Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying biological mechanisms, but is a complex mathematical problem. We present an efficient approach to determine a basic topological property of the parameter region of multistationary, namely whether it is connected or not. The connectivity of this region can be interpreted in terms of the biological mechanisms underlying bistability and the switch-like patterns that the system can create. We provide an algorithm to assert that the parameter region of multistationarity is connected, targeting reaction networks with mass-action kinetics. We show that this is the case for numerous relevant cell signaling motifs, previously described to exhibit bistability. However, we show that for a motif displaying a phosphorylation cycle with allosteric enzyme regulation, the region of multistationarity has two distinct connected components, corresponding to two different, but symmetric, biological mechanisms. The method relies on linear programming and bypasses the expensive computational cost of direct and generic approaches to study parametric polynomial systems. This characteristic makes it suitable for mass-screening of reaction networks.
Statistical Shape Modeling (SSM) is a valuable tool for investigating and quantifying anatomical variations within populations of anatomies. However, traditional correspondence-based SSM generation methods require a time-consuming re-optimization process each time a new subject is added to the cohort, making the inference process prohibitive for clinical research. Additionally, they require complete geometric proxies (e.g., high-resolution binary volumes or surface meshes) as input shapes to construct the SSM. Unordered 3D point cloud representations of shapes are more easily acquired from various medical imaging practices (e.g., thresholded images and surface scanning). Point cloud deep networks have recently achieved remarkable success in learning permutation-invariant features for different point cloud tasks (e.g., completion, semantic segmentation, classification). However, their application to learning SSM from point clouds is to-date unexplored. In this work, we demonstrate that existing point cloud encoder-decoder-based completion networks can provide an untapped potential for SSM, capturing population-level statistical representations of shapes while reducing the inference burden and relaxing the input requirement. We discuss the limitations of these techniques to the SSM application and suggest future improvements. Our work paves the way for further exploration of point cloud deep learning for SSM, a promising avenue for advancing shape analysis literature and broadening SSM to diverse use cases.
Inferring causal structures from time series data is the central interest of many scientific inquiries. A major barrier to such inference is the problem of subsampling, i.e., the frequency of measurements is much lower than that of causal influence. To overcome this problem, numerous model-based and model-free methods have been proposed, yet either limited to the linear case or failed to establish identifiability. In this work, we propose a model-free algorithm that can identify the entire causal structure from subsampled time series, without any parametric constraint. The idea is that the challenge of subsampling arises mainly from \emph{unobserved} time steps and therefore should be handled with tools designed for unobserved variables. Among these tools, we find the proxy variable approach particularly fits, in the sense that the proxy of an unobserved variable is naturally itself at the observed time step. Following this intuition, we establish comprehensive structural identifiability results. Our method is constraint-based and requires no more regularities than common continuity and differentiability. Theoretical advantages are reflected in experimental results.
A good understanding of the heat transfer in fused filament fabrication is crucial for an accurate stress prediction and subsequently for repetitive, high quality printing. This work focuses on two challenges that have been presented when it comes to the accuracy and efficiency in simulating the heat transfer in the fused filament fabrication process. With the prospect of choosing correct thermal boundary conditions expressing the natural convection between printed material and its environment, values for the convective heat transfer coefficient and ambient temperature were calibrated through numerical data fitting of experimental thermal measurements. Furthermore, modeling simplifications were proposed for an efficient numerical discretization of infill structures. Samples were printed with varying infill characteristics, such as varying air void size, infill densities and infill patterns. Thermal measurements were performed to investigate the role of these parameters on the heat transfer and based on these observations, possible modeling simplifications were studied in the numerical simulations.
Harnessing complex body dynamics has been a long-standing challenge in robotics. Soft body dynamics is a typical example of high complexity in interacting with the environment. An increasing number of studies have reported that these dynamics can be used as a computational resource. This includes the McKibben pneumatic artificial muscle, which is a typical soft actuator. This study demonstrated that various dynamics, including periodic and chaotic dynamics, could be embedded into the pneumatic artificial muscle, with the entire bifurcation structure using the framework of physical reservoir computing. These results suggest that dynamics that are not presented in training data could be embedded by using this capability of bifurcation embeddment. This implies that it is possible to embed various qualitatively different patterns into pneumatic artificial muscle by learning specific patterns, without the need to design and learn all patterns required for the purpose. Thus, this study sheds new light on a novel pathway to simplify the robotic devices and training of the control by reducing the external pattern generators and the amount and types of training data for the control.
The Fisher-Kolmogorov equation is a diffusion-reaction PDE that is used to model the accumulation of prionic proteins, which are responsible for many different neurological disorders. Likely, the most important and studied misfolded protein in literature is the Amyloid-$\beta$, responsible for the onset of Alzheimer disease. Starting from medical images we construct a reduced-order model based on a graph brain connectome. The reaction coefficient of the proteins is modelled as a stochastic random field, taking into account all the many different underlying physical processes, which can hardly be measured. Its probability distribution is inferred by means of the Monte Carlo Markov Chain method applied to clinical data. The resulting model is patient-specific and can be employed for predicting the disease's future development. Forward uncertainty quantification techniques (Monte Carlo and sparse grid stochastic collocation) are applied with the aim of quantifying the impact of the variability of the reaction coefficient on the progression of protein accumulation within the next 20 years.
Arguably, the largest class of stochastic processes generated by means of a finite memory consists of those that are sequences of observations produced by sequential measurements in a suitable generalized probabilistic theory (GPT). These are constructed from a finite-dimensional memory evolving under a set of possible linear maps, and with probabilities of outcomes determined by linear functions of the memory state. Examples of such models are given by classical hidden Markov processes, where the memory state is a probability distribution, and at each step it evolves according to a non-negative matrix, and hidden quantum Markov processes, where the memory state is a finite dimensional quantum state, and at each step it evolves according to a completely positive map. Here we show that the set of processes admitting a finite-dimensional explanation do not need to be explainable in terms of either classical probability or quantum mechanics. To wit, we exhibit families of processes that have a finite-dimensional explanation, defined manifestly by the dynamics of explicitly given GPT, but that do not admit a quantum, and therefore not even classical, explanation in finite dimension. Furthermore, we present a family of quantum processes on qubits and qutrits that do not admit a classical finite-dimensional realization, which includes examples introduced earlier by Fox, Rubin, Dharmadikari and Nadkarni as functions of infinite dimensional Markov chains, and lower bound the size of the memory of a classical model realizing a noisy version of the qubit processes.
現代生物醫學數據集——從基因表達的分子測量到病理圖像——為發現新的治療方法和探索有關細胞行為的基本問題提供了希望。對這些復雜的高維數據進行深思熟慮的統計建模,對于闡明可靠的科學發現至關重要。數據分析中一個常見的假設是數據樣本是獨立同分布的。然而,這個假設在實踐中幾乎總是被違背。在生物醫學數據的設置中尤其如此,生物醫學數據通常表現出一定的結構,例如患者的亞群、細胞或組織類型或樣本之間的其他相關結構。
在這項工作中,我提出了數據分析和實驗設計框架,以解釋幾種類型的高度結構化生物醫學數據。這些方法采用貝葉斯模型和相關推理算法的形式,是專門為具有組結構、多種數據模態和樣本空間組織的數據集量身定制的。在第一行工作中,我提出了一個對比降維模型,該模型分解了屬于案例和控制條件的樣本的變異源。其次,提出了一種計算框架,用于將空間分辨的基因組數據對齊到一個共同的坐標系中,該坐標系考慮了樣本之間的空間相關性,并對多種數據模態進行建模。最后,我提出了一系列方法,用于優化設計空間分辨基因組學實驗,這些方法是為這些研究的高度結構化數據收集過程量身定制的。通過開發直接利用這些數據中常見結構類型的模型,并展示這些建模方法在各種數據類型中的優勢,這些工作推進了生物醫學數據分析領域。 //dataspace.princeton.edu/handle/88435/dsp01bn9999982
Learning on big data brings success for artificial intelligence (AI), but the annotation and training costs are expensive. In future, learning on small data is one of the ultimate purposes of AI, which requires machines to recognize objectives and scenarios relying on small data as humans. A series of machine learning models is going on this way such as active learning, few-shot learning, deep clustering. However, there are few theoretical guarantees for their generalization performance. Moreover, most of their settings are passive, that is, the label distribution is explicitly controlled by one specified sampling scenario. This survey follows the agnostic active sampling under a PAC (Probably Approximately Correct) framework to analyze the generalization error and label complexity of learning on small data using a supervised and unsupervised fashion. With these theoretical analyses, we categorize the small data learning models from two geometric perspectives: the Euclidean and non-Euclidean (hyperbolic) mean representation, where their optimization solutions are also presented and discussed. Later, some potential learning scenarios that may benefit from small data learning are then summarized, and their potential learning scenarios are also analyzed. Finally, some challenging applications such as computer vision, natural language processing that may benefit from learning on small data are also surveyed.
論文題目: Automatic structured variational inference
摘要: 概率編程的目的是在任意概率模型(程序)中自動概率推理的各個方面,這樣用戶就可以將注意力集中在建模上,而不需要處理特定的推理方法。基于梯度的自動微分隨機變分推理是一種有效的概率規劃方法。然而,任何(參數)變分方法的性能取決于適當的變分族的選擇。在這里,我們介紹了一種完全自動化的方法來構建結構化的變分族,其靈感來自于共軛模型的封閉形式更新。這些偽共軛族包含了輸入概率程序的前向傳遞,可以捕獲復雜的統計相關性。偽共軛族具有與輸入概率程序相同的空間和時間復雜度,因此在很大的一類模型中是可處理的。我們將自動變分方法應用于包括深度學習組件在內的多種高維推理問題。