@inproceedings{20729, abstract = {Persistence modules (defined as a sequence of vector spaces and linear maps between them) are a key tool in topological data analysis. They are easy to interpret and fast to compute. However, when considering persistence maps (i.e. maps between persistence modules), these properties are lost. We propose a new invariant for persistence maps consisting of a partial matching such that: it is easy to interpret, it is more discriminative than the image of the persistence map, and can be calculated with cubical complexity.}, author = {Gonzalez-Diaz, Rocio and Soriano Trigueros, Manuel and Torras-Casas, Alvaro}, booktitle = {Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation}, isbn = {9798400720758}, location = {Guanajuato, Mexico}, pages = {188--196}, publisher = {Association for Computing Machinery}, title = {{Additive partial matchings for persistent homology}}, doi = {10.1145/3747199.3747561}, year = {2025}, } @article{20730, abstract = {Radio-frequency measurements could satisfy DiVincenzo’s readout criterion in future large-scale solid-state quantum processors, as they allow for high bandwidths and frequency multiplexing. However, the scalability potential of this readout technique can only be leveraged if quantum device tuning is performed using exclusively radio-frequency measurements, that is, without resorting to current measurements. We demonstrate an algorithm that performs automatic coarse tuning of double quantum dots with only radio-frequency measurements by exploiting their bandwidth and impedance matching. The tuning was completed within a few minutes with minimal prior knowledge about the device. Our results show that it is possible to eliminate the need for transport measurements for quantum-dot tuning, paving the way for more scalable device architectures.}, author = {Van Straaten, Barnaby and Fedele, Federico and Vigneau, Florian and Hickie, Joseph and Jirovec, Daniel and Ballabio, Andrea and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios and Ares, Natalia}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {5}, publisher = {American Physical Society}, title = {{All-rf-based coarse-tuning algorithm for quantum devices using machine learning}}, doi = {10.1103/v11m-dbhm}, volume = {24}, year = {2025}, } @article{20731, abstract = {The adult human brain, under resting conditions, consumes approximately 20% of total body glucose, a demand that is even higher during the first decade of life. The brain metabolic landscape is intricately regulated throughout development, and each cell type exhibits distinct metabolic signatures at each specific stage. This picture becomes even more intricate when considering that metabolism is dynamically modulated to sustain critical biological processes, such as cell proliferation and differentiation and synaptic activity–dependent processes. The orchestration between metabolic regulation and the aforementioned physiological processes often relies on metabolism-dependent changes in the epigenetic landscape, which shape gene expression patterns to trigger selected downstream biological responses. Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental disorders. This review explores the latest insights into the regulation of brain metabolism in health and disease.}, author = {Marano, Domenico and Mariano, Vittoria and Novarino, Gaia}, issn = {1545-2948}, journal = {Annual Review of Genetics}, pages = {415--434}, publisher = {Annual Reviews}, title = {{Fueling the mind: Brain metabolism in health and neurodevelopmental disorders}}, doi = {10.1146/annurev-genet-111523-102424}, volume = {59}, year = {2025}, } @article{20732, abstract = {We investigate the real-time dynamics of a quenched quantum impurity immersed in a one-dimensional ultracold Fermi gas, focusing on the breakdown of the adiabatic Born-Oppenheimer approximation due to nonadiabatic effects. Despite a sizable impurity-bath mass imbalance, increasing interactions induce strong nonadiabatic couplings, disrupting adiabatic motion and enabling population transfer between the adiabatic potential energy curves. These transitions are governed by conical intersections arising from the pseudo Jahn-Teller effect, dynamically shaping the impurity's motion through the bath. Using ab initio simulations via the multilayer multiconfiguration time-dependent Hartree method and a multichannel Born-Oppenheimer framework, we track the impurity's evolution and directly prove the dynamical manifestation of the pseudo Jahn-Teller effect. We analyze two key scenarios: (i) a small initial shift, where a single avoided crossing drives transitions, and (ii) a large shift, where multiple avoided crossings lead to enhanced nonadiabaticity, self-trapping, and energy redistribution. Our findings establish ultracold fermionic few-body systems as tunable platforms for studying nonadiabatic quantum dynamics, opening new avenues for controlled impurity transport in strongly correlated environments.}, author = {Becker, A. and Koutentakis, Georgios and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {3}, publisher = {American Physical Society}, title = {{Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined fermions}}, doi = {10.1103/2fr6-b59y}, volume = {7}, year = {2025}, } @article{20733, abstract = {The conversion of thermal energy into work is usually more efficient in the slow-driving regime, where the power output is vanishingly small. Efficient work extraction for fast-driving protocols remains an outstanding challenge at the nanoscale, where fluctuations play a significant role. In this Letter, we use a quantum-dot Szilard engine to extract work from thermal fluctuations with maximum efficiency over two decades of driving speed. We design and implement a family of optimized protocols ranging from the slow- to the fast-driving regime, and we measure the engine's efficiency as well as the mean and variance of its power output in each case. These optimized protocols exhibit significant improvements in power and efficiency compared to the naive approach. Our results also show that, when optimizing for efficiency, boosting the power output of a Szilard engine inevitably comes at the cost of increased power fluctuations.}, author = {Aggarwal, Kushagra and Rolandi, Alberto and Yang, Yikai and Hickie, Joseph and Jirovec, Daniel and Ballabio, Andrea and Chrastina, Daniel and Isella, Giovanni and Mitchison, Mark T. and Perarnau-Llobet, Martí and Ares, Natalia}, issn = {2643-1564}, journal = {Physical Review Research}, number = {3}, publisher = {American Physical Society}, title = {{Rapid optimal work extraction from a quantum-dot information engine}}, doi = {10.1103/q3dx-kyqj}, volume = {7}, year = {2025}, } @article{20734, abstract = {We consider the problem of parameter estimation in a high-dimensional generalized linear model. Spectral methods obtained via the principal eigenvector of a suitable data-dependent matrix provide a simple yet surprisingly effective solution. However, despite their wide use, a rigorous performance characterization, as well as a principled way to preprocess the data, are available only for unstructured (i.i.d. Gaussian and Haar orthogonal) designs. In contrast, real-world data matrices are highly structured and exhibit non-trivial correlations. To address the problem, we consider correlated Gaussian designs capturing the anisotropic nature of the features via a covariance matrix Σ. Our main result is a precise asymptotic characterization of the performance of spectral estimators. This allows us to identify the optimal preprocessing that minimizes the number of samples needed for parameter estimation. Surprisingly, such preprocessing is universal across a broad set of designs, which partly addresses a conjecture on optimal spectral estimators for rotationally invariant models. Our principled approach vastly improves upon previous heuristic methods, including for designs common in computational imaging and genetics. The proposed methodology, based on approximate message passing, is broadly applicable and opens the way to the precise characterization of spiked matrices and of the corresponding spectral methods in a variety of settings.}, author = {Zhang, Yihan and Ji, Hong Chang and Venkataramanan, Ramji and Mondelli, Marco}, issn = {2520-2324}, journal = {Mathematical Statistics and Learning}, number = {3-4}, pages = {193--304}, publisher = {EMS Press}, title = {{Spectral estimators for structured generalized linear models via approximate message passing}}, doi = {10.4171/MSL/52}, volume = {8}, year = {2025}, } @phdthesis{20737, author = {Casado Polanco, Raquel}, isbn = {978-3-99078-072-5}, issn = {2663-337X}, keywords = {NOTCH, radial glial progenitor, lineage progression, cortical development}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Role of NOTCH signaling in radial glial progenitor lineage progression}}, doi = {10.15479/AT-ISTA-20737}, year = {2025}, } @phdthesis{20741, abstract = {Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. Firstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. Next, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. Finally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. }, author = {Kojic, Marko}, isbn = {978-3-99078-073-2}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria}}, doi = {10.15479/AT-ISTA-20741}, year = {2025}, } @misc{20749, abstract = {Datasets and code for publication "Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter"}, author = {Shi, Sue}, publisher = {Zenodo}, title = {{Datasets and code for manuscript "Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter"}}, doi = {10.5281/ZENODO.15752991}, year = {2025}, } @misc{20750, author = {Van Straaten, Barnaby and Fedele, Federico and Vigneau, Florian and Hickie, Joseph and Jirovec, Daniel and Chrastina, Daniel and Isella, Giovanni and Ares, Natalia}, publisher = {Zenodo}, title = {{All rf-based tuning algorithm for quantum devices using machine learning}}, doi = {10.5281/ZENODO.17352653}, year = {2025}, } @article{20755, abstract = {We report the development of a continuous flow approach to nitrogen atom insertion. The setup is modular, enabling the rapid optimization of reaction conditions for a wide range of substrates. The milder reaction conditions led to an improved substrate scope and functional group tolerance compared to batch conditions. The reactions can also be safely scaled up to preparative scale.}, author = {Moon, Sooyeon and Reisenbauer, Julia and Paschke, Ann-Sophie K. and Scotto, Alessandro and Terraneo, Luca and Brenner, Niklas and Lefebvre, Quentin and Fessard, Thomas C. and Morandi, Bill}, issn = {1364-548X}, journal = {Chemical Communications}, number = {87}, pages = {16993--16996}, publisher = {Royal Society of Chemistry}, title = {{Efficient optimization and synthesis of diverse azaarenes via nitrogen atom insertion under continuous flow conditions}}, doi = {10.1039/d5cc03194j}, volume = {61}, year = {2025}, } @article{20767, abstract = {Chemistry education at the graduate level and beyond faces the formidable challenge of a boundless and constantly expanding frontier of knowledge on many fronts. While modern learners have an increasingly broad range of resources available at their disposal (including open access text-based references, online videos, training problems, and other digital learning materials), there are comparatively fewer such materials aimed at the highest levels of study. With the goal of producing widely accessible graduate-level learning content, we created a community-based approach to online course design that is easily digestible to meet the expectations of modern learners. Herein, we report the development of an open access Advanced Organic Chemistry video-based online course and several other specialized minicourses using the Synthesis Workshop YouTube channel.}, author = {Horwitz, Matthew A. and Al-Ahmad, Reem and Bai, Xingfeng and Balletti, Matteo and Bellotti, Peter and Ben-Tal, Yael and Campbell, Mark W. and Cheasty, Kathleen and Crossley, Steven W. M. and Day, Craig S. and Deneny, Patrick J. and Forbes, Katherine C. and Gogarnoiu, Emma S. and Grant, Phillip S. and Halder, Riya and Harris, Georgia R. and Hernández-Lladó, Pol and Jouanneau, Morgan and Jost, Vera and Kutateladze, Dennis A. and Laudadio, Gabriele and Liu, Chun and Looby, Aidan P. and Maestro, Aitor and McCallum, Terry and Palkowitz, Maximilian D. and Paolillo, Joshua M. and Perry, Matthew W. D. and Reisenbauer, Julia and Reyes, Cesar and Sharma, Hayden A. and Sheong, Fu Kit and Thoma, Benjamin and Tran, Andrew V. and Tran, Duc N. and Aguilar Troyano, Francisco José and Verheyen, Thomas and Walsh, Mark P. and Wagner, Alicia and Wearing, Emily R. and Wuitschik, Georg}, issn = {1938-1328}, journal = {Journal of Chemical Education}, number = {9}, pages = {3777--3783}, publisher = {American Chemical Society}, title = {{Reimagining advanced chemistry education: A community-based approach to course design for modern learners}}, doi = {10.1021/acs.jchemed.5c00555}, volume = {102}, year = {2025}, } @misc{20780, abstract = {Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.}, author = {Layana Franco, Lorena Alexandra and Toups, Melissa A and Vicoso, Beatriz}, keywords = {Schizophora, sex chromosomes, sex-chromosome turnover, Diptera, genomic features, out-of-X movement.}, publisher = {Institute of Science and Technology Austria}, title = {{Causes and consequences of sex-chromosome turnovers in Diptera}}, doi = {10.15479/AT-ISTA-20780}, year = {2025}, } @article{20795, abstract = {The tropical climate variability is characterized by various oscillations across a range of timescales. Oscillations that imprint the tropical mean state are generally attributed to slow processes, such as the seasonal cycle or interannual variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation (TWISO) in satellite observations and reanalyses. This oscillation, with a period of 30 to 60 d, is evident across multiple variables and involves interactions between convection, radiation, surface fluxes, and large-scale circulation. It is primarily manifested as convective perturbations in the tropical Indo-Pacific warm pool accompanied by oscillations in the large-scale tropical overturning circulation. Here, we examine the relationship between TWISO, the Madden–Julian Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain phases of TWISO coincide with specific phases of the MJO, suggesting a potential connection between the two. However, although the MJO can amplify the oscillation amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its broad manifestation across the tropics, TWISO potentially exerts widespread influence on tropical weather and climate at regional scales.}, author = {Bao, Jiawei and Bony, Sandrine and Takasuka, Daisuke and Muller, Caroline J}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {48}, publisher = {National Academy of Sciences}, title = {{Tropics-wide intraseasonal oscillations}}, doi = {10.1073/pnas.2511549122}, volume = {122}, year = {2025}, } @article{20796, abstract = {Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements.}, author = {Paouneskou, Dimitra and Baudrimont, Antoine and Kelemen, Réka K and Elkrewi, Marwan N and Graf, Angela and Moukbel Ali Aldawla, Shehab and Kölbl, Claudia and Tiemann-Boege, Irene and Vicoso, Beatriz and Jantsch, Verena}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity}}, doi = {10.1038/s41467-025-65420-9}, volume = {16}, year = {2025}, } @article{20816, abstract = {Background: DNA methylation (DNAm) can regulate gene expression, and its genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for complex traits. The relative stability of methylation profiles may enable better assessment of chronic exposures compared to single time-point protein measures. We present the first large-scale epigenetic study of the highly-abundant serum proteome measured via ultra-high throughput mass spectrometry in 14,671 samples from the Generation Scotland cohort. We further demonstrate the first large-scale comparison of protein EpiScores and their respective proteins as predictors of incident cardiovascular disease. Results: Marginal epigenome-wide association models, adjusting for age, sex, measurement batch, estimated white cell proportions, BMI, smoking and methylation principal components, reveal 15,855 significant CpG – protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10. Bayesian epigenome-wide association studies of the same 133 proteins reveal 697 CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein EpiScores correlate significantly with their respective protein in a holdout test-set. Of these, sixteen associate significantly with incident all-cause cardiovascular disease (Nevents=191) compared to one measured protein. Conclusions: We highlight a complex interplay between the blood-based methylome and proteome. Importantly, we show that protein EpiScores correlate with measured proteins and demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically relevant biomarkers. The protein EpiScores demonstrate more significant associations with cardiovascular disease than directly measured proteins, suggesting their potential as clinical biomarkers for monitoring or predicting disease risk. We suggest that biomarker development could be enhanced by the consideration of protein EpiScores alongside measured proteins.}, author = {Robertson, Josephine A. and Bajzik, Jakub and Vernardis, Spyros and Chybowska, Aleksandra D. and Mccartney, Daniel L. and Grauslys, Arturas and Mur, Jure and Smith, Hannah M. and Campbell, Archie and Drake, Camilla and Grant, Hannah and Pearce, Jamie and Russ, Tom C. and Adkin, Poppy and White, Matthew and Brigden, Charles and Messner, Christoph B. and Porteous, David J. and Hayward, Caroline and Cox, Simon R. and Zelezniak, Aleksej and Ralser, Markus and Robinson, Matthew Richard and Marioni, Riccardo E.}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {Springer Nature}, title = {{Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants}}, doi = {10.1186/s13059-025-03892-0}, volume = {26}, year = {2025}, } @inproceedings{20817, abstract = {We present Mechanistic PDE Networks -- a model for discovery of governing partial differential equations from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent linear partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations.}, author = {Pervez, Adeel A and Gavves, Efstratios and Locatello, Francesco}, booktitle = {42nd International Conference on Machine Learning}, issn = {2640-3498}, location = {Vancouver, Canada}, pages = {48962--48973}, publisher = {ML Research Press}, title = {{Mechanistic PDE networks for discovery of governing equations}}, volume = {267}, year = {2025}, } @inproceedings{20819, abstract = {Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for -means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success.}, author = {Scott, Jonathan A and Lampert, Christoph and Saulpic, David}, booktitle = {42nd International Conference on Machine Learning}, issn = {2640-3498}, location = {Vancouver, Canada}, pages = {53757--53790}, publisher = {ML Research Press}, title = {{Differentially private federated k-means clustering with server-side data}}, volume = {267}, year = {2025}, } @article{10045, abstract = {Given a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs. }, author = {Dvorak, Martin and Kolmogorov, Vladimir}, issn = {1436-4646}, journal = {Mathematical Programming}, keywords = {minimum 0-extension problem, metric labeling problem, discrete metric spaces, metric extensions, computational complexity, valued constraint satisfaction problems, discrete convex analysis, L-convex functions}, pages = {279--322}, publisher = {Springer Nature}, title = {{Generalized minimum 0-extension problem and discrete convexity}}, doi = {10.1007/s10107-024-02064-5}, volume = {209}, year = {2025}, } @article{8125, abstract = {Biological memory is known to be flexible—memory formation and recall depend on factors such as the behavioral context of the organism. However, this property is often ignored in associative memory models, leaving it unclear how memories can be organized and recalled when subject to contextual control. Because of the lack of a rigorous analytical framework, it is also unknown how contextual control affects memory stability, storage capacity, and information content. Here, we bring the dynamic nature of memory to the fore by introducing a novel model of associative memory, which we refer to as the context-modular memory network. In our model, stored memory patterns are associated to one of several background network states, or contexts. Memories are accessible when their corresponding context is active, and are otherwise inaccessible. Context modulates the effective network connectivity by imposing a specific configuration of neuronal and synaptic gating—gated neurons (synapses) have their activity (weights) momentarily silenced, thereby reducing interference from memories belonging to other contexts. Memory patterns are randomly and independently chosen, while neuronal and synaptic gates may be selected randomly or optimized through a process of contextual synaptic refinement. Through analytic and numerical results, we show that context-modular memory networks can exhibit both improved memory capacity and differential control of memory stability with random gating (especially for neuronal gating). For contextual synaptic refinement, we devise a method in which synapses are gated off for a given context if they destabilize the memory patterns in that context, drastically improving memory capacity and enabling even more precise control over memory stability. Notably, synaptic refinement allows for patterns to be accessible in multiple contexts, stabilizing memory patterns even for weight matrices that alone do not contain any information about the memory patterns, such as Gaussian random matrices. Overall, our model integrates recent ideas about context-dependent memory organization with classic associative memory models and proposes a rigorous theory which can act as a framework for future work. Furthermore, our work carries important implications for the understanding of biological memory storage and recall in the brain, such as highlighting an intriguing trade-off between memory capacity and accessibility.}, author = {Podlaski, William F. and Agnes, Everton J. and Vogels, Tim P}, issn = {2160-3308}, journal = {Physical Review X}, publisher = {American Physical Society}, title = {{High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating}}, doi = {10.1103/PhysRevX.15.011057}, volume = {15}, year = {2025}, }