SearcharxivSearch

arXiv subjects

Anna Ritz

Publications and source records attributed to Anna Ritz.

7 recordsLinked to original sources

Determinants of hyperparameter robustness in connectome reservoir computing

Reservoir computing provides a controlled setting for studying how recurrent network architectureshapes computation: input signals are projected into a high-dimensional state space by a fixed nonlinear dynamical system, and only the readout is trained. However, reservoir performance can be dependent on hyperparameters; this paper asks which recurrent network features support robustness to those parameter changes. We characterize computational performance using memory capacity (MC), truncated single-delay information-processing capacity (IPC), and kernel rank (KR). Generalization across input histories is measured using generalization rank (GR), while hyperparameter robustness is quantified using the coefficient of variation (CV) of each metric across sweeps of target spectral radius, input scaling, leak rate, and neuron bias. To examine the architectural determinants of robustness, we construct perturbations that alter connectivity topology, excitatory/inhibitory sign structure, weight magnitudes, and weight placement while preserving complementary properties. Across these experiments, the C. elegans connectome consistently occupies a relatively low-variance regime. The central result is a performance-robustness tradeoff: architecture variants with higher task-agnostic performance also tend to exhibit greater hyperparameter sensitivity and poorer common-tail generalization. Across the E/I edge balance sweeps and shuffle controls, this tradeoff is closely associated with the raw spectral radius before normalization. Because every perturbed matrix is rescaled to the same target radius, matrices with lower raw spectral radius receive greater global amplification of their recurrent weights. The observed differences among architectures therefore characterize the joint effects of structural variation and architecture-specific global rescaling under spectral-radius normalization.

q-bio.NC

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These challenges stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology and highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on the future directions of network biology. Additionally, we offer insights into scientific communities, educational initiatives, and the importance of fostering diversity within the field. This paper establishes a roadmap for an immediate and long-term vision for network biology.

q-bio.MN

Graphery: Interactive Tutorials for Biological Network Algorithms

Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver designed to help biological researchers understand the fundamental concepts behind commonly-used graph algorithms. Each tutorial describes a graph concept along with executable Python code that visualizes the concept in a code view and a graph view. Graphery tutorials help researchers understand graph statistics (such as degree distribution and network modularity) and classic graph algorithms (such as shortest paths and random walks). Users navigate each tutorial using their choice of real-world biological networks, ranging in scale from molecular interaction graphs to ecological networks. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Discipline-focused tutorials will be essential to help researchers interpret their biological data. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Availability: Graphery is available at https://graphery.reedcompbio.org/.

q-bio.MN

Ten Simple Rules for Attending Your First Conference

Conferences are a mainstay of most scientific disciplines, where scientists of all career stages come together to share cutting-edge ideas and approaches. If you do research, chances are you will attend one or more of these meetings in your career. Conferences are a microcosm of their discipline, and while conferences offer different perspectives in different disciplines, they all offer experiences that range from a casual chat waiting in line for coffee to watching someone present their groundbreaking, hot-off-the-press research. The authors of this piece have attended our fair share of conferences and have collectively mentored hundreds of students in understanding the "unwritten rules" and pro-tips of conference attendance. As you head to your first scientific conference, these rules will help you navigate the conference environment and make the most of your experience. We have also developed a web portal which contains far more information about these rules, tables of professional societies and conferences in different disciplines, and other resources that may come in handy for first-time conference attendees and their mentors. We encourage any reader to use, adapt, and contribute to these materials.

cs.DL

Improved Differentially Private Analysis of Variance

Hypothesis testing is one of the most common types of data analysis and forms the backbone of scientific research in many disciplines. Analysis of variance (ANOVA) in particular is used to detect dependence between a categorical and a numerical variable. Here we show how one can carry out this hypothesis test under the restrictions of differential privacy. We show that the $F$-statistic, the optimal test statistic in the public setting, is no longer optimal in the private setting, and we develop a new test statistic $F_1$ with much higher statistical power. We show how to rigorously compute a reference distribution for the $F_1$ statistic and give an algorithm that outputs accurate $p$-values. We implement our test and experimentally optimize several parameters. We then compare our test to the only previous work on private ANOVA testing, using the same effect size as that work. We see an order of magnitude improvement, with our test requiring only 7% as much data to detect the effect.

cs.CR

Mass bias evolution in tSZ cluster cosmology

Galaxy clusters observed through the thermal Sunyaev-Zeldovich (tSZ) effect are a recent cosmological probe. The precision on the cosmological constraints is affected mainly by the current knowledge of cluster physics, which enters the analysis through the scaling relations. Here we aim to study one of the most important sources of systematic uncertainties, the mass bias, $b$. We have analysed the effects of a mass-redshift dependence, adopting a power-law parametrisation. We applied this parametrisation to the combination of tSZ number counts and power spectrum, finding a hint of redshift dependence that leads to a decreasing value of the mass bias for higher redshift. We tested the robustness of our results for different mass bias calibrations and a discrete redshift dependence. We find our results to be dependent on the clusters sample that we are considering, in particular obtaining an inverse (decreasing) redshift dependence when neglecting $z<0.2$ clusters. We analysed the effects of this parametrisation on the combination of cosmic microwave background (CMB) primary anisotropies and tSZ galaxy clusters. We find a preferred constant value of mass bias, having $(1-b) =0.62 \pm 0.05$. The corresponding value of $b$ is too high with respect to weak lensing and numerical simulations estimations. Therefore we conclude that this mass-redshift parametrisation does not help in solving the remaining discrepancy between CMB and tSZ clusters observations.

astro-ph.CO

Differentially Private ANOVA Testing

Modern society generates an incredible amount of data about individuals, and releasing summary statistics about this data in a manner that provably protects individual privacy would offer a valuable resource for researchers in many fields. We present the first algorithm for analysis of variance (ANOVA) that preserves differential privacy, allowing this important statistical test to be conducted (and the results released) on databases of sensitive information. In addition to our private algorithm for the F test statistic, we show a rigorous way to compute p-values that accounts for the added noise needed to preserve privacy. Finally, we present experimental results quantifying the statistical power of this differentially private version of the test, finding that a sample of several thousand observations is frequently enough to detect variation between groups. The differentially private ANOVA algorithm is a promising approach for releasing a common test statistic that is valuable in fields in the sciences and social sciences.

cs.CR