Josue Ortega Caro

Nikos Karantzas, Emma Besier, Josue Ortega Caro et al.

Despite the enormous success of artificial neural networks (ANNs) in many disciplines, the characterization of their computations and the origin of key properties such as generalization and robustness remain open questions. Recent literature suggests that robust networks with good generalization properties tend to be biased towards processing low frequencies in images. To explore the frequency bias hypothesis further, we develop an algorithm that allows us to learn modulatory masks highlighting the essential input frequencies needed for preserving a trained network's performance. We achieve this by imposing invariance in the loss with respect to such modulations in the input frequencies. We first use our method to test the low-frequency preference hypothesis of adversarially trained or data-augmented networks. Our results suggest that adversarially robust networks indeed exhibit a low-frequency bias but we find this bias is also dependent on directions in frequency space. However, this is not necessarily true for other types of data augmentation. Our results also indicate that the essential frequencies in question are effectively the ones used to achieve generalization in the first place. Surprisingly, images seen through these modulatory masks are not recognizable and resemble texture-like patterns.

Emanuele Zappala, Antonio Henrique de Oliveira Fonseca, Josue Ortega Caro et al.

Nonlinear operators with long distance spatiotemporal dependencies are fundamental in modeling complex systems across sciences, yet learning these nonlocal operators remains challenging in machine learning. Integral equations (IEs), which model such nonlocal systems, have wide ranging applications in physics, chemistry, biology, and engineering. We introduce Neural Integral Equations (NIE), a method for learning unknown integral operators from data using an IE solver. To improve scalability and model capacity, we also present Attentional Neural Integral Equations (ANIE), which replaces the integral with self-attention. Both models are grounded in the theory of second kind integral equations, where the indeterminate appears both inside and outside the integral operator. We provide theoretical analysis showing how self-attention can approximate integral operators under mild regularity assumptions, further deepening previously reported connections between transformers and integration, and deriving corresponding approximation results for integral operators. Through numerical benchmarks on synthetic and real world data, including Lotka-Volterra, Navier-Stokes, and Burgers' equations, as well as brain dynamics and integral equations, we showcase the models' capabilities and their ability to derive interpretable dynamics embeddings. Our experiments demonstrate that ANIE outperforms existing methods, especially for longer time intervals and higher dimensional problems. Our work addresses a critical gap in machine learning for nonlocal operators and offers a powerful tool for studying unknown complex systems with long range dependencies.

Syed Asad Rizvi, Nazreen Pallikkavaliyaveetil, David Zhang et al.

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation models challenging. In this work, we propose Foundation-Informed Message Passing (FIMP), a Graph Neural Network (GNN) message-passing framework that leverages pretrained non-textual foundation models in graph-based tasks. We show that the self-attention layers of foundation models can effectively be repurposed on graphs to perform cross-node attention-based message-passing. Our model is evaluated on a real-world image network dataset and two biological applications (single-cell RNA sequencing data and fMRI brain activity recordings) in both finetuned and zero-shot settings. FIMP outperforms strong baselines, demonstrating that it can effectively leverage state-of-the-art foundation models in graph tasks.

Antonio H. de O. Fonseca, Emanuele Zappala, Josue Ortega Caro et al.

Modeling spatiotemporal dynamical systems is a fundamental challenge in machine learning. Transformer models have been very successful in NLP and computer vision where they provide interpretable representations of data. However, a limitation of transformers in modeling continuous dynamical systems is that they are fundamentally discrete time and space models and thus have no guarantees regarding continuous sampling. To address this challenge, we present the Continuous Spatiotemporal Transformer (CST), a new transformer architecture that is designed for the modeling of continuous systems. This new framework guarantees a continuous and smooth output via optimization in Sobolev space. We benchmark CST against traditional transformers as well as other spatiotemporal dynamics modeling methods and achieve superior performance in a number of tasks on synthetic and real systems, including learning brain dynamics from calcium imaging data.

Hao Liang, Josue Ortega Caro, Vikram Maheshri et al.

Training dataset biases are by far the most scrutinized factors when explaining algorithmic biases of neural networks. In contrast, hyperparameters related to the neural network architecture have largely been ignored even though different network parameterizations are known to induce different implicit biases over learned features. For example, convolutional kernel size is known to affect the frequency content of features learned in CNNs. In this work, we present a causal framework for linking an architectural hyperparameter to out-of-distribution algorithmic bias. Our framework is experimental, in that we train several versions of a network with an intervention to a specific hyperparameter, and measure the resulting causal effect of this choice on performance bias when a particular out-of-distribution image perturbation is applied. In our experiments, we focused on measuring the causal relationship between convolutional kernel size and face analysis classification bias across different subpopulations (race/gender), with respect to high-frequency image details. We show that modifying kernel size, even in one layer of a CNN, changes the frequency content of learned features significantly across data subgroups leading to biased generalization performance even in the presence of a balanced dataset.

Josue Ortega Caro, Yongxu Zhang, Hannah M Batchelor et al.

Many biological systems evolve through continuous local dynamics while switching between latent regimes defined by learning, stimulus context, internal state, or developmental stage. These processes are often observed only as unpaired longitudinal snapshots: the same cells, neurons, or animals are not tracked as matched trajectories, even though population states are sampled across successive stages. This creates two coupled challenges. First, trajectories must respect curved low-dimensional manifolds embedded in high-dimensional biological measurements. Second, the model must identify when the transport mechanism itself changes. We introduce FLUX (FLow matching for Unpaired longitudinal data with miXture-of-experts), a geometry-aware longitudinal flow-matching framework for joint transport modeling and unsupervised regime discovery. FLUX learns a data-dependent metric from pooled labeled and unlabeled observations, uses that metric to construct geometry-aware conditional paths between adjacent marginals, and decomposes the resulting velocity field into sparse expert vector fields selected by a Straight-Through Gumbel-Softmax router. Across manifold controls, a regime-switching Lorenz system, widefield cortical calcium imaging during associative learning, and embryoid body single-cell differentiation, FLUX reconstructs longitudinal transport while recovering interpretable regime structure. Ablations show that mixture-of-experts routing alone is insufficient: FLUX without geometric learning can fit local transport but fails or weakens regime discovery when regimes are encoded in local dynamics. These results suggest that geometry-aware velocity decomposition provides a general strategy for discovering latent biological state transitions from unpaired longitudinal snapshots.

Justin Sahs, Ryan Pyle, Aneel Damaraju et al.

Understanding the learning dynamics and inductive bias of neural networks (NNs) is hindered by the opacity of the relationship between NN parameters and the function represented. We propose reparametrizing ReLU NNs as continuous piecewise linear splines. Using this spline lens, we study learning dynamics in shallow univariate ReLU NNs, finding unexpected insights and explanations for several perplexing phenomena. We develop a surprisingly simple and transparent view of the structure of the loss surface, including its critical and fixed points, Hessian, and Hessian spectrum. We also show that standard weight initializations yield very flat functions, and that this flatness, together with overparametrization and the initial weight scale, is responsible for the strength and type of implicit regularization, consistent with recent work arXiv:1906.05827. Our implicit regularization results are complementary to recent work arXiv:1906.07842, done independently, which showed that initialization scale critically controls implicit regularization via a kernel-based argument. Our spline-based approach reproduces their key implicit regularization results but in a far more intuitive and transparent manner. Going forward, our spline-based approach is likely to extend naturally to the multivariate and deep settings, and will play a foundational role in efforts to understand neural networks. Videos of learning dynamics using a spline-based visualization are available at http://shorturl.at/tFWZ2.

Josue Ortega Caro, Yilong Ju, Ryan Pyle et al.

Adversarial Attacks are still a significant challenge for neural networks. Recent work has shown that adversarial perturbations typically contain high-frequency features, but the root cause of this phenomenon remains unknown. Inspired by theoretical work on linear full-width convolutional models, we hypothesize that the local (i.e. bounded-width) convolutional operations commonly used in current neural networks are implicitly biased to learn high frequency features, and that this is one of the root causes of high frequency adversarial examples. To test this hypothesis, we analyzed the impact of different choices of linear and nonlinear architectures on the implicit bias of the learned features and the adversarial perturbations, in both spatial and frequency domains. We find that the high-frequency adversarial perturbations are critically dependent on the convolution operation because the spatially-limited nature of local convolutions induces an implicit bias towards high frequency features. The explanation for the latter involves the Fourier Uncertainty Principle: a spatially-limited (local in the space domain) filter cannot also be frequency-limited (local in the frequency domain). Furthermore, using larger convolution kernel sizes or avoiding convolutions (e.g. by using Vision Transformers architecture) significantly reduces this high frequency bias, but not the overall susceptibility to attacks. Looking forward, our work strongly suggests that understanding and controlling the implicit bias of architectures will be essential for achieving adversarial robustness.

Hanlin Tang, Martin Schrimpf, Bill Lotter et al.

Making inferences from partial information constitutes a critical aspect of cognition. During visual perception, pattern completion enables recognition of poorly visible or occluded objects. We combined psychophysics, physiology and computational models to test the hypothesis that pattern completion is implemented by recurrent computations and present three pieces of evidence that are consistent with this hypothesis. First, subjects robustly recognized objects even when rendered <15% visible, but recognition was largely impaired when processing was interrupted by backward masking. Second, invasive physiological responses along the human ventral cortex exhibited visually selective responses to partially visible objects that were delayed compared to whole objects, suggesting the need for additional computations. These physiological delays were correlated with the effects of backward masking. Third, state-of-the-art feed-forward computational architectures were not robust to partial visibility. However, recognition performance was recovered when the model was augmented with attractor-based recurrent connectivity. These results provide a strong argument of plausibility for the role of recurrent computations in making visual inferences from partial information.