OpenRaiser/Intern-Atlas huggingface dataset:
Efficient Multimodal Transformer with Dual-Level Feature Restoration for Robust Multimodal Sentiment Analysis
Venue: arXiv cs.LG 2023
Year: 2023

With the proliferation of user-generated online videos, Multimodal Sentiment Analysis (MSA) has attracted increasing attention recently. Despite significant progress, there are still two major challenges on the way towards robust MSA: 1) inefficiency when modeling cross-modal interactions in unaligned multimodal data; and 2) vulnerability to random modality feature missing which typically occurs in realistic settings. In this paper, we propose a generic and unified framework to address them, named Efficient Multimodal Transformer with Dual-Level Feature Restoration (EMT-DLFR). Concretely, EMT employs utterance-level representations from each modality as the global multimodal context to interact with local unimodal features and mutually promote each other. It not only avoids the quadratic scaling cost of previous local-local cross-modal interaction methods but also leads to better performance. To improve model robustness in the incomplete modality setting, on the one hand, DLFR performs low-level feature reconstruction to implicitly encourage the model to learn semantic information from incomplete data. On the other hand, it innovatively regards complete and incomplete data as two different views of one sample and utilizes siamese representation learning to explicitly attract their high-level representations. Comprehensive experiments on three popular datasets demonstrate that our method achieves superior performance in both complete and incomplete modality settings.
Demonstrating Software Reliability using Possibly Correlated Tests: Insights from a Conservative Bayesian Approach
Venue: arXiv cs.SE 2023
Year: 2023

This paper presents Bayesian techniques for conservative claims about software reliability, particularly when evidence suggests the software's executions are not statistically independent. We formalise informal notions of "doubting" that the executions are independent, and incorporate such doubts into reliability assessments. We develop techniques that reveal the extent to which independence assumptions can undermine conservatism in assessments, and identify conditions under which this impact is not significant. These techniques - novel extensions of conservative Bayesian inference (CBI) approaches - give conservative confidence bounds on the software's failure probability per execution. With illustrations in two application areas - nuclear power-plant safety and autonomous vehicle (AV) safety - our analyses reveals: 1) the confidence an assessor should possess before subjecting a system to operational testing. Otherwise, such testing is futile - favourable operational testing evidence will eventually decrease one's confidence in the system being sufficiently reliable; 2) the independence assumption supports conservative claims sometimes; 3) in some scenarios, observing a system operate without failure gives less confidence in the system than if some failures had been observed; 4) building confidence in a system is very sensitive to failures - each additional failure means significantly more operational testing is required, in order to support a reliability claim.
Which Factors are associated with Open Access Publishing? A Springer Nature Case Study
Venue: arXiv cs.DL 2023
Year: 2023

Open Access (OA) facilitates access to articles. But, authors or funders often must pay the publishing costs preventing authors who do not receive financial support from participating in OA publishing and citation advantage for OA articles. OA may exacerbate existing inequalities in the publication system rather than overcome them. To investigate this, we studied 522,411 articles published by Springer Nature. Employing correlation and regression analyses, we describe the relationship between authors affiliated with countries from different income levels, their choice of publishing model, and the citation impact of their papers. A machine learning classification method helped us to explore the importance of different features in predicting the publishing model. The results show that authors eligible for APC waivers publish more in gold-OA journals than others. In contrast, authors eligible for an APC discount have the lowest ratio of OA publications, leading to the assumption that this discount insufficiently motivates authors to publish in gold-OA journals. We found a strong correlation between the journal rank and the publishing model in gold-OA journals, whereas the OA option is mostly avoided in hybrid journals. Also, results show that the countries' income level, seniority, and experience with OA publications are the most predictive factors for OA publishing in hybrid journals.
Simplicity in Eulerian Circuits: Uniqueness and Safety
Venue: arXiv cs.DS 2023
Year: 2023

An Eulerian circuit in a directed graph is one of the most fundamental Graph Theory notions. Detecting if a graph $G$ has a unique Eulerian circuit can be done in polynomial time via the BEST theorem by de Bruijn, van Aardenne-Ehrenfest, Smith and Tutte, 1941-1951 (involving counting arborescences), or via a tailored characterization by Pevzner, 1989 (involving computing the intersection graph of simple cycles of $G$), both of which thus rely on overly complex notions for the simpler uniqueness problem. In this paper we give a new linear-time checkable characterization of directed graphs with a unique Eulerian circuit. This is based on a simple condition of when two edges must appear consecutively in all Eulerian circuits, in terms of cut nodes of the underlying undirected graph of $G$. As a by-product, we can also compute in linear-time all maximal $\textit{safe}$ walks appearing in all Eulerian circuits, for which Nagarajan and Pop proposed in 2009 a polynomial-time algorithm based on Pevzner characterization.
Learning Program Representations with a Tree-Structured Transformer
Venue: arXiv cs.SE 2023
Year: 2023

Learning vector representations for programs is a critical step in applying deep learning techniques for program understanding tasks. Various neural network models are proposed to learn from tree-structured program representations, e.g., abstract syntax tree (AST) and concrete syntax tree (CST). However, most neural architectures either fail to capture long-range dependencies which are ubiquitous in programs, or cannot learn effective representations for syntax tree nodes, making them incapable of performing the node-level prediction tasks, e.g., bug localization. In this paper, we propose Tree-Transformer, a novel recursive tree-structured neural network to learn the vector representations for source codes. We propose a multi-head attention mechanism to model the dependency between siblings and parent-children node pairs. Moreover, we propose a bi-directional propagation strategy to allow node information passing in two directions, bottom-up and top-down along trees. In this way, Tree-Transformer can learn the information of the node features as well as the global contextual information. The extensive experimental results show that our Tree-Transformer significantly outperforms the existing tree-based and graph-based program representation learning approaches in both the tree-level and node-level prediction tasks.
Learning Spatial-Frequency Transformer for Visual Object Tracking
Venue: arXiv cs.CV 2023
Year: 2023

Recent trackers adopt the Transformer to combine or replace the widely used ResNet as their new backbone network. Although their trackers work well in regular scenarios, however, they simply flatten the 2D features into a sequence to better match the Transformer. We believe these operations ignore the spatial prior of the target object which may lead to sub-optimal results only. In addition, many works demonstrate that self-attention is actually a low-pass filter, which is independent of input features or key/queries. That is to say, it may suppress the high-frequency component of the input features and preserve or even amplify the low-frequency information. To handle these issues, in this paper, we propose a unified Spatial-Frequency Transformer that models the Gaussian spatial Prior and High-frequency emphasis Attention (GPHA) simultaneously. To be specific, Gaussian spatial prior is generated using dual Multi-Layer Perceptrons (MLPs) and injected into the similarity matrix produced by multiplying Query and Key features in self-attention. The output will be fed into a Softmax layer and then decomposed into two components, i.e., the direct signal and high-frequency signal. The low- and high-pass branches are rescaled and combined to achieve all-pass, therefore, the high-frequency features will be protected well in stacked self-attention layers. We further integrate the Spatial-Frequency Transformer into the Siamese tracking framework and propose a novel tracking algorithm, termed SFTransT. The cross-scale fusion based SwinTransformer is adopted as the backbone, and also a multi-head cross-attention module is used to boost the interaction between search and template features. The output will be fed into the tracking head for target localization. Extensive experiments on both short-term and long-term tracking benchmarks all demonstrate the effectiveness of our proposed framework.
A Kind Introduction to Lexical and Grammatical Aspect, with a Survey of Computational Approaches
Venue: arXiv cs.CL 2023
Year: 2023

Aspectual meaning refers to how the internal temporal structure of situations is presented. This includes whether a situation is described as a state or as an event, whether the situation is finished or ongoing, and whether it is viewed as a whole or with a focus on a particular phase. This survey gives an overview of computational approaches to modeling lexical and grammatical aspect along with intuitive explanations of the necessary linguistic concepts and terminology. In particular, we describe the concepts of stativity, telicity, habituality, perfective and imperfective, as well as influential inventories of eventuality and situation types. We argue that because aspect is a crucial component of semantics, especially when it comes to reporting the temporal structure of situations in a precise way, future NLP approaches need to be able to handle and evaluate it systematically in order to achieve human-level language understanding.
Entropy Augmented Reinforcement Learning
Venue: arXiv cs.LG 2023
Year: 2023

Deep reinforcement learning was instigated with the presence of trust region methods, being scalable and efficient. However, the pessimism of such algorithms, among which it forces to constrain in a trust region by all means, has been proven to suppress the exploration and harm the performance. Exploratory algorithm such as SAC, while utilizes the entropy to encourage exploration, implicitly optimizing another objective yet. We first observed this inconsistency, and therefore put forward an analogous augmentation technique, which combines well with the on-policy algorithms, when a value critic is involved. Surprisingly, the proposed method consistently satisfies the soft policy improvement theorem, while being more extensible. As the analysis advises, it is crucial to control the temperature coefficient to balance the exploration and exploitation. Empirical tests on MuJoCo benchmark tasks show that the agent is heartened towards higher reward regions, and enjoys a finer performance. Furthermore, we verify the exploration bonus of our method on a set of custom environments.
Evaluating Explainability for Graph Neural Networks
Venue: arXiv cs.LG 2023
Year: 2023

As post hoc explanations are increasingly used to understand the behavior of graph neural networks (GNNs), it becomes crucial to evaluate the quality and reliability of GNN explanations. However, assessing the quality of GNN explanations is challenging as existing graph datasets have no or unreliable ground-truth explanations for a given task. Here, we introduce a synthetic graph data generator, ShapeGGen, which can generate a variety of benchmark datasets (e.g., varying graph sizes, degree distributions, homophilic vs. heterophilic graphs) accompanied by ground-truth explanations. Further, the flexibility to generate diverse synthetic datasets and corresponding ground-truth explanations allows us to mimic the data generated by various real-world applications. We include ShapeGGen and several real-world graph datasets into an open-source graph explainability library, GraphXAI. In addition to synthetic and real-world graph datasets with ground-truth explanations, GraphXAI provides data loaders, data processing functions, visualizers, GNN model implementations, and evaluation metrics to benchmark the performance of GNN explainability methods.
Diffusion-based Time Series Imputation and Forecasting with Structured State Space Models
Venue: arXiv cs.LG 2023
Year: 2023

The imputation of missing values represents a significant obstacle for many real-world data analysis pipelines. Here, we focus on time series data and put forward SSSD, an imputation model that relies on two emerging technologies, (conditional) diffusion models as state-of-the-art generative models and structured state space models as internal model architecture, which are particularly suited to capture long-term dependencies in time series data. We demonstrate that SSSD matches or even exceeds state-of-the-art probabilistic imputation and forecasting performance on a broad range of data sets and different missingness scenarios, including the challenging blackout-missing scenarios, where prior approaches failed to provide meaningful results.
Line Coverage with Multiple Robots: Algorithms and Experiments
Venue: arXiv cs.RO 2023
Year: 2023

The line coverage problem involves finding efficient routes for the coverage of linear features by one or more resource-constrained robots. Linear features model environments like road networks, power lines, and oil and gas pipelines. Two modes of travel are defined for robots: servicing and deadheading. A robot services a feature if it performs task-specific actions, such as taking images, as it traverses the feature; otherwise, it is deadheading. Traversing the environment incurs costs (e.g., travel time) and demands on resources (e.g., battery life). Servicing and deadheading can have different cost and demand functions, which can be direction-dependent. The environment is modeled as a graph, and an integer linear program is provided. As the problem is NP-hard, we design a fast and efficient heuristic algorithm, Merge-Embed-Merge (MEM). Exploiting the constructive property of the MEM algorithm, algorithms for line coverage of large graphs with multiple depots are developed. Furthermore, turning costs and nonholonomic constraints are efficiently incorporated into the algorithm. The algorithms are benchmarked on road networks and demonstrated in experiments with aerial robots.
Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction
Venue: arXiv cs.LG 2023
Year: 2023

Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and medical development. Determining accurate folding landscape using co-evolutionary information is fundamental to the success of modern protein structure prediction methods. As the state of the art, AlphaFold2 has dramatically raised the accuracy without performing explicit co-evolutionary analysis. Nevertheless, its performance still shows strong dependence on available sequence homologs. Based on the interrogation on the cause of such dependence, we presented EvoGen, a meta generative model, to remedy the underperformance of AlphaFold2 for poor MSA targets. By prompting the model with calibrated or virtually generated homologue sequences, EvoGen helps AlphaFold2 fold accurately in low-data regime and even achieve encouraging performance with single-sequence predictions. Being able to make accurate predictions with few-shot MSA not only generalizes AlphaFold2 better for orphan sequences, but also democratizes its use for high-throughput applications. Besides, EvoGen combined with AlphaFold2 yields a probabilistic structure generation method which could explore alternative conformations of protein sequences, and the task-aware differentiable algorithm for sequence generation will benefit other related tasks including protein design.
Minimizing Visible Edges in Polyhedra
Venue: arXiv cs.CG 2023
Year: 2023

We prove that, given a polyhedron $\mathcal P$ in $\mathbb{R}^3$, every point in $\mathbb R^3$ that does not see any vertex of $\mathcal P$ must see eight or more edges of $\mathcal P$, and this bound is tight. More generally, this remains true if $\mathcal P$ is any finite arrangement of internally disjoint polygons in $\mathbb{R}^3$. We also prove that every point in $\mathbb{R}^3$ can see six or more edges of $\mathcal{P}$ (possibly only the endpoints of some these edges) and every point in the interior of $\mathcal{P}$ can see a positive portion of at least six edges of $\mathcal{P}$. These bounds are also tight.
Wolfies at SemEval-2022 Task 8: Feature extraction pipeline with transformers for Multi-lingual news article similarity
Venue: arXiv cs.CL 2023
Year: 2023

This work is about finding the similarity between a pair of news articles. There are seven different objective similarity metrics provided in the dataset for each pair and the news articles are in multiple different languages. On top of the pre-trained embedding model, we calculated cosine similarity for baseline results and feed-forward neural network was then trained on top of it to improve the results. We also built separate pipelines for each similarity metric for feature extraction. We could see significant improvement from baseline results using feature extraction and feed-forward neural network.
A Survey on Transactional Stream Processing
Venue: arXiv cs.DB 2023
Year: 2023

Transactional stream processing (TSP) strives to create a cohesive model that merges the advantages of both transactional and stream-oriented guarantees. Over the past decade, numerous endeavors have contributed to the evolution of TSP solutions, uncovering similarities and distinctions among them. Despite these advances, a universally accepted standard approach for integrating transactional functionality with stream processing remains to be established. Existing TSP solutions predominantly concentrate on specific application characteristics and involve complex design trade-offs. This survey intends to introduce TSP and present our perspective on its future progression. Our primary goals are twofold: to provide insights into the diverse TSP requirements and methodologies, and to inspire the design and development of groundbreaking TSP systems.
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
Venue: arXiv cs.AR 2023
Year: 2023

Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is the recently proposed GenASM algorithm. We identify and address three inefficiencies in the GenASM algorithm: it has a high amount of data movement, a large memory footprint, and does some unnecessary work. We propose Scrooge, a fast and memory-frugal genomic sequence aligner. Scrooge includes three novel algorithmic improvements which reduce the data movement, memory footprint, and the number of operations in the GenASM algorithm. We provide efficient open-source implementations of the Scrooge algorithm for CPUs and GPUs, which demonstrate the significant benefits of our algorithmic improvements. For long reads, the CPU version of Scrooge achieves a 20.1x, 1.7x, and 2.1x speedup over KSW2, Edlib, and a CPU implementation of GenASM, respectively. The GPU version of Scrooge achieves a 4.0x 80.4x, 6.8x, 12.6x and 5.9x speedup over the CPU version of Scrooge, KSW2, Edlib, Darwin-GPU, and a GPU implementation of GenASM, respectively. We estimate an ASIC implementation of Scrooge to use 3.6x less chip area and 2.1x less power than a GenASM ASIC while maintaining the same throughput. Further, we systematically analyze the throughput and accuracy behavior of GenASM and Scrooge under various configurations. As the best configuration of Scrooge depends on the computing platform, we make several observations that can help guide future implementations of Scrooge. Availability: https://github.com/CMU-SAFARI/Scrooge
Review of Natural Language Processing in Pharmacology
Venue: arXiv cs.CL 2023
Year: 2023

Natural language processing (NLP) is an area of artificial intelligence that applies information technologies to process the human language, understand it to a certain degree, and use it in various applications. This area has rapidly developed in the last few years and now employs modern variants of deep neural networks to extract relevant patterns from large text corpora. The main objective of this work is to survey the recent use of NLP in the field of pharmacology. As our work shows, NLP is a highly relevant information extraction and processing approach for pharmacology. It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media. We split our coverage into five categories to survey modern NLP methodology, commonly addressed tasks, relevant textual data, knowledge bases, and useful programming libraries. We split each of the five categories into appropriate subcategories, describe their main properties and ideas, and summarize them in a tabular form. The resulting survey presents a comprehensive overview of the area, useful to practitioners and interested observers.
On the binary linear constant weight codes and their autormorphism groups
Venue: arXiv cs.IT 2023
Year: 2023

We give a characterization for the binary linear constant weight codes by using the symmetric difference of the supports of the codewords. This characterization gives a correspondence between the set of binary linear constant weight codes and the set of partitions for the union of supports of the codewords. By using this correspondence, we present a formula for the order of the automorphism group of a binary linear constant weight code in terms of its parameters. This formula is a key step to determine more algebraic structures on constant weight codes with given parameters. Bonisoli [Bonisoli, A.: Every equidistant linear code is a sequence of dual Hamming codes. Ars Combinatoria 18, 181--186 (1984)] proves that the $q$-ary linear constant weight codes with the same parameters are equivalent (for the binary case permutation equivalent). We also give an alternative proof for Bonisoli's theorem by presenting an explicit permutation on symmetric difference of the supports of the codewords which gives the permutation equivalence between the binary linear constant weight codes.
Latent Neural Stochastic Differential Equations for Change Point Detection
Venue: arXiv cs.LG 2023
Year: 2023

Automated analysis of complex systems based on multiple readouts remains a challenge. Change point detection algorithms are aimed to locating abrupt changes in the time series behaviour of a process. In this paper, we present a novel change point detection algorithm based on Latent Neural Stochastic Differential Equations (SDE). Our method learns a non-linear deep learning transformation of the process into a latent space and estimates a SDE that describes its evolution over time. The algorithm uses the likelihood ratio of the learned stochastic processes in different timestamps to find change points of the process. We demonstrate the detection capabilities and performance of our algorithm on synthetic and real-world datasets. The proposed method outperforms the state-of-the-art algorithms on the majority of our experiments.