arXiv subjects

Luciano Dyballa

Publications and source records attributed to Luciano Dyballa.

10 recordsLinked to original sources

arXiv2026

Bracketing Uncertainty in Clustering Under the Manifold Hypothesis

The manifold hypothesis suggests a natural criterion for clustering: partition data according to the manifold component from which each point is drawn. Whether two components are separable depends on a geometric tradeoff: the ambient separation between components versus the largest gap in sampling. In practice, this tradeoff is rarely assessed explicitly, leading standard methods to over-commit to a single clustering assignment even when the data do not support a unique answer. We formalize this tradeoff by combining intrinsic manifold geometry (volume growth and reach) with sample-level quantities (fill distance and density), yielding a threshold phenomenon for mutual-$k$-nearest-neighbor graphs: when the offset-to-fill ratio exceeds a conservative upper threshold, component separation is preserved; below a lower threshold, components fuse. The gap between these thresholds defines a geometric uncertainty zone in which the number of clusters is not identifiable from the data. Nevertheless, conventional approaches still seek one: sweeping parameters (an engineering approach) or fitting a generative mixture model (a model-based approach). Rather than forcing a single estimate of the number of clusters, we propose Manifold-Based Clustering (MBC), which returns an explicit bracket interval to quantify the underlying data uncertainty. This bracket acts as an empirically calibrated diagnostic: it narrows when a single resolution is supported, widens when multiple resolutions coexist, and collapses to one when no separated structure is detectable. Empirically, we find that many real datasets lie within the uncertainty zone rather than admitting one clear answer. Our results suggest that ambiguity in cluster number is often intrinsic, and should be quantified rather than resolved.

stat.ML↗

arXiv2026

Inferring Active Neural Circuits Using Diffusion Scores

In biological systems, neural circuits compute through directed, short-latency interactions whose effects unfold across multiple time scales and behavioral contexts. We address the problem of inferring these local, lag-specific interactions from sampled neural population activity under varying stimuli, without assuming a parametric form for the underlying dynamics. Our approach leverages denoising score models by estimating joint-window scores over consecutive activity snapshots (i.e., brain states) and converting these scores into calibrated, directed edge tests via cross-block score products. The key insight is that these products recover the Jacobian of the transition map between brain states under nonlinear dynamics. To cleanly separate lag-specific effects, we introduce minimal multi-block windows that condition on intermediate time points, avoiding the omitted-lag bias inherent in pairwise analyses. The resulting method, Score--Block Time Graphs (SBTG), identifies lag-specific directed interactions in sampled neuronal population data. We specifically apply SBTG to whole-brain C. elegans calcium imaging data to recover lag-specific circuit structure not resolved by current methods, including improved alignment with independent connectomes, cell-type-specific temporal organization, and neuromodulatory profiles consistent with known receptor kinetics. These findings highlight the potential for SBTG to serve as a practical ``AI for science'' tool by turning high-dimensional neural population recordings into statistically testable circuit hypotheses.

q-bio.NC↗

arXiv2026

Decoding Alignment without Encoding Alignment: A critique of similarity analysis in neuroscience

Decoding approaches are widely used in neuroscience and machine learning to compare stimulus representations across neural systems, such as different brain regions, organisms, and deep learning models. Popular methods include decoding (perceptual) manifolds and alignment metrics such as Representational Similarity Analysis (RSA) and Dynamic Similarity Analysis (DSA), where similarity in decoding representations is interpreted as evidence for similar computation. This paper demonstrates a fundamental weakness behind this approach: it is misleading to assume that representational geometry is representative of a neuronal population as a whole, when such representations may actually be shaped by a very small subset of neurons. We show that the complementary encoding paradigm addresses this issue directly: it characterizes how neurons are organized globally in terms of their responses to a set of data, providing insight into how the decoding representation is implemented by neurons within a population. We demonstrate across experiments in biological systems and deep learning models that (i) surprisingly, similar decoding behavior and high representational alignment can arise from small, non-representative subpopulations of neurons; and critically, (ii) alignment metrics are insensitive to encoding manifold topology (how function is distributed across neurons), despite this being a key signature of differentiation across biological systems. A controlled MNIST experiment provides causal evidence: decoding metrics remain unchanged even when encoding topology is causally manipulated via the training loss. Overall, similarity in decoding behavior, as measured by classic alignment metrics, does not imply similarity in function or computation, motivating the use of encoding manifolds as a complementary tool for comparing neural systems.

q-bio.NC↗

arXiv2026

How 'Neural' is a Neural Foundation Model?

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. Our 'tubularity' metric quantifies this stimulus-dependent development of neural activity as biologically plausible. The readout module achieves high fidelity by using numerous specialized feature maps rather than biologically plausible mechanisms. Overall, this study provides a window into 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. Our findings suggest design changes that could bring neural foundation models into closer alignment with biological systems: introducing recurrence in early encoder stages, and constraining features in the readout module.

q-bio.NC↗

arXiv2025

Manifolds and Modules: How Function Develops in a Neural Foundation Model

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.

q-bio.NC↗

arXiv2024

A separability-based approach to quantifying generalization: which layer is best?

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

cs.LG↗

arXiv2024

Zero-shot generalization across architectures for visual classification

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.

cs.CV↗

arXiv2024

Learning dynamic representations of the functional connectome in neurobiological networks

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.

q-bio.NC↗

arXiv2023

IAN: Iterated Adaptive Neighborhoods for manifold learning and dimensionality estimation

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

cs.LG↗

arXiv2014

Further insights into the interareal connectivity of a cortical network

Over the past years, network science has proven invaluable as a means to better understand many of the processes taking place in the brain. Recently, interareal connectivity data of the macaque cortex was made available with great richness of detail. We explore new aspects of this dataset, such as a correlation between connection weights and cortical hierarchy. We also look at the link-community structure that emerges from the data to uncover the major communication pathways in the network, and moreover investigate its reciprocal connections, showing that they share similar properties.

q-bio.NC↗