The Conditional Gaussian Nonlinear System (CGNS) is a broad class of nonlinear stochastic dynamical systems. Given the trajectories for a subset of state variables, the remaining follow a Gaussian distribution. Despite the conditionally linear structure, the CGNS exhibits strong nonlinearity, thus capturing many non-Gaussian characteristics observed in nature through its joint and marginal distributions. Desirably, it enjoys closed analytic formulae for the time evolution of its conditional Gaussian statistics, which facilitate the study of data assimilation and other related topics. In this paper, we develop a martingale-free approach to improve the understanding of CGNSs. This methodology provides a tractable approach to proving the time evolution of the conditional statistics by deriving results through time discretization schemes, with the continuous-time regime obtained via a formal limiting process as the discretization time-step vanishes. This discretized approach further allows for developing analytic formulae for optimal posterior sampling of unobserved state variables with correlated noise. These tools are particularly valuable for studying extreme events and intermittency and apply to high-dimensional systems. Moreover, the approach improves the understanding of different sampling methods in characterizing uncertainty. The effectiveness of the framework is demonstrated through a physics-constrained, triad-interaction climate model with cubic nonlinearity and state-dependent cross-interacting noise.
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The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.
Computed tomography from a low radiation dose (LDCT) is challenging due to high noise in the projection data. Popular approaches for LDCT image reconstruction are two-stage methods, typically consisting of the filtered backprojection (FBP) algorithm followed by a neural network for LDCT image enhancement. Two-stage methods are attractive for their simplicity and potential for computational efficiency, typically requiring only a single FBP and a neural network forward pass for inference. However, the best reconstruction quality is currently achieved by unrolled iterative methods (Learned Primal-Dual and ItNet), which are more complex and thus have a higher computational cost for training and inference. We propose a method combining the simplicity and efficiency of two-stage methods with state-of-the-art reconstruction quality. Our strategy utilizes a neural network pretrained for Gaussian noise removal from natural grayscale images, fine-tuned for LDCT image enhancement. We call this method FBP-DTSGD (Domain and Task Shifted Gaussian Denoisers) as the fine-tuning is a task shift from Gaussian denoising to enhancing LDCT images and a domain shift from natural grayscale to LDCT images. An ablation study with three different pretrained Gaussian denoisers indicates that the performance of FBP-DTSGD does not depend on a specific denoising architecture, suggesting future advancements in Gaussian denoising could benefit the method. The study also shows that pretraining on natural images enhances LDCT reconstruction quality, especially with limited training data. Notably, pretraining involves no additional cost, as existing pretrained models are used. The proposed method currently holds the top mean position in the LoDoPaB-CT challenge.
Large language models (LLMs) have shown remarkable capability in numerous tasks and applications. However, fine-tuning LLMs using high-quality datasets under external supervision remains prohibitively expensive. In response, LLM self-improvement approaches have been vibrantly developed recently. The typical paradigm of LLM self-improvement involves training LLM on self-generated data, part of which may be detrimental and should be filtered out due to the unstable data quality. While current works primarily employs filtering strategies based on answer correctness, in this paper, we demonstrate that filtering out correct but with high distribution shift extent (DSE) samples could also benefit the results of self-improvement. Given that the actual sample distribution is usually inaccessible, we propose a new metric called DS weight to approximate DSE, inspired by the Importance Weighting methods. Consequently, we integrate DS weight with self-consistency to comprehensively filter the self-generated samples and fine-tune the language model. Experiments show that with only a tiny valid set (up to 5\% size of the training set) to compute DS weight, our approach can notably promote the reasoning ability of current LLM self-improvement methods. The resulting performance is on par with methods that rely on external supervision from pre-trained reward models.
We consider the computational efficiency of Monte Carlo (MC) and Multilevel Monte Carlo (MLMC) methods applied to partial differential equations with random coefficients. These arise, for example, in groundwater flow modelling, where a commonly used model for the unknown parameter is a random field. We make use of the circulant embedding procedure for sampling from the aforementioned coefficient. To improve the computational complexity of the MLMC estimator in the case of highly oscillatory random fields, we devise and implement a smoothing technique integrated into the circulant embedding method. This allows to choose the coarsest mesh on the first level of MLMC independently of the correlation length of the covariance function of the random field, leading to considerable savings in computational cost. We illustrate this with numerical experiments, where we see a saving of factor 5-10 in computational cost for accuracies of practical interest.
Computed Tomography (CT) is a widely used imaging technique that provides detailed cross-sectional views of objects. Over the past decade, Deep Learning-based Reconstruction (DLR) methods have led efforts to enhance image quality and reduce noise, yet they often require large amounts of data and are computationally intensive. Inspired by recent advancements in scene reconstruction, some approaches have adapted NeRF and 3D Gaussian Splatting (3DGS) techniques for CT reconstruction. However, these methods are not ideal for direct 3D volume reconstruction. In this paper, we reconsider the representation of CT reconstruction and propose a novel Discretized Gaussian Representation (DGR) specifically designed for CT. Unlike the popular 3D Gaussian Splatting, our representation directly reconstructs the 3D volume using a set of discretized Gaussian functions in an end-to-end manner. Additionally, we introduce a Fast Volume Reconstruction technique that efficiently aggregates the contributions of these Gaussians into a discretized volume. Extensive experiments on both real-world and synthetic datasets demonstrate the effectiveness of our method in improving reconstruction quality and computational efficiency. Our code has been provided for review purposes and will be made publicly available upon acceptance.
Soft robots have the potential to interact with sensitive environments and perform complex tasks effectively. However, motion plans and trajectories for soft manipulators are challenging to calculate due to their deformable nature and nonlinear dynamics. This article introduces a fast real-time trajectory generation approach for soft robot manipulators, which creates dynamically-feasible motions for arbitrary kinematically-feasible paths of the robot's end effector. Our insight is that piecewise constant curvature (PCC) dynamics models of soft robots can be differentially flat, therefore control inputs can be calculated algebraically rather than through a nonlinear differential equation. We prove this flatness under certain conditions, with the curvatures of the robot as the flat outputs. Our two-step trajectory generation approach uses an inverse kinematics procedure to calculate a motion plan of robot curvatures per end-effector position, then, our flatness diffeomorphism generates corresponding control inputs that respect velocity. We validate our approach through simulations of our representative soft robot manipulator along three different trajectories, demonstrating a margin of 23x faster than real-time at a frequency of 100 Hz. This approach could allow fast verifiable replanning of soft robots' motions in safety-critical physical environments, crucial for deployment in the real world.
Federated Learning (FL) is a decentralized machine-learning paradigm, in which a global server iteratively averages the model parameters of local users without accessing their data. User heterogeneity has imposed significant challenges to FL, which can incur drifted global models that are slow to converge. Knowledge Distillation has recently emerged to tackle this issue, by refining the server model using aggregated knowledge from heterogeneous users, other than directly averaging their model parameters. This approach, however, depends on a proxy dataset, making it impractical unless such a prerequisite is satisfied. Moreover, the ensemble knowledge is not fully utilized to guide local model learning, which may in turn affect the quality of the aggregated model. Inspired by the prior art, we propose a data-free knowledge distillation} approach to address heterogeneous FL, where the server learns a lightweight generator to ensemble user information in a data-free manner, which is then broadcasted to users, regulating local training using the learned knowledge as an inductive bias. Empirical studies powered by theoretical implications show that, our approach facilitates FL with better generalization performance using fewer communication rounds, compared with the state-of-the-art.
Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis.
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