The following input profile is derived from election data of the 2009 mayoral election in Burlington, Vermont, which is known to exhibit interesting voting theoretic properties. One of them, James Simpson for the Green Party, gathered almost no votes (35 first-place votes compared to 1,306 first-place votes for the next-lowest candidate), so we ignore this candidate for convenience. The other four candidates are K = Bob Kiss M = Andy Montroll H = Dan Smith W = Kurt Wright. The resulting profile consists of the following 3,352 votes. For instance, the plurality winner (W) is different from the winner under Instant Runoff Voting rule (K) which Burlington used, and both are different from the Condorcet winner (M).

The following input profile is derived from election data of the 2009 mayoral election in Burlington, Vermont, which is known to exhibit interesting voting theoretic properties. One of them, James Simpson for the Green Party, gathered almost no votes (35 first-place votes compared to 1,306 first-place votes for the next-lowest candidate), so we ignore this candidate for convenience. The other four candidates are K = Bob Kiss M = Andy Montroll H = Dan Smith W = Kurt Wright. The resulting profile consists of the following 3,352 votes. For instance, the plurality winner (W) is different from the winner under Instant Runoff Voting rule (K) which Burlington used, and both are different from the Condorcet winner (M).

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Tokenization is a necessary component within the current architecture of many language models, including the transformer-based large language models (LLMs) of Generative AI, yet its impact on the model's cognition is often overlooked. We argue that LLMs demonstrate that the Distributional Hypothesis (DH) is sufficient for reasonably human-like language performance, and that the emergence of human-meaningful linguistic units among tokens motivates linguistically-informed interventions in existing, linguistically-agnostic tokenization techniques, particularly with respect to their roles as (1) semantic primitives and as (2) vehicles for conveying salient distributional patterns from human language to the model. We explore tokenizations from a BPE tokenizer; extant model vocabularies obtained from Hugging Face and tiktoken; and the information in exemplar token vectors as they move through the layers of a RoBERTa (large) model. Besides creating sub-optimal semantic building blocks and obscuring the model's access to the necessary distributional patterns, we describe how tokenization pretraining can be a backdoor for bias and other unwanted content, which current alignment practices may not remediate. Additionally, we relay evidence that the tokenization algorithm's objective function impacts the LLM's cognition, despite being meaningfully insulated from the main system intelligence.

Hyperbolic models can reproduce the heavy-tailed degree distribution, high clustering, and hierarchical structure of empirical networks. Current algorithms for finding the hyperbolic coordinates of networks, however, do not quantify uncertainty in the inferred coordinates. We present BIGUE, a Markov chain Monte Carlo (MCMC) algorithm that samples the posterior distribution of a Bayesian hyperbolic random graph model. We show that combining random walk and random cluster transformations significantly improves mixing compared to the commonly used and state-of-the-art dynamic Hamiltonian Monte Carlo algorithm. Using this algorithm, we also provide evidence that the posterior distribution cannot be approximated by a multivariate normal distribution, thereby justifying the use of MCMC to quantify the uncertainty of the inferred parameters.

Network scientists often use complex dynamic processes to describe network contagions, but tools for fitting contagion models typically assume simple dynamics. Here, we address this gap by developing a nonparametric method to reconstruct a network and dynamics from a series of node states, using a model that breaks the dichotomy between simple pairwise and complex neighborhood-based contagions. We then show that a network is more easily reconstructed when observed through the lens of complex contagions if it is dense or the dynamic saturates, and that simple contagions are better otherwise.

Finding controllers that perform well across multiple morphologies is an important milestone for large-scale robotics, in line with recent advances via foundation models in other areas of machine learning. However, the challenges of learning a single controller to control multiple morphologies make the `one robot one task' paradigm dominant in the field. To alleviate these challenges, we present a pipeline that: (1) leverages Quality Diversity algorithms like MAP-Elites to create a dataset of many single-task/single-morphology teacher controllers, then (2) distills those diverse controllers into a single multi-morphology controller that performs well across many different body plans by mimicking the sensory-action patterns of the teacher controllers via supervised learning. The distilled controller scales well with the number of teachers/morphologies and shows emergent properties. It generalizes to unseen morphologies in a zero-shot manner, providing robustness to morphological perturbations and instant damage recovery. Lastly, the distilled controller is also independent of the teacher controllers -- we can distill the teacher's knowledge into any controller model, making our approach synergistic with architectural improvements and existing training algorithms for teacher controllers.

Apple, in its latest update to its App Store developer guidelines for iPhones and iPads, flagged by 9to5Mac, says it will allow game console emulators – and even downloadable games. Apple warns developers, however, they "are responsible for all such software offered in [their] app, including ensuring that such software complies with these Guidelines and all applicable laws." So don't expect to play Super Mario, Spyro, or a third game series that starts with an'S'. Meanwhile, we have a guide to watching (and recording) the total eclipse in North America later today. The best chance of good viewing along the path of eclipse totality is still in northeastern parts of the US (Buffalo, NY, Burlington, VT) and southeast Canada (Niagara Falls and Montreal).

Evolving virtual creatures is a field with a rich history and recently it has been getting more attention, especially in the soft robotics domain. The compliance of soft materials endows soft robots with complex behavior, but it also makes their design process unintuitive and in need of automated design. Despite the great interest, evolved virtual soft robots lack the complexity, and co-optimization of morphology and control remains a challenging problem. Prior work identifies and investigates a major issue with the co-optimization process -- fragile co-adaptation of brain and body resulting in premature convergence of morphology. In this work, we expand the investigation of this phenomenon by comparing learnable controllers with proprioceptive observations and fixed controllers without any observations, whereas in the latter case, we only have the optimization of the morphology. Our experiments in two morphology spaces and two environments that vary in complexity show, concrete examples of the existence of high-performing regions in the morphology space that are not able to be discovered during the co-optimization of the morphology and control, yet exist and are easily findable when optimizing morphologies alone. Thus this work clearly demonstrates and characterizes the challenges of optimizing morphology during co-optimization. Based on these results, we propose a new body-centric framework to think about the co-optimization problem which helps us understand the issue from a search perspective. We hope the insights we share with this work attract more attention to the problem and help us to enable efficient brain-body co-optimization.

We study the problem of clustering networks whose nodes have imputed or physical positions in a single dimension, for example prestige hierarchies or the similarity dimension of hyperbolic embeddings. Existing algorithms, such as the critical gap method and other greedy strategies, only offer approximate solutions to this problem. Here, we introduce a dynamic programming approach that returns provably optimal solutions in polynomial time -- O(n^2) steps -- for a broad class of clustering objectives. We demonstrate the algorithm through applications to synthetic and empirical networks and show that it outperforms existing heuristics by a significant margin, with a similar execution time.