Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective Self-Assembly using Re-Programmable Magnetic Pixels

This paper introduces a method to generate highly selective encodings that can be magnetically “programmed” onto physical modules to enable them to self-assemble in chosen configurations. We generate these encodings based on Hadamard matrices, and show how to design the faces of modules to be maximally attractive to their intended mate, while remaining maximally agnostic to other faces. We derive guarantees on these bounds, and verify their attraction and agnosticism experimentally. Using cubic modules whose faces have been covered in soft magnetic material, we show how inexpensive, passive modules with planar faces can be used to selectively self-assemble into target shapes without geometric guides. We show that these modules can be easily re-programmed for new target shapes using a CNC-based magnetic plotter, and demonstrate self-assembly of 8 cubes in a water tank.
Sparse representation learning with modified q-VAE towards minimal realization of world model

Extraction of low-dimensional latent space from high-dimensional observation data is essential to construct a real-time robot controller with a world model on the extracted latent space. However, there is no established method for tuning the dimension size of the latent space automatically, suffering from finding the necessary and sufficient dimension size, i.e. the minimal realization of the world model. In this study, we analyze and improve Tsallis-based variational autoencoder (q-VAE), and reveal that, under an appropriate configuration, it always facilitates making the latent space sparse. Even if the dimension size of the pre-specified latent space is redundant compared to the minimal realization, this sparsification collapses unnecessary dimensions, allowing for easy removal of them. We experimentally verified the benefits of the sparsification by the proposed method that it can easily find the necessary and sufficient six dimensions for a reaching task with a mobile manipulator that requires a six-dimensional state space. Moreover, by planning with such a minimal-realization world model learned in the extracted dimensions, the proposed method was able to exert a more optimal action sequence in real-time, reducing the reaching accomplishment time by around 20%. GRAPHICAL ABSTRACT
Modeling Extremal Streamflow using Deep Learning Approximations and a Flexible Spatial Process

Quantifying changes in the probability and magnitude of extreme flooding events is key to mitigating their impacts. While hydrodynamic data are inherently spatially dependent, traditional spatial models such as Gaussian processes are poorly suited for modeling extreme events. Spatial extreme value models with more realistic tail dependence characteristics are under active development. They are theoretically justified, but give intractable likelihoods, making computation challenging for small datasets and prohibitive for continental-scale studies. We propose a process mixture model (PMM) which specifies spatial dependence in extreme values as a convex combination of a Gaussian process and a max-stable process, yielding desirable tail dependence properties but intractable likelihoods. To address this, we employ a unique computational strategy where a feed-forward neural network is embedded in a density regression model to approximate the conditional distribution at one spatial location given a set of neighbors. We then use this univariate density function to approximate the joint likelihood for all locations by way of a Vecchia approximation. The PMM is used to analyze changes in annual maximum streamflow within the US over the last 50 years, and is able to detect areas which show increases in extreme streamflow over time.
Generating Negative Samples for Sequential Recommendation

To make Sequential Recommendation (SR) successful, recent works focus on designing effective sequential encoders, fusing side information, and mining extra positive self-supervision signals. The strategy of sampling negative items at each time step is less ex-plored. Due to the dynamics of users’ interests and model updates during training, considering randomly sampled items from a user’s non-interacted item set as negatives can be uninformative. As a result, the model will inaccurately learn user preferences toward items. Identifying informative negatives is challenging because informative negative items are tied with both dynamically changed interests and model parameters (and sampling process should also be efficient). To this end, we propose to Gen erate N egative Samples ( i tems) for SR ( GenNi ). A negative item is sampled at each time step based on the current SR model’s learned user preferences toward items. An efficient implementation is proposed to further accelerate the generation process, making it scalable to large-scale recommendation tasks. Extensive experiments on four public datasets verify the importance of providing high-quality negative samples for SR and demonstrate the effectiveness and efficiency of GenNi .
Bug-Fix Variants: Visualizing Unique Source Code Changes across GitHub Forks

Forking is a common practice for developers when building upon on already existing projects. These forks create variants, which have a common code base but then evolve the code in different directions, which is specific to that forked project requirements. An interesting side-effect of having multiple forks is the ability to select between different evolution directions of the code which is based on developers fixing bugs in the code base. However, the key issue that this decentralized form of information is difficult to analyze. In this study, we propose a visualization to analyze active changes in fork repositories that have not been merged back to the original project. Our visualization shows code commit activities in multiple forks with highlight on bug fix commits in the history of forks. While the commit activity of each repository is visualized similarly to the code frequency view of GitHub, our view shows only commits unique to fork repositories. To illustrate the effectiveness of our visualization, we have applied our view to two use cases: identifying forks from a repository no longer maintained, and identifying a bug fix among forks. In the first case, we identify a fork of a suspended project named Obfuscator-LLVM. Our view shows the original repository and its most active fork that continue the development on the top. In the second case, we identify a bug fix in a fork of Clipy project. Our view shows that the most active fork has its own bug fixes; we could easily identify a patch for the bug highlighted in the view. As a new ideas paper, we then present our outline of three research questions to spark real world use-cases and goals for our visualization has the potential to uncover. A prototype of our visualization is available at https://naist-se.github. io/vissoft2022/
Perception-Distortion Balanced ADMM Optimization for Single-Image Super-Resolution

In image super-resolution, both pixel-wise accuracy and perceptual fidelity are desirable. However, most deep learning methods only achieve high performance in one aspect due to the perception-distortion trade-off, and works that successfully balance the trade-off rely on fusing results from separately trained models with ad-hoc post-processing. In this paper, we propose a novel super-resolution model with a low-frequency constraint (LFc-SR), which balances the objective and perceptual quality through a single model and yields super-resolved images with high PSNR and perceptual scores. We further introduce an ADMM-based alternating optimization method for the non-trivial learning of the constrained model. Experiments showed that our method, without cumbersome post-processing procedures, achieved the state-of-the-art performance. The code is available at https://github.com/Yuehan717/PDASR.
Decomposable Non-Smooth Convex Optimization with Nearly-Linear Gradient Oracle Complexity

Many fundamental problems in machine learning can be formulated by the convex program \[ \min_{\theta\in R^d}\ \sum_{i=1}^{n}f_{i}(\theta), \] where each $f_i$ is a convex, Lipschitz function supported on a subset of $d_i$ coordinates of $\theta$. One common approach to this problem, exemplified by stochastic gradient descent, involves sampling one $f_i$ term at every iteration to make progress. This approach crucially relies on a notion of uniformity across the $f_i$'s, formally captured by their condition number. In this work, we give an algorithm that minimizes the above convex formulation to $\epsilon$-accuracy in $\widetilde{O}(\sum_{i=1}^n d_i \log (1 /\epsilon))$ gradient computations, with no assumptions on the condition number. The previous best algorithm independent of the condition number is the standard cutting plane method, which requires $O(nd \log (1/\epsilon))$ gradient computations. As a corollary, we improve upon the evaluation oracle complexity for decomposable submodular minimization by Axiotis et al. (ICML 2021). Our main technical contribution is an adaptive procedure to select an $f_i$ term at every iteration via a novel combination of cutting-plane and interior-point methods.
Testing the “Freight Landscape” Concept for Paris

The concept of “freight landscape,” the basis for a modeling approach for urban freight traffic estimation using commonly available datasets, was proposed in 2017 with a case study applying it to the Los Angeles metropolitan area. To extend the scope of that research, we conduct another case study using data from the Paris region, France. We estimate spatial lag models using population, employment, or establishment transportation accessibilities as explanatory variables and network-based truck traffic as the dependent variable, modifying the approach used in the Los Angeles study. We identify differences in the characteristics of the variables and the models between the Los Angeles and Paris cases, each having a distinctively different urban structure. While the models estimated for the Paris region provide beneficial insights into the relationships between freight landscape indicators and urban freight traffic, the complex correlation structure among indicators, as well as the limitation of the models for specifying the areas of very high truck traffic, underlines the need for further research on the modeling framework and for more case studies.
DESIGN AND TESTING OF A METHODOLOGY FOR THESIS ADVISORY AS AN APPROACH FROM PROJECT MANAGEMENT

After applying several project management and quality methodologies to industry, consulting and academic projects of different complexity levels for several years, a methodology for thesis advisory was designed and implemented using an approach from projects management, for increasing the quantity and quality of terminal efficiency when facing the fact of having many students requesting thesis advisors and few professors as advisors at superior education institutions. This methodology also looks reduction of risk of academic abortion pushing a cultural change directed by the advisor using social media and digital resources. Methodology, maturity stages and test results applied to bachelor students when developing thesis advisory based on learning based projects is discussed. This methodology was applied to a small under graduated students group for a two-years project, those students got their grades successfully after the project. Now this methodology is being applied to groups of under graduated and graduated students. Methodology looks for a win to win game for students, advisors, but also research groups increasing productivity and quality reducing invested time.
Data-centric AI approach to improve optic nerve head segmentation and localization in OCT en face images

The automatic detection and localization of anatomical features in retinal imaging data are relevant for many aspects. In this work, we follow a data-centric approach to optimize classiﬁer training for optic nerve head detection and localization in optical coherence tomography en face images of the retina. We examine the eﬀect of domain knowledge driven spatial complexity reduction on the resulting optic nerve head segmentation and localization performance. We present a machine learning approach for segmenting optic nerve head in 2D en face projections of 3D wideﬁeld swept source optical coherence tomography scans that enables the automated assessment of large amounts of data. Evaluation on manually annotated 2D en face images of the retina demonstrates that training of a standard U-Net can yield improved optic nerve head segmentation and localization performance when the underlying pixel-level binary classiﬁcation task is spatially relaxed through domain knowledge.
Granger Causality using Neural Networks

The Granger Causality (GC) test is a famous statistical hypothesis test for investigating if the past of one time series affects the future of the other. It helps in answering the question whether one time series is helpful in forecasting -another (Granger, 1969). Standard traditional approaches to Granger causality detection commonly assume linear dynamics, but such simpliﬁca-tion does not hold in many real-world applications, e.g., neuroscience or ge-nomics that are inherently non-linear. In such cases, imposing linear models such as Vector Autoregressive (VAR) models can lead to inconsistent estimation of true Granger Causal interactions. Machine Learning (ML) can learn the hidden patterns in the datasets speciﬁcally Deep Learning (DL) has shown tremendous promise in learning the non-linear dynamics of complex systems. Recent work of Tank et al. (2018) propose to overcome the issue of linear sim-pliﬁcation in VAR models by using neural networks combined with sparsity-inducing penalties on the learn-able weights. The authors propose a class of non-linear methods by applying structured multilayer perceptrons (MLPs) or recurrent neural networks (RNNs) for prediction of each time series sepa-rately using Component Wise MLPs and RNNs. Sparsity is achieved through the use of convex group-lasso penalties. The sparsity penalties encourage speciﬁc sets of weights to be zero (or very small), allowing the Granger Causal structure to be extracted. In this work, we build upon ideas introduced by Tank et al. We propose several new classes of models that can handle underlying non-linearity. Firstly, we present the Learned Kernal VAR(LeKVAR) model—an extension of VAR models that also learns kernel parametrized by a neural net. Sec-ondly, we show one can directly decouple lags and individual time series importance via decoupled penalties. This decoupling provides better scaling and allows us to embed lag selection into RNNs. Lastly, we propose a new training algorithm that supports mini-batching, and it is compatible with commonly used adaptive optimizers such as Adam (Kingma and Ba, 2014). The proposed techniques are evaluated on several simulated datasets in-spired by real-world applications.We also apply these methods to the Electro-Encephalogram (EEG) data for an epilepsy patient to study the evolution of GC before , during and after seizure across the 19 EEG channels. and batch size 1024 . We tune learning rate ( { 1 ., 0 . 1 , 0 . 01 , 0 . 001 , 0 . 0001 } ) and sparsity-inducing penalty parameter ( { 1 e − 2 , 1 e − 3 , 1 e − 4 , 1 e − 5 , 1 e − 6 , 1 e − 7 } ). Lag is ﬁxed at value ﬁve if not otherwise stated, and we apply group lasso across individual series and lags as the sparsity-inducing penalty. Results are the mean across three initializations, with one standard deviation.
Generalized Glauber Dynamics for Inference in Biology

Large interacting systems in biology often exhibit emergent dynamics, such as coexistence of multiple time scales, manifested by fat tails in the distribution of waiting times. While existing tools in statistical inference, such as maximum entropy models, reproduce the empirical steady state distributions, it remains challenging to learn dynamical models. We present a novel inference method, called generalized Glauber dynamics. Constructed through a non-Markovian fluctuation dissipation theorem, generalized Glauber dynamics tunes the dynamics of an interacting system, while keeping the steady state distribution fixed. We motivate the need for the method on real data from Eco-HAB, an automated habitat for testing behavior in groups of mice under semi-naturalistic conditions, and present it on simple Ising spin systems. We show its applicability for experimental data, by inferring dynamical models of social interactions in a group of mice that reproduce both its collective behavior and the long tails observed in individual dynamics.
IDLat: An Importance-Driven Latent Generation Method for Scientific Data

Deep learning based latent representations have been widely used for numerous scientific visualization applications such as isosurface similarity analysis, volume rendering, flow field synthesis, and data reduction, just to name a few. However, existing latent representations are mostly generated from raw data in an unsupervised manner, which makes it difficult to incorporate domain interest to control the size of the latent representations and the quality of the reconstructed data. In this paper, we present a novel importance-driven latent representation to facilitate domain-interest-guided scientific data visualization and analysis. We utilize spatial importance maps to represent various scientific interests and take them as the input to a feature transformation network to guide latent generation. We further reduced the latent size by a lossless entropy encoding algorithm trained together with the autoencoder, improving the storage and memory efficiency. We qualitatively and quantitatively evaluate the effectiveness and efficiency of latent representations generated by our method with data from multiple scientific visualization applications.
OnlineHybridTrafficClassifierforPeer-to-PeerSystemsBasedonNetwork Processors

It is estimated that 70 percent or more of broadband bandwidth is consumed by transmitting music, games, video and other content through P2P clients. In order to detect, identify, and manage P2P traffic, some port, payload and transport layer f eature based methods were proposed. Most of them were applied to offline traffic classification mainly due to the performance reason. In this paper, a network processors (NPs) based online hybrid traffic classifier is proposed. The designed hardware classifier is able to classify P2P traffic based on the static characteristic namely on line speed, and the Flexible Neural Network(FNT) based software classifier helps learning and selecting P2P traffic attributes from the statistical characteristics of the P2P traffic. Experiment results illustrate that the hybrid classifier performs well for online classification of P2P traffic from gigabit network.The proposed framework also depicts good expansion capabilities to add new P2P features and to adapt to new P2P applications online.
Information bottleneck theory of high-dimensional regression: relevancy, efficiency and optimality

Avoiding overfitting is a central challenge in machine learning, yet many large neural networks readily achieve zero training loss. This puzzling contradiction necessitates new approaches to the study of overfitting. Here we quantify overfitting via residual information, defined as the bits in fitted models that encode noise in training data. Information efficient learning algorithms minimize residual information while maximizing the relevant bits, which are predictive of the unknown generative models. We solve this optimization to obtain the information content of optimal algorithms for a linear regression problem and compare it to that of randomized ridge regression. Our results demonstrate the fundamental trade-off between residual and relevant information and characterize the relative information efficiency of randomized regression with respect to optimal algorithms. Finally, using results from random matrix theory, we reveal the information complexity of learning a linear map in high dimensions and unveil information-theoretic analogs of double and multiple descent phenomena.
Federated Learning for Medical Applications: A Taxonomy, Current Trends, Challenges, and Future Research Directions

With the advent of the Internet of Things (IoT), artificial intelligence (AI), machine learning (ML), and deep learning (DL) algorithms, the landscape of data-driven medical applications has emerged as a promising avenue for designing robust and scalable diagnostic and prognostic models from medical data. This has gained a lot of attention from both academia and industry, leading to significant improvements in healthcare quality. However, the adoption of AI-driven medical applications still faces tough challenges, including meeting security, privacy, and Quality-of-Service (QoS) standards. Recent developments in federated learning (FL) have made it possible to train complex machine-learned models in a distributed manner and have become an active research domain, particularly processing the medical data at the edge of the network in a decentralized way to preserve privacy and address security concerns. To this end, in this article, we explore the present and future of FL technology in medical applications where data sharing is a significant challenge. We delve into the current research trends and their outcomes, unraveling the complexities of designing reliable and scalable FL models. This article outlines the fundamental statistical issues in FL, tackles device-related problems, addresses security challenges, and navigates the complexity of privacy concerns, all while highlighting its transformative potential in the medical field. Our study primarily focuses on medical applications of FL, particularly in the context of global cancer diagnosis. We highlight the potential of FL to enable computer-aided diagnosis tools that address this challenge with greater effectiveness than traditional data-driven methods. Recent literature has shown that FL models are robust and generalize well to new data, which is essential for medical applications. We hope that this comprehensive review will serve as a checkpoint for the field, summarizing the current state of the art and identifying open problems and future research directions.
Bridging the Gap: Commonality and Differences between Online and Offline COVID-19 Data

With the onset of the COVID-19 pandemic, news outlets and social media have become central tools for disseminating and consuming information. Because of their ease of access, users seek COVID-19-related information from online social media (i.e., online news) and news outlets (i.e., offline news). Online and offline news are often connected, sharing common topics while each has unique, different topics. A gap between these two news sources can lead to misinformation propagation. For instance, according to the Guardian, most COVID-19 misinformation comes from users on social media. Without fact-checking social media news, misinformation can lead to health threats. In this paper, we focus on the novel problem of bridging the gap between online and offline data by monitoring their common and distinct topics generated over time. We employ Twitter (online) and local news (offline) data for a time span of two years. Using online matrix factorization, we analyze and study online and offline COVID-19-related data differences and commonalities. We design experiments to show how online and offline data are linked together and what trends they follow.