximate inference method that allows us to efficiently optimize the latent path while marginalizing over tuning curves. We show that this method outperforms previous Laplace-approximation-based inference methods in both the speed of convergence and accuracy. We apply the model to spike trains recorded from hippocampal place cells and show that it compares favorably to a variety of previous methods for latent structure discovery, including variational auto-encoder (VAE) based methods that parametrize the nonlinear mapping from latent space to spike rates with a deep neural network.

Subunit models provide a powerful yet parsimonious description of neural spike responses to complex stimuli. They can be expressed by a cascade of two linear-nonlinear (LN) stages, with the first linear stage defined by convolution with one or more filters. Recent interest in such models has surged due to their biological plausibility and accuracy for characterizing early sensory responses. However, fitting subunit models poses a difficult computational challenge due to the expense of evaluating the log-likelihood and the ubiquity of local optima. Here we address this problem by forging a theoretical connection between spike-triggered covariance analysis and nonlinear subunit models. Specifically, we show that a ''convolutional'' decomposition of the spike-triggered average (STA) and covariance (STC) provides an asymptotically efficient estimator for the subunit model under certain technical conditions. We also prove the identifiability of such convolutional decomposition under mild assumptions. Our moment-based methods outperform highly regularized versions of the GQM on neural data from macaque primary visual cortex, and achieves nearly the same prediction performance as the full maximum-likelihood estimator, yet with substantially lower cost.