With the Open Science approach becoming important for research, the evolution towards open scientific-paper reviews is making an impact on the scientific community. However, there is a lack of publicly available resources for conducting research activities related to this subject, as only a limited number of journals and conferences currently allow access to their review process for interested parties. In this paper, we introduce the new comprehensive Open Review-Based dataset (ORB); it includes a curated list of more than 36,000 scientific papers with their more than 89,000 reviews and final decisions. We gather this information from two sources: the OpenReview.net and SciPost.org websites. However, given the volatile nature of this domain, the software infrastructure that we introduce to supplement the ORB dataset is designed to accommodate additional resources in the future. The ORB deliverables include (1) Python code (interfaces and implementations) to translate document data and metadata into a structured and high-level representation, (2) an ETL process (Extract, Transform, Load) to facilitate the automatic updates from defined sources and (3) data files representing the structured data. The paper presents our data architecture and an overview of the collected data along with relevant statistics. For illustration purposes, we also discuss preliminary Natural-Language-Processing-based experiments that aim to predict (1) papers' acceptance based on their textual embeddings, and (2) grading statistics inferred from embeddings as well. We believe ORB provides a valuable resource for researchers interested in open science and review, with our implementation easing the use of this data for further analysis and experimentation. We plan to update ORB as the field matures as well as introduce new resources even more fitted to dedicated scientific domains such as High-Energy Physics.

Instagram, a social media platform, has in the vicinity of 2 billion active users in 2023. The platform allows users to post photos and videos with one another. However, cyberbullying remains a significant problem for about 50% of young Indonesians. To address this issue, sentiment analysis for comment filtering uses a Support Vector Machine (SVM) and Easy Data Augmentation (EDA). EDA will augment the dataset, enabling robust prediction and analysis of cyberbullying by introducing more variation. Based on the tests, SVM combination with EDA results in a 2.52% increase in the k-Fold Cross Validation score. Our proposed approach shows an improved accuracy of 92.5%, 2.5% higher than that of the existing state-of-the-art method. To maintain the reproducibility and replicability of this research, the source code can be accessed at uns.id/eda_svm.

In this paper, we prove that an Adam-type algorithm with smooth clipping approaches the global minimizer of the regularized non-convex loss function. Adding smooth clipping and taking the state space as the set of all trajectories, we can apply the ergodic theory of Markov semigroups for this algorithm and investigate its asymptotic behavior. The ergodic theory we establish in this paper reduces the problem of evaluating the convergence, generalization error and discretization error of this algorithm to the problem of evaluating the difference between two functional stochastic differential equations (SDEs) with different drift coefficients. As a result of our analysis, we have shown that this algorithm minimizes the the regularized non-convex loss function with errors of the form $n^{-1/2}$, $\eta^{1/4}$, $\beta^{-1} \log (\beta + 1)$ and $e^{- c t}$. Here, $c$ is a constant and $n$, $\eta$, $\beta$ and $t$ denote the size of the training dataset, learning rate, inverse temperature and time, respectively.

Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be overly time-consuming for the development of new algorithms, and the $\textit{in silico}$ validation with recovery and perplexity metrics is efficient but may not precisely reflect true foldability. To address this gap, we introduce two novel metrics: refoldability-based metric, which leverages high-accuracy protein structure prediction models as a proxy for wet lab experiments, and stability-based metric, which assesses whether models can assign high likelihoods to experimentally stable proteins. We curate datasets from high-quality CATH protein data, high-throughput $\textit{de novo}$ designed proteins, and mega-scale experimental mutagenesis experiments, and in doing so, present the $\textbf{PDB-Struct}$ benchmark that evaluates both recent and previously uncompared protein design methods. Experimental results indicate that ByProt, ProteinMPNN, and ESM-IF perform exceptionally well on our benchmark, while ESM-Design and AF-Design fall short on the refoldability metric. We also show that while some methods exhibit high sequence recovery, they do not perform as well on our new benchmark. Our proposed benchmark paves the way for a fair and comprehensive evaluation of protein design methods in the future. Code is available at https://github.com/WANG-CR/PDB-Struct.

Large Vision Foundation Models (VFMs) pretrained on massive datasets exhibit impressive performance on various downstream tasks, especially with limited labeled target data. However, due to their high memory and compute requirements, these models cannot be deployed in resource constrained settings. This raises an important question: How can we utilize the knowledge from a large VFM to train a small task-specific model for a new target task with limited labeled training data? In this work, we answer this question by proposing a simple and highly effective task-oriented knowledge transfer approach to leverage pretrained VFMs for effective training of small task-specific models. Our experimental results on four target tasks under limited labeled data settings show that the proposed knowledge transfer approach outperforms task-agnostic VFM distillation, web-scale CLIP pretraining and supervised ImageNet pretraining by 1-10.5%, 2-22% and 2-14%, respectively. We also show that the dataset used for transferring knowledge has a significant effect on the final target task performance, and propose an image retrieval-based approach for curating effective transfer sets. Currently, the computer vision community is witnessing the emergence of various vision and multimodal foundation models pretrained on massive datasets (Radford et al., 2021; Yuan et al., 2021; Alayrac et al., 2022; Kirillov et al., 2023; Oquab et al., 2023; Li et al., 2023b; Wang et al., 2023b). These models have been shown to work well for many downstream computer vision tasks, especially, when task-specific labeled data is limited (Radford et al., 2021). While a single large foundation model could serve many applications, it cannot be directly used in resource constrained settings due to its high memory and compute requirements. Also, many real-world applications such as autonomous driving, medical image diagnostics, and industrial automation, focus on specific tasks and need small task-specific models rather than a large foundation model.

Spectral Graph Neural Networks (GNNs), also referred to as graph filters have gained increasing prevalence for heterophily graphs. Optimal graph filters rely on Laplacian eigendecomposition for Fourier transform. In an attempt to avert the prohibitive computations, numerous polynomial filters by leveraging distinct polynomials have been proposed to approximate the desired graph filters. However, polynomials in the majority of polynomial filters are predefined and remain fixed across all graphs, failing to accommodate the diverse heterophily degrees across different graphs. To tackle this issue, we first investigate the correlation between polynomial bases of desired graph filters and the degrees of graph heterophily via a thorough theoretical analysis. Afterward, we develop an adaptive heterophily basis by incorporating graph heterophily degrees. Subsequently, we integrate this heterophily basis with the homophily basis, creating a universal polynomial basis UniBasis. In consequence, we devise a general polynomial filter UniFilter. Comprehensive experiments on both real-world and synthetic datasets with varying heterophily degrees significantly support the superiority of UniFilter, demonstrating the effectiveness and generality of UniBasis, as well as its promising capability as a new method for graph analysis.

Forecasting building energy consumption has become a promising solution in Building Energy Management Systems for energy saving and optimization. Furthermore, it can play an important role in the efficient management of the operation of a smart grid. Different data-driven approaches to forecast the future energy demand of buildings at different scale, and over various time horizons, can be found in the scientific literature, including extensive Machine Learning and Deep Learning approaches. However, the identification of the most accurate forecaster model which can be utilized to predict the energy demand of such a building is still challenging.In this paper, the design and implementation of a data-driven approach to predict how forecastable the future energy demand of a building is, without first utilizing a data-driven forecasting model, is presented. The investigation utilizes a historical electricity consumption time series data set with a half-hour interval that has been collected from a group of residential buildings located in the City of London, United Kingdom

High-dimensional time series data poses challenges due to its dynamic nature, varying lengths, and presence of missing values. This kind of data requires extensive preprocessing, limiting the applicability of existing Time Series Classification and Time Series Extrinsic Regression techniques. For this reason, we propose BORF, a Bag-Of-Receptive-Fields model, which incorporates notions from time series convolution and 1D-SAX to handle univariate and multivariate time series with varying lengths and missing values. We evaluate BORF on Time Series Classification and Time Series Extrinsic Regression tasks using the full UEA and UCR repositories, demonstrating its competitive performance against state-of-the-art methods. Finally, we outline how this representation can naturally provide saliency and feature-based explanations.

Vision Transformers (ViTs) have achieved state-of-the-art performance for various vision tasks. One reason behind the success lies in their ability to provide plausible innate explanations for the behavior of neural architectures. However, ViTs suffer from issues with explanation faithfulness, as their focal points are fragile to adversarial attacks and can be easily changed with even slight perturbations on the input image. In this paper, we propose a rigorous approach to mitigate these issues by introducing Faithful ViTs (FViTs). Briefly speaking, an FViT should have the following two properties: (1) The top-$k$ indices of its self-attention vector should remain mostly unchanged under input perturbation, indicating stable explanations; (2) The prediction distribution should be robust to perturbations. To achieve this, we propose a new method called Denoised Diffusion Smoothing (DDS), which adopts randomized smoothing and diffusion-based denoising. We theoretically prove that processing ViTs directly with DDS can turn them into FViTs. We also show that Gaussian noise is nearly optimal for both $\ell_2$ and $\ell_\infty$-norm cases. Finally, we demonstrate the effectiveness of our approach through comprehensive experiments and evaluations. Specifically, we compare our FViTs with other baselines through visual interpretation and robustness accuracy under adversarial attacks. Results show that FViTs are more robust against adversarial attacks while maintaining the explainability of attention, indicating higher faithfulness.

Micro RNAs (miRNA) are a type of non-coding RNA, which are involved in gene regulation and can be associated with diseases such as cancer, cardiovascular and neurological diseases. As such, identifying the entire genome of miRNA can be of great relevance. Since experimental methods for novel precursor miRNA (pre-miRNA) detection are complex and expensive, computational detection using ML could be useful. Existing ML methods are often complex black boxes, which do not create an interpretable structural description of pre-miRNA. In this paper, we propose a novel framework, which makes use of generative modeling through Variational Auto-Encoders to uncover the generative factors of pre-miRNA. After training the VAE, the pre-miRNA description is developed using a decision tree on the lower dimensional latent space. Applying the framework to miRNA classification, we obtain a high reconstruction and classification performance, while also developing an accurate miRNA description.