pwc-archive/papers-with-abstracts huggingface dataset:
Guaranteed Nonconvex Factorization Approach for Tensor Train Recovery
Authors: Zhen Qin, Michael B. Wakin, Zhihui Zhu
Date: 2024-01-05 00:00:00

In this paper, we provide the first convergence guarantee for the factorization approach. Specifically, to avoid the scaling ambiguity and to facilitate theoretical analysis, we optimize over the so-called left-orthogonal TT format which enforces orthonormality among most of the factors. To ensure the orthonormal structure, we utilize the Riemannian gradient descent (RGD) for optimizing those factors over the Stiefel manifold. We first delve into the TT factorization problem and establish the local linear convergence of RGD. Notably, the rate of convergence only experiences a linear decline as the tensor order increases. We then study the sensing problem that aims to recover a TT format tensor from linear measurements. Assuming the sensing operator satisfies the restricted isometry property (RIP), we show that with a proper initialization, which could be obtained through spectral initialization, RGD also converges to the ground-truth tensor at a linear rate. Furthermore, we expand our analysis to encompass scenarios involving Gaussian noise in the measurements. We prove that RGD can reliably recover the ground truth at a linear rate, with the recovery error exhibiting only polynomial growth in relation to the tensor order. We conduct various experiments to validate our theoretical findings.
Optimal Chaining of Vehicle Plans with Time Windows
Authors: David Fiedler, Fabio V. Difonzo, Jan Mrkos
Date: 2024-01-05 00:00:00

For solving problems from the domain of Mobility-on-Demand (MoD), we often need to connect vehicle plans into plans spanning longer time, a process we call plan chaining. As we show in this work, chaining of the plans can be used to reduce the size of MoD providers' fleet (fleet-sizing problem) but also to reduce the total driven distance by providing high-quality vehicle dispatching solutions in MoD systems. Recently, a solution that uses this principle has been proposed to solve the fleet-sizing problem. The method does not consider the time flexibility of the plans. Instead, plans are fixed in time and cannot be delayed. However, time flexibility is an essential property of all vehicle problems with time windows. This work presents a new plan chaining formulation that considers delays as allowed by the time windows and a solution method for solving it. Moreover, we prove that the proposed plan chaining method is optimal, and we analyze its complexity. Finally, we list some practical applications and perform a demonstration for one of them: a new heuristic vehicle dispatching method for solving the static dial-a-ride problem. The demonstration results show that our proposed method provides a better solution than the two heuristic baselines for the majority of instances that cannot be solved optimally. At the same time, our method does not have the largest computational time requirements compared to the baselines. Therefore, we conclude that the proposed optimal chaining method provides not only theoretically sound results but is also practically applicable.
Constrained Max Drawdown: a Fast and Robust Portfolio Optimization Approach
Authors: Albert Dorador
Date: 2024-01-05 00:00:00
Tasks: Portfolio Optimization, Sensitivity

We propose an alternative linearization to the classical Markowitz quadratic portfolio optimization model, based on maximum drawdown. This model, which minimizes maximum portfolio drawdown, is particularly appealing during times of financial distress, like during the COVID-19 pandemic. In addition, we will present a Mixed-Integer Linear Programming variation of our new model that, based on our out-of-sample results and sensitivity analysis, delivers a more profitable and robust solution with a 200 times faster solving time compared to the standard Markowitz quadratic formulation.
Structured Matrix Learning under Arbitrary Entrywise Dependence and Estimation of Markov Transition Kernel
Authors: Jinhang Chai, Jianqing Fan
Date: 2024-01-04 00:00:00

The problem of structured matrix estimation has been studied mostly under strong noise dependence assumptions. This paper considers a general framework of noisy low-rank-plus-sparse matrix recovery, where the noise matrix may come from any joint distribution with arbitrary dependence across entries. We propose an incoherent-constrained least-square estimator and prove its tightness both in the sense of deterministic lower bound and matching minimax risks under various noise distributions. To attain this, we establish a novel result asserting that the difference between two arbitrary low-rank incoherent matrices must spread energy out across its entries; in other words, it cannot be too sparse, which sheds light on the structure of incoherent low-rank matrices and may be of independent interest. We then showcase the applications of our framework to several important statistical machine learning problems. In the problem of estimating a structured Markov transition kernel, the proposed method achieves the minimax optimality and the result can be extended to estimating the conditional mean operator, a crucial component in reinforcement learning. The applications to multitask regression and structured covariance estimation are also presented. We propose an alternating minimization algorithm to approximately solve the potentially hard optimization problem. Numerical results corroborate the effectiveness of our method which typically converges in a few steps.
Graph-level Protein Representation Learning by Structure Knowledge Refinement
Authors: Ge Wang, Zelin Zang, Jiangbin Zheng, Jun Xia, Stan Z. Li
Date: 2024-01-05 00:00:00
Tasks: Contrastive Learning, Property Prediction, Representation Learning

This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-world issues such as molecule property prediction, protein structure feature extraction, and social network analysis. The mainstream method is utilizing contrastive learning to facilitate graph feature extraction, known as Graph Contrastive Learning (GCL). GCL, although effective, suffers from some complications in contrastive learning, such as the effect of false negative pairs. Moreover, augmentation strategies in GCL are weakly adaptive to diverse graph datasets. Motivated by these problems, we propose a novel framework called Structure Knowledge Refinement (SKR) which uses data structure to determine the probability of whether a pair is positive or negative. Meanwhile, we propose an augmentation strategy that naturally preserves the semantic meaning of the original data and is compatible with our SKR framework. Furthermore, we illustrate the effectiveness of our SKR framework through intuition and experiments. The experimental results on the tasks of graph-level classification demonstrate that our SKR framework is superior to most state-of-the-art baselines.
Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation
Authors: Can Xu, Haosen Wang, Weigang Wang, Pengfei Zheng, Hongyang Chen
Date: 2024-01-05 00:00:00
Tasks: 3D Molecule Generation, Denoising

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow connections to multiple atoms through single bonds, solely using pair-wise distance to model molecule geometries is insufficient. Therefore, the first one involves proposing an effective neural network as the denoising kernel that is capable to capture complex multi-body interatomic relationships and learn high-quality features. Due to the discrete nature of graphs, mainstream diffusion-based methods for molecules heavily rely on predefined rules and generate edges in an indirect manner. The second challenge involves accommodating molecule generation to diffusion and accurately predicting the existence of bonds. In our research, we view the iterative way of updating molecule conformations in diffusion process is consistent with molecular dynamics and introduce a novel molecule generation method named Geometric-Facilitated Molecular Diffusion (GFMDiff). For the first challenge, we introduce a Dual-Track Transformer Network (DTN) to fully excevate global spatial relationships and learn high quality representations which contribute to accurate predictions of features and geometries. As for the second challenge, we design Geometric-Facilitated Loss (GFLoss) which intervenes the formation of bonds during the training period, instead of directly embedding edges into the latent space. Comprehensive experiments on current benchmarks demonstrate the superiority of GFMDiff.
Large Language Models in Plant Biology
Authors: Hilbert Yuen In Lam, Xing Er Ong, Marek Mutwil
Date: 2024-01-05 00:00:00

Large Language Models (LLMs), such as ChatGPT, have taken the world by storm and have passed certain forms of the Turing test. However, LLMs are not limited to human language and analyze sequential data, such as DNA, protein, and gene expression. The resulting foundation models can be repurposed to identify the complex patterns within the data, resulting in powerful, multi-purpose prediction tools able to explain cellular systems. This review outlines the different types of LLMs and showcases their recent uses in biology. Since LLMs have not yet been embraced by the plant community, we also cover how these models can be deployed for the plant kingdom.
Memory, Consciousness and Large Language Model
Authors: Jitang Li, Jinzheng Li
Date: 2024-01-04 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model, model, Retrieval

With the development in cognitive science and Large Language Models (LLMs), increasing connections have come to light between these two distinct fields. Building upon these connections, we propose a conjecture suggesting the existence of a duality between LLMs and Tulving's theory of memory. We identify a potential correspondence between Tulving's synergistic ecphory model (SEM) of retrieval and the emergent abilities observed in LLMs, serving as supporting evidence for our conjecture. Furthermore, we speculate that consciousness may be considered a form of emergent ability based on this duality. We also discuss how other theories of consciousness intersect with our research.
Dynamic coexistence driven by physiological transitions in microbial communities
Authors: Avaneesh V. Narla, Terence Hwa, Arvind Murugan
Date: 2024-01-04 00:00:00

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.
Denoising Diffusion Variational Inference: Diffusion Models as Expressive Variational Posteriors
Authors: Wasu Top Piriyakulkij, Yingheng Wang, Volodymyr Kuleshov
Date: 2024-01-05 00:00:00
Tasks: Denoising, Variational Inference

We propose denoising diffusion variational inference (DDVI), a black-box variational inference algorithm for latent variable models which relies on diffusion models as flexible approximate posteriors. Specifically, our method introduces an expressive class of diffusion-based variational posteriors that perform iterative refinement in latent space; we train these posteriors with a novel regularized evidence lower bound (ELBO) on the marginal likelihood inspired by the wake-sleep algorithm. Our method is easy to implement (it fits a regularized extension of the ELBO), is compatible with black-box variational inference, and outperforms alternative classes of approximate posteriors based on normalizing flows or adversarial networks. We find that DDVI improves inference and learning in deep latent variable models across common benchmarks as well as on a motivating task in biology -- inferring latent ancestry from human genomes -- where it outperforms strong baselines on the Thousand Genomes dataset.
Elastic jump propagation across a blood vessel junction
Authors: Tamsin A. Spelman, Ifeanyi S. Onah, David MacTaggart, Peter S. Stewart
Date: 2024-01-04 00:00:00

The theory of small-amplitude waves propagating across a blood vessel junction has been well established with linear analysis. In this study we consider the propagation of large-amplitude, nonlinear waves (i.e. shocks and rarefactions) through a junction from a parent vessel into two (identical) daughter vessels using a combination of three approaches: numerical computations using a Godunov method with patching across the junction, analysis of a nonlinear Riemann problem in the neighbourhood of the junction and an analytical theory which extends the linear analysis to the following order in amplitude. A unified picture emerges: an abrupt (prescribed) increase in pressure at the inlet to the parent vessel generates a propagating shock wave along the parent vessel which interacts with the junction. For modest driving, this shock wave divides into propagating shock waves along the two daughter vessels and reflects a rarefaction wave back towards the inlet. However, for larger driving the reflected rarefaction wave becomes transcritical, generating an additional shock wave. Just beyond criticality this new shock wave has zero speed, pinned to the junction, but for further increases in driving this additional shock divides into two new propagating shock waves in the daughter vessels.
Predicting Future States with Spatial Point Processes in Single Molecule Resolution Spatial Transcriptomics
Authors: Biraaj Rout, Priyanshi Borad, Parisa Boodaghi Malidarreh, Mohammad Sadegh Nasr, Jillur Rahman Saurav, Kelli Fenelon, Jai Prakash Veerla, Jacob M. Luber, Theodora Koromila
Date: 2024-01-04 00:00:00
Tasks: Point Processes, regression, Super-Resolution

In this paper, we introduce a pipeline based on XGboost to predict the future distribution of cells that are expressed by the Sog-D gene (active cells) in both the Anterior to posterior (AP) and the Dorsal to Ventral (DV) axis of the Drosophila in embryogenesis process. This method provides insights about how cells and living organisms control gene expression in super resolution whole embryo spatial transcriptomics imaging at sub cellular, single molecule resolution. An XGboost model was used to predict the next stage active distribution based on the previous one. To achieve this goal, we leveraged temporally resolved, spatial point processes by including Ripley's K-function in conjunction with the cell's state in each stage of embryogenesis, and found average predictive accuracy of active cell distribution. This tool is analogous to RNA Velocity for spatially resolved developmental biology, from one data point we can predict future spatially resolved gene expression using features from the spatial point processes.
Displaying risk in mergers: a diagrammatic approach for exchange ratio determination
Authors: Alessandra Mainini, Enrico Moretto, Daniela Visetti
Date: 2024-01-05 00:00:00

This article extends, in a stochastic setting, previous results in the determination of feasible exchange ratios for merging companies. A first outcome is that shareholders of the companies involved in the merging process face both an upper and a lower bounds for acceptable exchange ratios. Secondly, in order for the improved `bargaining region' to be intelligibly displayed, the diagrammatic approach developed by Kulpa is exploited.
Model-Agnostic Interpretation Framework in Machine Learning: A Comparative Study in NBA Sports
Authors: Shun Liu
Date: 2024-01-05 00:00:00
Tasks: Computational Efficiency, Decision Making

The field of machine learning has seen tremendous progress in recent years, with deep learning models delivering exceptional performance across a range of tasks. However, these models often come at the cost of interpretability, as they operate as opaque "black boxes" that obscure the rationale behind their decisions. This lack of transparency can limit understanding of the models' underlying principles and impede their deployment in sensitive domains, such as healthcare or finance. To address this challenge, our research team has proposed an innovative framework designed to reconcile the trade-off between model performance and interpretability. Our approach is centered around modular operations on high-dimensional data, which enable end-to-end processing while preserving interpretability. By fusing diverse interpretability techniques and modularized data processing, our framework sheds light on the decision-making processes of complex models without compromising their performance. We have extensively tested our framework and validated its superior efficacy in achieving a harmonious balance between computational efficiency and interpretability. Our approach addresses a critical need in contemporary machine learning applications by providing unprecedented insights into the inner workings of complex models, fostering trust, transparency, and accountability in their deployment across diverse domains.
Quantitative Technology Forecasting: a Review of Trend Extrapolation Methods
Authors: Peng-Hung Tsai, Daniel Berleant, Richard S. Segall, Hyacinthe Aboudja, Venkata Jaipal R. Batthula, Sheela Duggirala, Michael Howell
Date: 2024-01-04 00:00:00
Tasks: Time Series

Quantitative technology forecasting uses quantitative methods to understand and project technological changes. It is a broad field encompassing many different techniques and has been applied to a vast range of technologies. A widely used approach in this field is trend extrapolation. Based on the publications available to us, there has been little or no attempt made to systematically review the empirical evidence on quantitative trend extrapolation techniques. This study attempts to close this gap by conducting a systematic review of technology forecasting literature addressing the application of quantitative trend extrapolation techniques. We identified 25 studies relevant to the objective of this research and classified the techniques used in the studies into different categories, among which growth curves and time series methods were shown to remain popular over the past decade, while newer methods, such as machine learning-based hybrid models, have emerged in recent years. As more effort and evidence are needed to determine if hybrid models are superior to traditional methods, we expect to see a growing trend in the development and application of hybrid models to technology forecasting.
Hyperparameter Estimation for Sparse Bayesian Learning Models
Authors: Feng Yu, Lixin Shen, Guohui Song
Date: 2024-01-04 00:00:00

Sparse Bayesian Learning (SBL) models are extensively used in signal processing and machine learning for promoting sparsity through hierarchical priors. The hyperparameters in SBL models are crucial for the model's performance, but they are often difficult to estimate due to the non-convexity and the high-dimensionality of the associated objective function. This paper presents a comprehensive framework for hyperparameter estimation in SBL models, encompassing well-known algorithms such as the expectation-maximization (EM), MacKay, and convex bounding (CB) algorithms. These algorithms are cohesively interpreted within an alternating minimization and linearization (AML) paradigm, distinguished by their unique linearized surrogate functions. Additionally, a novel algorithm within the AML framework is introduced, showing enhanced efficiency, especially under low signal noise ratios. This is further improved by a new alternating minimization and quadratic approximation (AMQ) paradigm, which includes a proximal regularization term. The paper substantiates these advancements with thorough convergence analysis and numerical experiments, demonstrating the algorithm's effectiveness in various noise conditions and signal-to-noise ratios.
Dagma-DCE: Interpretable, Non-Parametric Differentiable Causal Discovery
Authors: Daniel Waxman, Kurt Butler, Petar M. Djuric
Date: 2024-01-05 00:00:00
Tasks: Causal Discovery

We introduce Dagma-DCE, an interpretable and model-agnostic scheme for differentiable causal discovery. Current non- or over-parametric methods in differentiable causal discovery use opaque proxies of ``independence'' to justify the inclusion or exclusion of a causal relationship. We show theoretically and empirically that these proxies may be arbitrarily different than the actual causal strength. Juxtaposed to existing differentiable causal discovery algorithms, \textsc{Dagma-DCE} uses an interpretable measure of causal strength to define weighted adjacency matrices. In a number of simulated datasets, we show our method achieves state-of-the-art level performance. We additionally show that \textsc{Dagma-DCE} allows for principled thresholding and sparsity penalties by domain-experts. The code for our method is available open-source at https://github.com/DanWaxman/DAGMA-DCE, and can easily be adapted to arbitrary differentiable models.
Shared active subspace for multivariate vector-valued functions
Authors: Khadija Musayeva, Mickael Binois
Date: 2024-01-05 00:00:00

This paper proposes several approaches as baselines to compute a shared active subspace for multivariate vector-valued functions. The goal is to minimize the deviation between the function evaluations on the original space and those on the reconstructed one. This is done either by manipulating the gradients or the symmetric positive (semi-)definite (SPD) matrices computed from the gradients of each component function so as to get a single structure common to all component functions. These approaches can be applied to any data irrespective of the underlying distribution unlike the existing vector-valued approach that is constrained to a normal distribution. We test the effectiveness of these methods on five optimization problems. The experiments show that, in general, the SPD-level methods are superior to the gradient-level ones, and are close to the vector-valued approach in the case of a normal distribution. Interestingly, in most cases it suffices to take the sum of the SPD matrices to identify the best shared active subspace.