Xue-Xin Wei

Dehong Xu, Ruiqi Gao, Wen-Hao Zhang et al.

The activity of the grid cell population in the medial entorhinal cortex (MEC) of the mammalian brain forms a vector representation of the self-position of the animal. Recurrent neural networks have been proposed to explain the properties of the grid cells by updating the neural activity vector based on the velocity input of the animal. In doing so, the grid cell system effectively performs path integration. In this paper, we investigate the algebraic, geometric, and topological properties of grid cells using recurrent network models. Algebraically, we study the Lie group and Lie algebra of the recurrent transformation as a representation of self-motion. Geometrically, we study the conformal isometry of the Lie group representation where the local displacement of the activity vector in the neural space is proportional to the local displacement of the agent in the 2D physical space. Topologically, the compact abelian Lie group representation automatically leads to the torus topology commonly assumed and observed in neuroscience. We then focus on a simple non-linear recurrent model that underlies the continuous attractor neural networks of grid cells. Our numerical experiments show that conformal isometry leads to hexagon periodic patterns in the grid cell responses and our model is capable of accurate path integration. Code is available at \url{https://github.com/DehongXu/grid-cell-rnn}.

Hua-Dong Xiong, Li Ji-An, Robert C. Wilson et al.

Large language models (LLMs) exhibit remarkable flexibility: they can adapt to novel tasks from in-context examples without any parameter updates, a capability known as in-context learning (ICL). Prior work on synthetic tasks has shown that ICL can implement specific algorithms, demonstrating architectural competence, and mechanistic analyses have identified key circuits that support this behavior. However, because in-context computation -- regardless of its algorithmic form -- relies on transformations in high-dimensional representation space, it remains unclear how the geometry of that space shapes ICL effectiveness. Motivated by the neuroscience view of classification as the untangling of neural representations, we hypothesize that ICL depends on the successful online untangling of task-relevant representations. To test this idea, we study how LLMs classify in-context examples whose labels are defined by the model's own internal representations with known structure. We show that ICL performance correlates systematically with the representational structure of the underlying classification task and that successful ICL is accompanied by geometric reorganization that increases online separability. We further find that LLM behavior is well described by a prototype-like algorithm that integrates evidence while reshaping representations to support classification. These findings offer a geometric account of ICL in pretrained LLMs, establish representational geometry as a mechanistic constraint on ICL, and quantify the gap between what pretrained representations afford and what in-context learning can exploit.

Dehong Xu, Ruiqi Gao, Wen-Hao Zhang et al.

Grid cells in the entorhinal cortex of mammalian brains exhibit striking hexagon grid firing patterns in their response maps as the animal (e.g., a rat) navigates in a 2D open environment. In this paper, we study the emergence of the hexagon grid patterns of grid cells based on a general recurrent neural network (RNN) model that captures the navigation process. The responses of grid cells collectively form a high dimensional vector, representing the 2D self-position of the agent. As the agent moves, the vector is transformed by an RNN that takes the velocity of the agent as input. We propose a simple yet general conformal normalization of the input velocity of the RNN, so that the local displacement of the position vector in the high-dimensional neural space is proportional to the local displacement of the agent in the 2D physical space, regardless of the direction of the input velocity. We apply this mechanism to both a linear RNN and nonlinear RNNs. Theoretically, we provide an understanding that explains the connection between conformal normalization and the emergence of hexagon grid patterns. Empirically, we conduct extensive experiments to verify that conformal normalization is crucial for the emergence of hexagon grid patterns, across various types of RNNs. The learned patterns share similar profiles to biological grid cells, and the topological properties of the patterns also align with our theoretical understanding.

Hua-Dong Xiong, Li Ji-An, Jiaqi Huang et al.

Intelligent systems must maintain and manipulate task-relevant information online to adapt to dynamic environments and changing goals. This capacity, known as working memory, is fundamental to human reasoning and intelligence. Despite having on the order of 100 billion neurons, both biological and artificial systems exhibit limitations in working memory. This raises a key question: why do large language models (LLMs) show such limitations, given that transformers have full access to prior context through attention? We find that although a two-layer transformer can be trained to solve working memory tasks perfectly, a diverse set of pretrained LLMs continues to show working memory limitations. Notably, LLMs reproduce interference signatures observed in humans: performance degrades with increasing memory load and is biased by recency and stimulus statistics. Across models, stronger working memory capacity correlates with broader competence on standard benchmarks, mirroring its link to general intelligence in humans. Yet despite substantial variability in working memory performance, LLMs surprisingly converge on a common computational mechanism. Rather than directly copying the relevant memory item from context, models encode multiple memory items in entangled representations, such that successful recall depends on interference control -- actively suppressing task-irrelevant content to isolate the target for readout. Moreover, a targeted intervention that suppresses stimulus content information improves performance, providing causal support for representational interference. Together, these findings identify representational interference as a core constraint on working memory in pretrained LLMs, suggesting that working-memory limits in biological and artificial systems may reflect a shared computational challenge: selecting task-relevant information under interference.

Ruiqi Gao, Jianwen Xie, Xue-Xin Wei et al.

Understanding how grid cells perform path integration calculations remains a fundamental problem. In this paper, we conduct theoretical analysis of a general representation model of path integration by grid cells, where the 2D self-position is encoded as a higher dimensional vector, and the 2D self-motion is represented by a general transformation of the vector. We identify two conditions on the transformation. One is a group representation condition that is necessary for path integration. The other is an isotropic scaling condition that ensures locally conformal embedding, so that the error in the vector representation translates conformally to the error in the 2D self-position. Then we investigate the simplest transformation, i.e., the linear transformation, uncover its explicit algebraic and geometric structure as matrix Lie group of rotation, and explore the connection between the isotropic scaling condition and a special class of hexagon grid patterns. Finally, with our optimization-based approach, we manage to learn hexagon grid patterns that share similar properties of the grid cells in the rodent brain. The learned model is capable of accurate long distance path integration. Code is available at https://github.com/ruiqigao/grid-cell-path.

Elizabeth Pavlova, Xue-Xin Wei

Recent work on diffusion models proposed that they operate in two regimes: memorization, in which models reproduce their training data, and generalization, in which they generate novel samples. While this has been tested in high-noise settings, the behavior of diffusion models as effective denoisers when the corruption level is small remains unclear. To address this gap, we systematically investigated the behavior of diffusion models under low-noise diffusion dynamics, with implications for model robustness and interpretability. Using (i) CelebA subsets of varying sample sizes and (ii) analytic Gaussian mixture benchmarks, we reveal that models trained on disjoint data diverge near the data manifold even when their high-noise outputs converge. We quantify how training set size, data geometry, and model objective choice shape denoising trajectories and affect score accuracy, providing insights into how these models actually learn representations of data distributions. This work starts to address gaps in our understanding of generative model reliability in practical applications where small perturbations are common.

Xin Tong, Thi Thu Uyen Hoang, Xue-Xin Wei et al.

Understanding the representation of probability in the human mind has been of great interest to understanding human decision making. Classical paradoxes in decision making suggest that human perception distorts probability magnitudes. Previous accounts postulate a Probability Weighting Function that transforms perceived probabilities; however, its motivation has been debated. Recent work has sought to motivate this function in terms of noisy representations of probabilities in the human mind. Here, we present an account of the Probability Weighting Function grounded in rational inference over optimal decoding from noisy neural encoding of quantities. We show that our model accurately accounts for behavior in a lottery task and a dot counting task. It further accounts for adaptation to a bimodal short-term prior. Taken together, our results provide a unifying account grounding the human representation of probability in rational inference.

Yu, Qian, Wilson S. Geisler et al.

Previous studies have compared the brain and deep neural networks trained on image classification. Intriguingly, while some suggest that their representations are highly similar, others argued the opposite. Here, we propose a new approach to characterize the similarity of the decision strategies of two observers (models or brains) using decision variable correlation (DVC). DVC quantifies the correlation between decoded decisions on individual samples in a classification task and thus can capture task-relevant information rather than general representational alignment. We evaluate this method using monkey V4/IT recordings and models trained on image classification tasks. We find that model--model similarity is comparable to monkey--monkey similarity, whereas model--monkey similarity is consistently lower and, surprisingly, decreases with increasing ImageNet-1k performance. While adversarial training enhances robustness, it does not improve model--monkey similarity in task-relevant dimensions; however, it markedly increases model--model similarity. Similarly, pre-training on larger datasets does not improve model--monkey similarity. These results suggest a fundamental divergence between the task-relevant representations in monkey V4/IT and those learned by models trained on image classification tasks.

Liu Yuezhang, Xue-Xin Wei

Recent findings suggest that diffusion models significantly enhance empirical adversarial robustness. While some intuitive explanations have been proposed, the precise mechanisms underlying these improvements remain unclear. In this work, we systematically investigate how and how well diffusion models improve adversarial robustness. First, we observe that diffusion models intriguingly increase, rather than decrease, the $\ell_p$ distance to clean samples--challenging the intuition that purification denoises inputs closer to the original data. Second, we find that the purified images are heavily influenced by the internal randomness of diffusion models, where a compression effect arises within each randomness configuration. Motivated by this observation, we evaluate robustness under fixed randomness and find that the improvement drops to approximately 24% on CIFAR-10--substantially lower than prior reports approaching 70%. Importantly, we show that this remaining robustness gain strongly correlates with the model's ability to compress the input space, revealing the compression rate as a reliable robustness indicator without requiring gradient-based analysis. Our findings provide novel insights into the mechanisms underlying diffusion-based purification, and offer guidance for developing more effective and principled adversarial purification systems.

Ding Zhou, Xue-Xin Wei

The ability to record activities from hundreds of neurons simultaneously in the brain has placed an increasing demand for developing appropriate statistical techniques to analyze such data. Recently, deep generative models have been proposed to fit neural population responses. While these methods are flexible and expressive, the downside is that they can be difficult to interpret and identify. To address this problem, we propose a method that integrates key ingredients from latent models and traditional neural encoding models. Our method, pi-VAE, is inspired by recent progress on identifiable variational auto-encoder, which we adapt to make appropriate for neuroscience applications. Specifically, we propose to construct latent variable models of neural activity while simultaneously modeling the relation between the latent and task variables (non-neural variables, e.g. sensory, motor, and other externally observable states). The incorporation of task variables results in models that are not only more constrained, but also show qualitative improvements in interpretability and identifiability. We validate pi-VAE using synthetic data, and apply it to analyze neurophysiological datasets from rat hippocampus and macaque motor cortex. We demonstrate that pi-VAE not only fits the data better, but also provides unexpected novel insights into the structure of the neural codes.

Xue-Xin Wei, Ding Zhou, Andres Grosmark et al.

Calcium imaging is a critical tool for measuring the activity of large neural populations. Much effort has been devoted to developing "pre-processing" tools for calcium video data, addressing the important issues of e.g., motion correction, denoising, compression, demixing, and deconvolution. However, statistical modeling of deconvolved calcium signals (i.e., the estimated activity extracted by a pre-processing pipeline) is just as critical for interpreting calcium measurements, and for incorporating these observations into downstream probabilistic encoding and decoding models. Surprisingly, these issues have to date received significantly less attention. In this work we examine the statistical properties of the deconvolved activity estimates, and compare probabilistic models for these random signals. In particular, we propose a zero-inflated gamma (ZIG) model, which characterizes the calcium responses as a mixture of a gamma distribution and a point mass that serves to model zero responses. We apply the resulting models to neural encoding and decoding problems. We find that the ZIG model outperforms simpler models (e.g., Poisson or Bernoulli models) in the context of both simulated and real neural data, and can therefore play a useful role in bridging calcium imaging analysis methods with tools for analyzing activity in large neural populations.

Christopher J. Cueva, Peter Y. Wang, Matthew Chin et al.

Recent work suggests goal-driven training of neural networks can be used to model neural activity in the brain. While response properties of neurons in artificial neural networks bear similarities to those in the brain, the network architectures are often constrained to be different. Here we ask if a neural network can recover both neural representations and, if the architecture is unconstrained and optimized, the anatomical properties of neural circuits. We demonstrate this in a system where the connectivity and the functional organization have been characterized, namely, the head direction circuits of the rodent and fruit fly. We trained recurrent neural networks (RNNs) to estimate head direction through integration of angular velocity. We found that the two distinct classes of neurons observed in the head direction system, the Compass neurons and the Shifter neurons, emerged naturally in artificial neural networks as a result of training. Furthermore, connectivity analysis and in-silico neurophysiology revealed structural and mechanistic similarities between artificial networks and the head direction system. Overall, our results show that optimization of RNNs in a goal-driven task can recapitulate the structure and function of biological circuits, suggesting that artificial neural networks can be used to study the brain at the level of both neural activity and anatomical organization.

Christopher J. Cueva, Xue-Xin Wei

Decades of research on the neural code underlying spatial navigation have revealed a diverse set of neural response properties. The Entorhinal Cortex (EC) of the mammalian brain contains a rich set of spatial correlates, including grid cells which encode space using tessellating patterns. However, the mechanisms and functional significance of these spatial representations remain largely mysterious. As a new way to understand these neural representations, we trained recurrent neural networks (RNNs) to perform navigation tasks in 2D arenas based on velocity inputs. Surprisingly, we find that grid-like spatial response patterns emerge in trained networks, along with units that exhibit other spatial correlates, including border cells and band-like cells. All these different functional types of neurons have been observed experimentally. The order of the emergence of grid-like and border cells is also consistent with observations from developmental studies. Together, our results suggest that grid cells, border cells and others as observed in EC may be a natural solution for representing space efficiently given the predominant recurrent connections in the neural circuits.