We develop a topological model of site-specific recombination that applies to substrates which are the connected sum of two torus links of the form . Then we use our model to prove that all knots and links that can be produced by site-specific recombination on such substrates are contained in one of two…
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48 results for “Computational Substrate”
Graph Element Networks adaptively model spatial processes without prior graph structure.
problem Modeling spatial processes without a priori graphical structure.
method Assign nodes to spatial locations, optimize their connectivity, and use GNNs as a computational substrate.
result Optimized GNN nodes focus on complex parts of the space, allowing generalization and varying precision.
Deep neural networks map brain lesions to deficits for better brain function understanding.
problem Mapping the functional brain organization from pathological lesions.
method Deep generative neural network architectures, specifically variational convolutional volumetric auto-encoders.
result Our model outperforms established methods in lesion-deficit inference across various scenarios.
We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer , the…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and …
We develop a topological model of knots and links arising from a single (or multiple processive) round(s) of recombination starting with an unknot, unlink, or (2,m)-torus knot or link substrate. We show that all knotted or linked products fall into a single family, and prove that the size of this family grows linearly …
A new method approximates deep neural networks using Kalman Filters.
problem Approximating deep neural networks with limited data.
method Matrix Ensemble Kalman Filter-based multi-arm ANN (MEnKF-ANN).
result MEnKF-ANN can adequately approximate LSTM networks and provide uncertainty estimates.
A Quantifiable Information-Processing Hierarchy Provides a Necessary Condition for Detecting Agencyq-bio.NC
A new hierarchy quantifies agency in systems based on information processing.
problem Lack of a measurable, universal definition for agency in intelligent systems.
method Developed a bottom-up framework based on information processing hierarchy.
result Identified three orders of information processing (I, II, III) as necessary for agency.
METRO predicts reactions using minimal templates, reducing computational overhead and achieving state-of-the-art results.
problem Predicting possible reaction substrates for complex molecules from simpler precursors.
method METRO (Molecule-Edit Templates for RetrOsynthesis) uses minimal templates to predict reactions efficiently and accurately.
result METRO achieves state-of-the-art results on standard benchmarks, reducing computational overhead.
Conformal Smectics and their Many Metricscond-mat.soft
We establish that equally-spaced smectic configurations enjoy an infinite-dimensional conformal symmetry and show that there is a natural map between them and null hypersurfaces in maximally-symmetric spacetimes. By choosing the appropriate conformal factor it is possible to restore additional symmetries of focal struc…
Novel graph network learns hierarchical network structure.
problem Lack of information in hierarchical network topology.
method Hierarchical clustering for multiscale decomposition, graph convolutional layers.
result Competitive performance on citation network benchmark.
New Heintze-Karcher inequality helps understand droplet shapes.
problem Characterize the shape of droplets inside smooth containers.
method Obtained a new form of the Heintze-Karcher inequality for mean convex hypersurfaces with boundary on curved substrates.
result New mathematical inequality aids in understanding droplet shapes.
GNNs improve brain activity forecasting in fMRI studies.
problem Understanding neural dynamics in the brain.
method Comparison of GNN architectures for modeling fMRI data.
result GNNs outperform VAR models in robustly scaling to large network studies.
Boosting classifiers improve accuracy with noisy inputs.
problem Noisy communication or computation degrades boosting classifier accuracy.
method Optimize resource allocation for base classifiers based on importance metrics.
result Optimized noisy boosting classifiers are more robust than bagging.
How spiking networks are able to perform probabilistic inference is an intriguing question, not only for understanding information processing in the brain, but also for transferring these computational principles to neuromorphic silicon circuits. A number of computationally powerful spiking network models have been pro…
AgensFlow learns multi-agent coordination policies from experience.
problem Difficult coordination choices in multi-agent systems built on LLMs.
method Online policy learning from repeated trajectories, treating decisions as learnable.
result Learned routing improves coordination-heavy workflows over static wiring.
Study reveals optimal scaling conditions for photonic neural networks.
problem Impact of reservoir size and learning routines on convergence-speed during learning.
method Used a greedy algorithm to train a photonic neural network for chaotic signals prediction.
result Determined convergence speed of learning as a function of reservoir size and found close to linear scaling.
Quantum systems with scrambling improve temporal information processing, but scaling requires exponential overhead.
problem Scalability and memory retention of quantum reservoirs in temporal information processing.
method Examined a quantum reservoir processing framework with scrambling reservoirs modeled by high-order unitary designs, analyzed in noiseless and noisy settings.
result Memory retention improves exponentially with reservoir size but worsens with reservoir iterations, requiring exponential shot overhead for scaling.
Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the si…
We consider a disk-shaped thin elastic sheet bonded to a compliant sphere. (Our sheet can slip along the sphere; the bonding controls only its normal displacement.) If the bonding is stiff (but not too stiff), the geometry of the sphere makes the sheet wrinkle to avoid azimuthal compression. The total energy of this sy…
BNNs enhance reservoir computing by acting as generalization filters.
problem Understanding how BNNs integrate with reservoir computing.
method Optogenetics and calcium imaging to record BNNs, reservoir computing framework.
result BNNs improve reservoir computing performance through generalization.
Graphs predict reaction conditions for organic chemistry.
problem Predicting specific reaction conditions in organic chemistry.
method Graph Neural Networks (GNNs) for modeling reaction graphs.
result GNNs can identify specific graph features affecting reaction conditions.
Financial asset markets are sociotechnical systems whose constituent agents are subject to evolutionary pressure as unprofitable agents exit the marketplace and more profitable agents continue to trade assets. Using a population of evolving zero-intelligence agents and a frequent batch auction price-discovery mechanism…
Instrumented data enables causal scientific machine learning
problem Insufficient data for causal scientific machine learning
method Instrumented data with explicit model, uncertainty, and counterfactuals
result Supports causal interventions through Pearl's do-operator
Enhances disease progression modeling using LLMs for complex brain connectivity.
problem Inaccurate predictions of disease spread due to oversimplified brain connectivity models.
method Uses LLMs to synthesize multi-modal relationships and learn disease trajectories from longitudinal data.
result Superior prediction accuracy and interpretability compared to traditional methods.
This thesis explores emergent intelligence in disordered systems like spin glasses and neural networks.
problem Understanding the principles behind emergent intelligent behaviors in disordered systems.
method Statistical physics approach to charting learning mechanisms and dynamics.
result Uncovering relationships between learning mechanisms and physical dynamics.
GeomHerd predicts herding behavior before market prices move, using Ricci curvature of agent interaction graphs.
problem Quantifying herding behavior in markets that lags behind actual price movements.
method Develops a geometric framework to track coordination on agent interaction graphs, bypassing lag in price-correlation statistics.
result GeomHerd anticipates herding long before market baselines, with significant lead times in predictions.
NSMs use always-on stochasticity to normalize activations, improving convergence and performance.
problem Improving the robustness and generalizability of deep neural networks.
method Developed Neural Sampling Machines (NSMs) using always-on multiplicative stochasticity and simple threshold neurons.
result NSMs exhibit self-normalizing properties similar to Weight Normalization, speeding up convergence and preventing internal covariate shift.
Agent-to-Agent Finance: Blockchain Payments and Trust Infrastructure for Autonomous AI Agentsq-fin.GN
Agent-to-agent finance aims to manage payments and trust for AI agents.
problem Managing financial interactions between autonomous AI agents.
method Develops agent-to-agent finance concept and explores blockchain solutions.
result Agent-to-agent finance can address coordination frictions in financial markets.
How do we assign value to economic transactions? To answer this question, we must consider whether the value of objects is inherent, is a product of social interaction, or involves other mechanisms. Economic theory predicts that there is an optimal price for any market transaction, and can be observed during auctions o…
An increasing body of evidence suggests that the trial-to-trial variability of spiking activity in the brain is not mere noise, but rather the reflection of a sampling-based encoding scheme for probabilistic computing. Since the precise statistical properties of neural activity are important in this context, many model…
We show that some pieces of cylinders bounded by two parallel straight-lines bifurcate in a family of periodic non-rotational surfaces with constant mean curvature and with the same boundary conditions. These cylinders are initial interfaces in a problem of microscale range modeling the morphologies that adopt a liquid…
Adapts MBDOE for real-time parameter estimation in complex systems.
problem Costly posterior inference and design optimization in nonlinear systems.
method Combines DAD with differentiable mechanistic models for real-time parameter estimation.
result Demonstrated on four systems, including a DC motor.
Intelligence emerges from stabilizing invariant cycles in memory.
problem Understanding the nature of intelligence and its emergence.
method Structural-dynamical account rooted in a topological closure law: \(\partial^2=0\).
result Memory-amortized inference (MAI) mechanism that implements SbS \(
ightarrow\) CCUP.
Functional brain networks exhibit dynamics on the sub-second temporal scale and are often assumed to embody the physiological substrate of cognitive processes. Here we analyse the temporal and spatial dynamics of these states, as measured by EEG, with a hidden Markov model and compare this approach to classical EEG mic…
GPMI method interpolates uncertain atrial conduction velocity on non-Euclidean manifolds.
problem Uncertainty in atrial conduction velocity calculations.
method Gaussian Process Manifold Interpolation (GPMI) on human atrial manifolds.
result GPMI accounts for atrial topology and calculates CV uncertainty.
A neural atlas simplifies 3D geometry simulation by avoiding meshing.
problem Simulation of complex 3D geometries with thin features or non-trivial topology.
method Learned geometric representation of overlapping volumetric coordinate charts, trained from point-cloud or level-set data.
result The learned atlas enables different solvers without re-meshing or re-parametrization.
Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more statistical power; yet the current brain-imaging analytic framework cannot be used at…
Inferring Microbial Biomass Yield and Cell Weight using Probabilistic Macrochemical Modelingq-bio.QM
Method improves microbial biomass yield estimation from noisy data.
problem Estimating microbial biomass yields from noisy cell counts and substrate measurements.
method Probabilistic macrochemical modeling to relax cell weight assumptions and improve robustness.
result Model provides accurate uncertainty estimates of key parameters.
MEGAN models chemical reactions as graph edits, improving synthesis planning.
problem Generating and predicting chemical reactions under constraints.
method End-to-end encoder-decoder neural model inspired by arrow pushing formalism.
result State-of-the-art accuracy in standard benchmarks for retrosynthesis prediction.
A learning rule for first-spike times in neural networks reduces energy consumption and reaction times.
problem Energy efficiency and reaction time in neuromorphic systems.
method Derivation of a learning rule for first-spike times in leaky integrate-and-fire neurons, using only input and output spike times.
result Demonstrated that the approach can implement error backpropagation in hierarchical spiking networks and is capable of harnessing neuromorphic system's speed and energy characteristics.
The study learns neural update rules by remembering past experiences.
problem Developing efficient online learning rules for neural networks.
method Representing neurons with vectors, using meta-neural networks for updates, and training for remembering past experiences.
result The approach reveals insights into learning rules and could be used for complex tasks like episodic memory.
Online CPD for weighted and directed graphs using RDPG model.
problem Monitoring and detecting changes in weighted and directed graph data.
method Spectral embeddings of RDPG models for online updates and error-rate control.
result A lightweight online CPD algorithm with improved detection resolution and delay.
The paper models financial order books using geometric shears and directional liquidity.
problem Understanding the geometry and dynamics of financial order books.
method Structural framework modeling liquidity as emergent observables, geometric shears, and directional imbalances.
result The geometry of financial order books can be described by a rigid drift and geometric shear, leading to a gamma-like profile of projected liquidity.
The episodic, irregular and asynchronous nature of medical data render them difficult substrates for standard machine learning algorithms. We would like to abstract away this difficulty for the class of time-stamped categorical variables (or events) by modeling them as a renewal process and inferring a probability dens…
CLQT benchmarks LLM portfolio managers by evaluating their decision-making process, not just returns.
problem Most benchmarks rank LLMs by returns, ignoring their decision-making process and potential for look-ahead leakage.
method CLQT reframes evaluation as diagnosis, using a closed-loop, cost-aware, strategy-consistent environment with a five-stage cycle.
result CLQT provides a durable map of agent competencies and limitations, separating outcome from process.
Transformers mimic Bayesian reasoning in controlled settings, revealing geometric mechanisms.
problem Verifying if transformers perform Bayesian reasoning rigorously in natural data.
method Constructing Bayesian wind tunnels with known posteriors and proving memorization impossibility.
result Transformers achieve - bit accuracy in Bayesian posteriors, while MLPs fail.
Quantum ELMs use a quantum reservoir to learn from data, with limits on expressivity and scalability.
problem Understanding the limits of quantum ELMs for machine learning tasks.
method Decomposed QELM predictions into Fourier series to analyze expressivity and scalability.
result Expressivity of QELMs is limited by the number of Fourier frequencies and observables, and scalability is hindered by hardware noise and entanglement.