Luciano Dyballa

Luciano Dyballa, Steven W. Zucker

Invoking the manifold assumption in machine learning requires knowledge of the manifold's geometry and dimension, and theory dictates how many samples are required. However, in applications data are limited, sampling may not be uniform, and manifold properties are unknown and (possibly) non-pure; this implies that neighborhoods must adapt to the local structure. We introduce an algorithm for inferring adaptive neighborhoods for data given by a similarity kernel. Starting with a locally-conservative neighborhood (Gabriel) graph, we sparsify it iteratively according to a weighted counterpart. In each step, a linear program yields minimal neighborhoods globally and a volumetric statistic reveals neighbor outliers likely to violate manifold geometry. We apply our adaptive neighborhoods to non-linear dimensionality reduction, geodesic computation and dimension estimation. A comparison against standard algorithms using, e.g., k-nearest neighbors, demonstrates their usefulness. Code for our algorithm will be available at https://github.com/dyballa/IAN

Luciano Dyballa, Evan Gerritz, Steven W. Zucker

Generalization to unseen data remains poorly understood for deep learning classification and foundation models, especially in the open set scenario. How can one assess the ability of networks to adapt to new or extended versions of their input space in the spirit of few-shot learning, out-of-distribution generalization, domain adaptation, and category discovery? Which layers of a network are likely to generalize best? We provide a new method for evaluating the capacity of networks to represent a sampled domain, regardless of whether the network has been trained on all classes in that domain. Our approach is the following: after fine-tuning state-of-the-art pre-trained models for visual classification on a particular domain, we assess their performance on data from related but distinct variations in that domain. Generalization power is quantified as a function of the latent embeddings of unseen data from intermediate layers for both unsupervised and supervised settings. Working throughout all stages of the network, we find that (i) high classification accuracy does not imply high generalizability; and (ii) deeper layers in a model do not always generalize the best, which has implications for pruning. Since the trends observed across datasets are largely consistent, we conclude that our approach reveals (a function of) the intrinsic capacity of the different layers of a model to generalize. Our code is available at https://github.com/dyballa/generalization

Luciano Dyballa, Samuel Lang, Alexandra Haslund-Gourley et al.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Evan Gerritz, Luciano Dyballa, Steven W. Zucker

Generalization to unseen data is a key desideratum for deep networks, but its relation to classification accuracy is unclear. Using a minimalist vision dataset and a measure of generalizability, we show that popular networks, from deep convolutional networks (CNNs) to transformers, vary in their power to extrapolate to unseen classes both across layers and across architectures. Accuracy is not a good predictor of generalizability, and generalization varies non-monotonically with layer depth.

Johannes Bertram, Luciano Dyballa, T. Anderson Keller et al.

Foundation models have shown remarkable success in fitting biological visual systems; however, their black-box nature inherently limits their utility for understanding brain function. Here, we peek inside a SOTA foundation model of neural activity (Wang et al., 2025) as a physiologist might, characterizing each 'neuron' based on its temporal response properties to parametric stimuli. We analyze how different stimuli are represented in neural activity space by building decoding manifolds, and we analyze how different neurons are represented in stimulus-response space by building neural encoding manifolds. We find that the different processing stages of the model (i.e., the feedforward encoder, recurrent, and readout modules) each exhibit qualitatively different representational structures in these manifolds. The recurrent module shows a jump in capabilities over the encoder module by 'pushing apart' the representations of different temporal stimulus patterns; while the readout module achieves biological fidelity by using numerous specialized feature maps rather than biologically plausible mechanisms. Overall, we present this work as a study of the inner workings of a prominent neural foundation model, gaining insights into the biological relevance of its internals through the novel analysis of its neurons' joint temporal response patterns.