Biohybrid systems in which robotic lures interact with animals have become compelling tools for probing and identifying the mechanisms underlying collective animal behavior. One key challenge lies in the transfer of social interaction models from simulations to reality, using robotics to validate the modeling hypotheses. This challenge arises in bridging what we term the "biomimicry gap", which is caused by imperfect robotic replicas, communication cues and physics constrains not incorporated in the simulations that may elicit unrealistic behavioral responses in animals. In this work, we used a biomimetic lure of a rummy-nose tetra fish (Hemigrammus rhodostomus) and a neural network (NN) model for generating biomimetic social interactions. Through experiments with a biohybrid pair comprising a fish and the robotic lure, a pair of real fish, and simulations of pairs of fish, we demonstrate that our biohybrid system generates high-fidelity social interactions mirroring those of genuine fish pairs. Our analyses highlight that: 1) the lure and NN maintain minimal deviation in real-world interactions compared to simulations and fish-only experiments, 2) our NN controls the robot efficiently in real-time, and 3) a comprehensive validation is crucial to bridge the biomimicry gap, ensuring realistic biohybrid systems.
Logical modeling is a powerful tool in biology, offering a system-level understanding of the complex interactions that govern biological processes. A gap that hinders the scalability of logical models is the need to specify the update function of every vertex in the network depending on the status of its predecessors. To address this, we introduce in this paper the concept of strong regulation, where a vertex is only updated to active/inactive if all its predecessors agree in their influences; otherwise, it is set to ambiguous. We explore the interplay between active, inactive, and ambiguous influences in a network. We discuss the existence of phenotype attractors in such networks, where the status of some of the variables is fixed to active/inactive, while the others can have an arbitrary status, including ambiguous.
The spectral clustering algorithm is often used as a binary clustering method for unclassified data by applying the principal component analysis. To study theoretical properties of the algorithm, the assumption of conditional homoscedasticity is often supposed in existing studies. However, this assumption is restrictive and often unrealistic in practice. Therefore, in this paper, we consider the allometric extension model, that is, the directions of the first eigenvectors of two covariance matrices and the direction of the difference of two mean vectors coincide, and we provide a non-asymptotic bound of the error probability of the spectral clustering algorithm for the allometric extension model. As a byproduct of the result, we obtain the consistency of the clustering method in high-dimensional settings.
A myriad of approaches have been proposed to characterise the mesoscale structure of networks - most often as a partition based on patterns variously called communities, blocks, or clusters. Clearly, distinct methods designed to detect different types of patterns may provide a variety of answers to the network's mesoscale structure. Yet, even multiple runs of a given method can sometimes yield diverse and conflicting results, producing entire landscapes of partitions which potentially include multiple (locally optimal) mesoscale explanations of the network. Such ambiguity motivates a closer look at the ability of these methods to find multiple qualitatively different 'ground truth' partitions in a network. Here, we propose the stochastic cross-block model (SCBM), a generative model which allows for two distinct partitions to be built into the mesoscale structure of a single benchmark network. We demonstrate a use case of the benchmark model by appraising the power of stochastic block models (SBMs) to detect implicitly planted coexisting bi-community and core-periphery structures of different strengths. Given our model design and experimental set-up, we find that the ability to detect the two partitions individually varies by SBM variant and that coexistence of both partitions is recovered only in a very limited number of cases. Our findings suggest that in most instances only one - in some way dominating - structure can be detected, even in the presence of other partitions. They underline the need for considering entire landscapes of partitions when different competing explanations exist and motivate future research to advance partition coexistence detection methods. Our model also contributes to the field of benchmark networks more generally by enabling further exploration of the ability of new and existing methods to detect ambiguity in the mesoscale structure of networks.
Certifying the positivity of trigonometric polynomials is of first importance for design problems in discrete-time signal processing. It is well known from the Riesz-Fej\'ez spectral factorization theorem that any trigonometric univariate polynomial positive on the unit circle can be decomposed as a Hermitian square with complex coefficients. Here we focus on the case of polynomials with Gaussian integer coefficients, i.e., with real and imaginary parts being integers. We design, analyze and compare, theoretically and practically,three hybrid numeric-symbolic algorithms computing weighted sums of Hermitian squares decompositions for trigonometric univariate polynomials positive on the unit circle with Gaussian coefficients. The numerical steps the first and second algorithm rely on are complex root isolation and semidefinite programming, respectively. An exact sum of Hermitian squares decomposition is obtained thanks to compensation techniques. The third algorithm, also based on complex semidefinite programming, is an adaptation of the rounding and projection algorithm by Peyrl and Parrilo. For all three algorithms, we prove bit complexity and output size estimates that are polynomial in the degree of the input and linear in the maximum bitsize of its coefficients. We compare their performance on randomly chosen benchmarks, and further design a certified finite impulse filter.
Recently, advancements in deep learning-based superpixel segmentation methods have brought about improvements in both the efficiency and the performance of segmentation. However, a significant challenge remains in generating superpixels that strictly adhere to object boundaries while conveying rich visual significance, especially when cross-surface color correlations may interfere with objects. Drawing inspiration from neural structure and visual mechanisms, we propose a biological network architecture comprising an Enhanced Screening Module (ESM) and a novel Boundary-Aware Label (BAL) for superpixel segmentation. The ESM enhances semantic information by simulating the interactive projection mechanisms of the visual cortex. Additionally, the BAL emulates the spatial frequency characteristics of visual cortical cells to facilitate the generation of superpixels with strong boundary adherence. We demonstrate the effectiveness of our approach through evaluations on both the BSDS500 dataset and the NYUv2 dataset.
Motivated by the problem of detecting a change in the evolution of a network, we consider the preferential attachment random graph model with a time-dependent attachment function. Our goal is to detect whether the attachment mechanism changed over time, based on a single snapshot of the network and without directly observable information about the dynamics. We cast this question as a hypothesis testing problem, where the null hypothesis is a preferential attachment model with a constant affine attachment parameter $\delta_0$, and the alternative hypothesis is a preferential attachment model where the affine attachment parameter changes from $\delta_0$ to $\delta_1$ at an unknown changepoint time $\tau_n$. For our analysis we focus on the regime where $\delta_0$ and $\delta_1$ are fixed, and the changepoint occurs close to the observation time of the network (i.e., $\tau_n = n - c n^\gamma$ with $c>0$ and $\gamma \in (0, 1)$). This corresponds to the relevant scenario where we aim to detect the changepoint shortly after it has happened. We present two tests based on the number of vertices with minimal degree, and show that these are asymptotically powerful when $\tfrac{1}{2}<\gamma<1$. We conjecture that there is no powerful test based on the final network snapshot when $\gamma < \tfrac{1}{2}$. The first test we propose requires knowledge of $\delta_0$. The second test is significantly more involved, and does not require the knowledge of $\delta_0$ while still achieving the same performance guarantees. Furthermore, we prove that the test statistics for both tests are asymptotically normal, allowing for accurate calibration of the tests. This is demonstrated by numerical experiments, that also illustrate the finite sample test properties.
Agent-based models are widely used to predict infectious disease spread. For these predictions, one needs to understand how each input parameter affects the result. Here, some parameters may affect the sensitivities of others, requiring the analysis of higher order coefficients through e.g. Sobol sensitivity analysis. The geographical structures of real-world regions are distinct in that they are difficult to reduce to single parameter values, making a unified sensitivity analysis intractable. Yet analyzing the importance of geographical structure on the sensitivity of other input parameters is important because a strong effect would justify the use of models with real-world geographical representations, as opposed to stylized ones. Here we perform a grouped Sobol's sensitivity analysis on COVID-19 spread simulations across a set of three diverse real-world geographical representations. We study the differences in both results and the sensitivity of non-geographical parameters across these geographies. By comparing Sobol indices of parameters across geographies, we find evidence that infection rate could have more sensitivity in regions where the population is segregated, while parameters like recovery period of mild cases are more sensitive in regions with mixed populations. We also show how geographical structure affects parameter sensitivity changes over time.
Graph-centric artificial intelligence (graph AI) has achieved remarkable success in modeling interacting systems prevalent in nature, from dynamical systems in biology to particle physics. The increasing heterogeneity of data calls for graph neural architectures that can combine multiple inductive biases. However, combining data from various sources is challenging because appropriate inductive bias may vary by data modality. Multimodal learning methods fuse multiple data modalities while leveraging cross-modal dependencies to address this challenge. Here, we survey 140 studies in graph-centric AI and realize that diverse data types are increasingly brought together using graphs and fed into sophisticated multimodal models. These models stratify into image-, language-, and knowledge-grounded multimodal learning. We put forward an algorithmic blueprint for multimodal graph learning based on this categorization. The blueprint serves as a way to group state-of-the-art architectures that treat multimodal data by choosing appropriately four different components. This effort can pave the way for standardizing the design of sophisticated multimodal architectures for highly complex real-world problems.
The goal of explainable Artificial Intelligence (XAI) is to generate human-interpretable explanations, but there are no computationally precise theories of how humans interpret AI generated explanations. The lack of theory means that validation of XAI must be done empirically, on a case-by-case basis, which prevents systematic theory-building in XAI. We propose a psychological theory of how humans draw conclusions from saliency maps, the most common form of XAI explanation, which for the first time allows for precise prediction of explainee inference conditioned on explanation. Our theory posits that absent explanation humans expect the AI to make similar decisions to themselves, and that they interpret an explanation by comparison to the explanations they themselves would give. Comparison is formalized via Shepard's universal law of generalization in a similarity space, a classic theory from cognitive science. A pre-registered user study on AI image classifications with saliency map explanations demonstrate that our theory quantitatively matches participants' predictions of the AI.
Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.