The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.
Graph-structured data is ubiquitous in the world which models complex relationships between objects, enabling various Web applications. Daily influxes of unlabeled graph data on the Web offer immense potential for these applications. Graph self-supervised algorithms have achieved significant success in acquiring generic knowledge from abundant unlabeled graph data. These pre-trained models can be applied to various downstream Web applications, saving training time and improving downstream (target) performance. However, different graphs, even across seemingly similar domains, can differ significantly in terms of attribute semantics, posing difficulties, if not infeasibility, for transferring the pre-trained models to downstream tasks. Concretely speaking, for example, the additional task-specific node information in downstream tasks (specificity) is usually deliberately omitted so that the pre-trained representation (transferability) can be leveraged. The trade-off as such is termed as "transferability-specificity dilemma" in this work. To address this challenge, we introduce an innovative deployment module coined as GraphControl, motivated by ControlNet, to realize better graph domain transfer learning. Specifically, by leveraging universal structural pre-trained models and GraphControl, we align the input space across various graphs and incorporate unique characteristics of target data as conditional inputs. These conditions will be progressively integrated into the model during fine-tuning or prompt tuning through ControlNet, facilitating personalized deployment. Extensive experiments show that our method significantly enhances the adaptability of pre-trained models on target attributed datasets, achieving 1.4-3x performance gain. Furthermore, it outperforms training-from-scratch methods on target data with a comparable margin and exhibits faster convergence.
Satellite-based remote sensing missions have revolutionized our understanding of the Ocean state and dynamics. Among them, spaceborne altimetry provides valuable measurements of Sea Surface Height (SSH), which is used to estimate surface geostrophic currents. However, due to the sensor technology employed, important gaps occur in SSH observations. Complete SSH maps are produced by the altimetry community using linear Optimal Interpolations (OI) such as the widely-used Data Unification and Altimeter Combination System (DUACS). However, OI is known for producing overly smooth fields and thus misses some mesostructures and eddies. On the other hand, Sea Surface Temperature (SST) products have much higher data coverage and SST is physically linked to geostrophic currents through advection. We design a realistic twin experiment to emulate the satellite observations of SSH and SST to evaluate interpolation methods. We introduce a deep learning network able to use SST information, and a trainable in two settings: one where we have no access to ground truth during training and one where it is accessible. Our investigation involves a comparative analysis of the aforementioned network when trained using either supervised or unsupervised loss functions. We assess the quality of SSH reconstructions and further evaluate the network's performance in terms of eddy detection and physical properties. We find that it is possible, even in an unsupervised setting to use SST to improve reconstruction performance compared to SST-agnostic interpolations. We compare our reconstructions to DUACS's and report a decrease of 41\% in terms of root mean squared error.
Biomarker detection is an indispensable part in the diagnosis and treatment of low-grade glioma (LGG). However, current LGG biomarker detection methods rely on expensive and complex molecular genetic testing, for which professionals are required to analyze the results, and intra-rater variability is often reported. To overcome these challenges, we propose an interpretable deep learning pipeline, a Multi-Biomarker Histomorphology Discoverer (Multi-Beholder) model based on the multiple instance learning (MIL) framework, to predict the status of five biomarkers in LGG using only hematoxylin and eosin-stained whole slide images and slide-level biomarker status labels. Specifically, by incorporating the one-class classification into the MIL framework, accurate instance pseudo-labeling is realized for instance-level supervision, which greatly complements the slide-level labels and improves the biomarker prediction performance. Multi-Beholder demonstrates superior prediction performance and generalizability for five LGG biomarkers (AUROC=0.6469-0.9735) in two cohorts (n=607) with diverse races and scanning protocols. Moreover, the excellent interpretability of Multi-Beholder allows for discovering the quantitative and qualitative correlations between biomarker status and histomorphology characteristics. Our pipeline not only provides a novel approach for biomarker prediction, enhancing the applicability of molecular treatments for LGG patients but also facilitates the discovery of new mechanisms in molecular functionality and LGG progression.
Digital Twins (DT) are a promising concept in cyber-physical systems research due to their advanced features including monitoring and automated reasoning. Semantic technologies such as Knowledge Graphs (KG) are recently being utilized in DTs especially for information modelling. Building on this move, this paper proposes a pipeline for semantic association rule learning in DTs using KGs and time series data. In addition to this initial pipeline, we also propose new semantic association rule criterion. The approach is evaluated on an industrial water network scenario. Initial evaluation shows that the proposed approach is able to learn a high number of association rules with semantic information which are more generalizable. The paper aims to set a foundation for further work on using semantic association rule learning especially in the context of industrial applications.
The formulation of Mean Field Games (MFG) typically requires continuous differentiability of the Hamiltonian in order to determine the advective term in the Kolmogorov--Fokker--Planck equation for the density of players. However, in many cases of practical interest, the underlying optimal control problem may exhibit bang-bang controls, which typically lead to nondifferentiable Hamiltonians. We develop the analysis and numerical analysis of stationary MFG for the general case of convex, Lipschitz, but possibly nondifferentiable Hamiltonians. In particular, we propose a generalization of the MFG system as a Partial Differential Inclusion (PDI) based on interpreting the derivative of the Hamiltonian in terms of subdifferentials of convex functions. We establish existence of a weak solution to the MFG PDI system, and we further prove uniqueness under a similar monotonicity condition to the one considered by Lasry and Lions. We then propose a monotone finite element discretization of the problem, and we prove strong $H^1$-norm convergence of the approximations to the value function and strong $L^q$-norm convergence of the approximations of the density function. We illustrate the performance of the numerical method in numerical experiments featuring nonsmooth solutions.
In the quest to advance human-centric natural language generation (NLG) systems, ensuring alignment between NLG models and human preferences is crucial. For this alignment, current popular methods leverage a reinforcement learning (RL) approach with a reward model trained on feedback from humans. However, inherent disagreements due to the subjective nature of human preferences pose a significant challenge for training the reward model, resulting in a deterioration of the NLG performance. To tackle this issue, previous approaches typically rely on majority voting or averaging to consolidate multiple inconsistent preferences into a merged one. Although straightforward to understand and execute, such methods suffer from an inability to capture the nuanced degrees of disaggregation among humans and may only represent a specialized subset of individuals, thereby lacking the ability to quantitatively disclose the universality of human preferences. To address this challenge, this paper proposes a novel approach, which employs a Bayesian framework to account for the distribution of disagreements among human preferences as training a preference model, and names it as d-PM. Besides, considering the RL strategy's inefficient and complex training process over the training efficiency, we further propose utilizing the contrastive learning strategy to train the NLG model with the preference scores derived from the d-PM model. Extensive experiments on two human-centric NLG tasks, i.e., emotional support conversation and integrity "Rule-of-Thumb" generation, show that our method consistently exceeds previous SOTA models in both automatic and human evaluations.
In the recently emerging field of nonabelian group-based cryptography, a prominently used one-way function is the Conjugacy Search Problem (CSP), and two important classes of platform groups are polycyclic and matrix groups. In this paper, we discuss the complexity of the conjugacy search problem (CSP) in these two classes of platform groups using the three protocols in [10], [26], and [29] as our starting point. We produce a polynomial time solution for the CSP in a finite polycyclic group with two generators, and show that a restricted CSP is reducible to a DLP. In matrix groups over finite fields, we usedthe Jordan decomposition of a matrix to produce a polynomial time reduction of an A-restricted CSP, where A is a cyclic subgroup of the general linear group, to a set of DLPs over an extension of Fq. We use these general methods and results to describe concrete cryptanalysis algorithms for these three systems. In particular, we show that in the group of invertible matrices over finite fields and in polycyclic groups with two generators, a CSP where conjugators are restricted to a cyclic subgroup is reducible to a set of O(n2) discrete logarithm problems. Using our general results, we demonstrate concrete cryptanalysis algorithms for each of these three schemes. We believe that our methods and findings are likely to allow for several other heuristic attacks in the general case.
Causal DAGs (also known as Bayesian networks) are a popular tool for encoding conditional dependencies between random variables. In a causal DAG, the random variables are modeled as vertices in the DAG, and it is stipulated that every random variable is independent of its ancestors conditioned on its parents. It is possible, however, for two different causal DAGs on the same set of random variables to encode exactly the same set of conditional dependencies. Such causal DAGs are said to be Markov equivalent, and equivalence classes of Markov equivalent DAGs are known as Markov Equivalent Classes (MECs). Beautiful combinatorial characterizations of MECs have been developed in the past few decades, and it is known, in particular that all DAGs in the same MEC must have the same ''skeleton'' (underlying undirected graph) and v-structures (induced subgraph of the form $a\rightarrow b \leftarrow c$). These combinatorial characterizations also suggest several natural algorithmic questions. One of these is: given an undirected graph $G$ as input, how many distinct Markov equivalence classes have the skeleton $G$? Much work has been devoted in the last few years to this and other closely related problems. However, to the best of our knowledge, a polynomial time algorithm for the problem remains unknown. In this paper, we make progress towards this goal by giving a fixed parameter tractable algorithm for the above problem, with the parameters being the treewidth and the maximum degree of the input graph $G$. The main technical ingredient in our work is a construction we refer to as shadow, which lets us create a "local description'' of long-range constraints imposed by the combinatorial characterizations of MECs.
Assistive devices, such as exoskeletons and prostheses, have revolutionized the field of rehabilitation and mobility assistance. Efficiently detecting transitions between different activities, such as walking, stair ascending and descending, and sitting, is crucial for ensuring adaptive control and enhancing user experience. We here present an approach for real-time transition detection, aimed at optimizing the processing-time performance. By establishing activity-specific threshold values through trained machine learning models, we effectively distinguish motion patterns and we identify transition moments between locomotion modes. This threshold-based method improves real-time embedded processing time performance by up to 11 times compared to machine learning approaches. The efficacy of the developed finite-state machine is validated using data collected from three different measurement systems. Moreover, experiments with healthy participants were conducted on an active pelvis orthosis to validate the robustness and reliability of our approach. The proposed algorithm achieved high accuracy in detecting transitions between activities. These promising results show the robustness and reliability of the method, reinforcing its potential for integration into practical applications.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.