Two Best Paper Awards at BIBE 2025
Researchers from the Archimedes Unit of the Athena Research Center, Greece, together with researchers from the Computer Science Department of the University of Crete, Greece; Stelios M. Smirnakis, Associate Neurologist at Brigham and Women’s Hospital, USA and Associate Professor at Harvard Medical School, USA; and Maria Papadopouli, Professor of Computer Science at the University of Crete, Greece, Affiliated Researcher at the Institute of Computer Science, FORTH, Crete, Greece and Lead Researcher at Archimedes, Athena Research Center, Greece, received two Best Paper Awards at the 25th annual IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2025), which took place on November 6-8, 2025 in Athens, Greece.
The publications, abstracts and bioRxiv links can be found below:
i. "Disentangling Stimulus & Population Dynamics in Mouse V1: Orthogonal Subspace Decomposition for Neural Representation"
Nikolaos Tzanakis, Alexandros Barberis, Ioanna Chourdaki, Mario Alexio Savaglio, Stelios Manolis Smirnakis, and Maria Papadopouli
Abstract: Understanding how the primary visual cortex of mice represents the external sensory input separately from the internal states is a fundamental challenge in systems neuroscience. Our work contributes to the problem of decoupling the stimulus-driven and internally generated components of neural activity in the primary visual cortex. Internally generated (or intrinsic) activity refers to neural dynamics that are not directly driven by sensory stimuli, reflecting the brain's ongoing, endogenous processes. Neuronal activity encodes both external stimuli and internal cortical states. The internally modulated activity, though not directly observable, can be inferred from the shared structure in population responses, and thus, serves as a proxy for the internal cortical state. We developed a two-phase Partial Least Squares Regression (PLSR) framework that decomposes neural activity into two orthogonal low-dimensional subspaces: (1) a "population" subspace capturing global variability shared across neurons, and (2) a "stimulus" subspace containing dimensions that discriminate between stimulus conditions while being linearly uncorrelated with the population subspace. We focus on the granular (L4) and supragranular (L2/3) layers of awake mice exposed to visual stimuli consisting of optical flow directions, using mesoscopic two-photon calcium imaging. In both L4 and L2/3 layers, many components individually yield above-chance decoding accuracy, yet a small low-dimensional subspace preserves nearly the full decoding performance of the high-dimensional population. Stimulus-driven components exhibit strong cross-mouse correlations, indicating a conserved coding scheme present in both L4 and L2/3. These components are stable across the entire recording session, reflecting robustness of the underlying representation over time. Removing the global modulation did not abolish stimulus discriminability in either layer, suggesting that information about stimulus direction is not dependent on this global signal. Both L4 and L2/3 stimulus components exhibit comparable decoding performance as well as similar tuning representations, suggesting common encoding of stimulus direction across layers.
BioRxiv link: https://www.biorxiv.org/content/10.1101/2025.11.10.687558v1
ii. "On Temporal Robustness & Brain-State Stability of Functional Connectivity in Mouse Primary Visual Area V1 compared to Higher Visual Area AL"
Mario Alexio Savaglio, Christina Brozi, Stelios Manolis Smirnakis, and Maria Papadopouli
Abstract: Understanding how the structure of functional connectivity in the visual cortex changes over time and across brain states is crucial for elucidating the mechanisms by which neurons coordinate to process information and support behavior. Higher-order visual areas in mice are known to exhibit more distinct, segregated functional roles compared to the primary visual cortex (V1), and they maintain stimulus representations over extended time scales. However, the stability of the architecture of their functional connectivity across time and brain states remains less understood. In vivo mesoscopic two-photon calcium imaging was used to simultaneously record activity from thousands of neurons across V1 and the extra-striate anterolateral area (AL) in mice, during both visual stimulation (optical-flow/motion) and at resting state (i.e., absence of stimulus). We then applied the spike time-tiling (STTC) coefficient to estimate the pairwise correlations of the neuronal firing and form the functional connectivity at the cell resolution. We then comparatively analyzed the functional connections within area AL and V1 under both stimulus-driven and resting-state conditions. The functional connectivity within AL remains consistently more robust over time than in area V1. Moreover, the structure of the functional connectivity in AL exhibits a smaller change between these two conditions compared to V1, indicating that functional connectivity derived from spontaneous activity more faithfully reflects the functional network architecture elicited by visual stimulation in this higher-order area. Finally, during the resting state, AL activity and functional connectivity are less dependent on pupil size than those of V1, indicating that arousal exerts a weaker modulatory effect on AL compared to V1.
BioRxiv link: https://www.biorxiv.org/content/10.1101/2025.11.10.687557v1
Official BIBE 2025 website can he found here.
