OpenRaiser/Intern-Atlas huggingface dataset:
RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules
Venue: arXiv cs.CE 2023
Year: 2023

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are continuously produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph encompassing biological knowledge about RNAs gathered from more than 50 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.
HeTriNet: Heterogeneous Graph Triplet Attention Network for Drug-Target-Disease Interaction
Venue: arXiv cs.LG 2023
Year: 2023

Modeling the interactions between drugs, targets, and diseases is paramount in drug discovery and has significant implications for precision medicine and personalized treatments. Current approaches frequently consider drug-target or drug-disease interactions individually, ignoring the interdependencies among all three entities. Within human metabolic systems, drugs interact with protein targets in cells, influencing target activities and subsequently impacting biological pathways to promote healthy functions and treat diseases. Moving beyond binary relationships and exploring tighter triple relationships is essential to understanding drugs' mechanism of action (MoAs). Moreover, identifying the heterogeneity of drugs, targets, and diseases, along with their distinct characteristics, is critical to model these complex interactions appropriately. To address these challenges, we effectively model the interconnectedness of all entities in a heterogeneous graph and develop a novel Heterogeneous Graph Triplet Attention Network (\texttt{HeTriNet}). \texttt{HeTriNet} introduces a novel triplet attention mechanism within this heterogeneous graph structure. Beyond pairwise attention as the importance of an entity for the other one, we define triplet attention to model the importance of pairs for entities in the drug-target-disease triplet prediction problem. Experimental results on real-world datasets show that \texttt{HeTriNet} outperforms several baselines, demonstrating its remarkable proficiency in uncovering novel drug-target-disease relationships.
Benchmarking and Enhancing Disentanglement in Concept-Residual Models
Venue: arXiv cs.LG 2023
Year: 2023

Concept bottleneck models (CBMs) are interpretable models that first predict a set of semantically meaningful features, i.e., concepts, from observations that are subsequently used to condition a downstream task. However, the model's performance strongly depends on the engineered features and can severely suffer from incomplete sets of concepts. Prior works have proposed a side channel -- a residual -- that allows for unconstrained information flow to the downstream task, thus improving model performance but simultaneously introducing information leakage, which is undesirable for interpretability. This work proposes three novel approaches to mitigate information leakage by disentangling concepts and residuals, investigating the critical balance between model performance and interpretability. Through extensive empirical analysis on the CUB, OAI, and CIFAR 100 datasets, we assess the performance of each disentanglement method and provide insights into when they work best. Further, we show how each method impacts the ability to intervene over the concepts and their subsequent impact on task performance.
Performance Analysis of Multi-Angle QAOA for p > 1
Venue: arXiv cs.ET 2023
Year: 2023

In this paper we consider the scalability of Multi-Angle QAOA with respect to the number of QAOA layers. We found that MA-QAOA is able to significantly reduce the depth of QAOA circuits, by a factor of up to 4 for the considered data sets. However, MA-QAOA is not optimal for minimization of the total QPU time. Different optimization initialization strategies are considered and compared for both QAOA and MA-QAOA. Among them, a new initialization strategy is suggested for MA-QAOA that is able to consistently and significantly outperform random initialization used in the previous studies.
Multi-Modal Video Topic Segmentation with Dual-Contrastive Domain Adaptation
Venue: arXiv cs.MM 2023
Year: 2023

Video topic segmentation unveils the coarse-grained semantic structure underlying videos and is essential for other video understanding tasks. Given the recent surge in multi-modal, relying solely on a single modality is arguably insufficient. On the other hand, prior solutions for similar tasks like video scene/shot segmentation cater to short videos with clear visual shifts but falter for long videos with subtle changes, such as livestreams. In this paper, we introduce a multi-modal video topic segmenter that utilizes both video transcripts and frames, bolstered by a cross-modal attention mechanism. Furthermore, we propose a dual-contrastive learning framework adhering to the unsupervised domain adaptation paradigm, enhancing our model's adaptability to longer, more semantically complex videos. Experiments on short and long video corpora demonstrate that our proposed solution, significantly surpasses baseline methods in terms of both accuracy and transferability, in both intra- and cross-domain settings.
RoboSync: Efficient Real-Time Operating System for Social Robots with Customizable Behaviour
Venue: arXiv cs.RO 2023
Year: 2023

Traditional robotic systems require complex implementations that are not always accessible or easy to use for Human-Robot Interaction (HRI) application developers. With the aim of simplifying the implementation of HRI applications, this paper introduces a novel real-time operating system (RTOS) designed for customizable HRI - RoboSync. By creating multi-level abstraction layers, the system enables users to define complex emotional and behavioral models without needing deep technical expertise. The system's modular architecture comprises a behavior modeling layer, a machine learning plugin configuration layer, a sensor checks customization layer, a scheduler that fits the need of HRI, and a communication and synchronization layer. This approach not only promotes ease of use without highly specialized skills but also ensures real-time responsiveness and adaptability. The primary functionality of the RTOS has been implemented for proof of concept and was tested on a CortexM4 microcontroller, demonstrating its potential for a wide range of lightweight simple-to-implement social robotics applications.
Improving Normalization with the James-Stein Estimator
Venue: arXiv cs.CV 2023
Year: 2023

Stein's paradox holds considerable sway in high-dimensional statistics, highlighting that the sample mean, traditionally considered the de facto estimator, might not be the most efficacious in higher dimensions. To address this, the James-Stein estimator proposes an enhancement by steering the sample means toward a more centralized mean vector. In this paper, first, we establish that normalization layers in deep learning use inadmissible estimators for mean and variance. Next, we introduce a novel method to employ the James-Stein estimator to improve the estimation of mean and variance within normalization layers. We evaluate our method on different computer vision tasks: image classification, semantic segmentation, and 3D object classification. Through these evaluations, it is evident that our improved normalization layers consistently yield superior accuracy across all tasks without extra computational burden. Moreover, recognizing that a plethora of shrinkage estimators surpass the traditional estimator in performance, we study two other prominent shrinkage estimators: Ridge and LASSO. Additionally, we provide visual representations to intuitively demonstrate the impact of shrinkage on the estimated layer statistics. Finally, we study the effect of regularization and batch size on our modified batch normalization. The studies show that our method is less sensitive to batch size and regularization, improving accuracy under various setups.
UAV-Aided Lifelong Learning for AoI and Energy Optimization in Non-Stationary IoT Networks
Venue: arXiv cs.NI 2023
Year: 2023

In this paper, a novel joint energy and age of information (AoI) optimization framework for IoT devices in a non-stationary environment is presented. In particular, IoT devices that are distributed in the real-world are required to efficiently utilize their computing resources so as to balance the freshness of their data and their energy consumption. To optimize the performance of IoT devices in such a dynamic setting, a novel lifelong reinforcement learning (RL) solution that enables IoT devices to continuously adapt their policies to each newly encountered environment is proposed. Given that IoT devices have limited energy and computing resources, an unmanned aerial vehicle (UAV) is leveraged to visit the IoT devices and update the policy of each device sequentially. As such, the UAV is exploited as a mobile learning agent that can learn a shared knowledge base with a feature base in its training phase, and feature sets of a zero-shot learning method in its testing phase, to generalize between the environments. To optimize the trajectory and flying velocity of the UAV, an actor-critic network is leveraged so as to minimize the UAV energy consumption. Simulation results show that the proposed lifelong RL solution can outperform the state-of-art benchmarks by enhancing the balanced cost of IoT devices by $8.3\%$ when incorporating warm-start policies for unseen environments. In addition, our solution achieves up to $49.38\%$ reduction in terms of energy consumption by the UAV in comparison to the random flying strategy.
Dynamic Matrix of Extremisms and Terrorism (DMET): A Continuum Approach Towards Identifying Different Degrees of Extremisms
Venue: arXiv cs.CY 2023
Year: 2023

We propose to extend the current binary understanding of terrorism (versus non-terrorism) with a Dynamic Matrix of Extremisms and Terrorism (DMET). DMET considers the whole ecosystem of content and actors that can contribute to a continuum of extremism (e.g., right-wing, left-wing, religious, separatist, single-issue). It organizes levels of extremisms by varying degrees of ideological engagement and the presence of violence identified (e.g., partisan, fringe, violent extremism, terrorism) based on cognitive and behavioral cues and group dynamics. DMET is globally applicable due to its comprehensive conceptualization of the levels of extremisms. It is also dynamic, enabling iterative mapping with the region- and time-specific classifications of extremist actors. Once global actors recognize DMET types and their distinct characteristics, they can comprehensively analyze the profiles of extremist actors (e.g., individuals, groups, movements), track these respective actors and their activities (e.g., social media content) over time, and launch targeted counter activities (e.g. de-platforming, content moderation, or redirects to targeted CVE narratives).
RTQ: Rethinking Video-language Understanding Based on Image-text Model
Venue: arXiv cs.CV 2023
Year: 2023

Recent advancements in video-language understanding have been established on the foundation of image-text models, resulting in promising outcomes due to the shared knowledge between images and videos. However, video-language understanding presents unique challenges due to the inclusion of highly complex semantic details, which result in information redundancy, temporal dependency, and scene complexity. Current techniques have only partially tackled these issues, and our quantitative analysis indicates that some of these methods are complementary. In light of this, we propose a novel framework called RTQ (Refine, Temporal model, and Query), which addresses these challenges simultaneously. The approach involves refining redundant information within frames, modeling temporal relations among frames, and querying task-specific information from the videos. Remarkably, our model demonstrates outstanding performance even in the absence of video-language pre-training, and the results are comparable with or superior to those achieved by state-of-the-art pre-training methods. Code is available at https://github.com/SCZwangxiao/RTQ-MM2023.
Student Activity Recognition in Classroom Environments using Transfer Learning
Venue: arXiv cs.CV 2023
Year: 2023

The recent advances in artificial intelligence and deep learning facilitate automation in various applications including home automation, smart surveillance systems, and healthcare among others. Human Activity Recognition is one of its emerging applications, which can be implemented in a classroom environment to enhance safety, efficiency, and overall educational quality. This paper proposes a system for detecting and recognizing the activities of students in a classroom environment. The dataset has been structured and recorded by the authors since a standard dataset for this task was not available at the time of this study. Transfer learning, a widely adopted method within the field of deep learning, has proven to be helpful in complex tasks like image and video processing. Pretrained models including VGG-16, ResNet-50, InceptionV3, and Xception are used for feature extraction and classification tasks. Xception achieved an accuracy of 93%, on the novel classroom dataset, outperforming the other three models in consideration. The system proposed in this study aims to introduce a safer and more productive learning environment for students and educators.
Towards Generalizable Referring Image Segmentation via Target Prompt and Visual Coherence
Venue: arXiv cs.CV 2023
Year: 2023

Referring image segmentation (RIS) aims to segment objects in an image conditioning on free-from text descriptions. Despite the overwhelming progress, it still remains challenging for current approaches to perform well on cases with various text expressions or with unseen visual entities, limiting its further application. In this paper, we present a novel RIS approach, which substantially improves the generalization ability by addressing the two dilemmas mentioned above. Specially, to deal with unconstrained texts, we propose to boost a given expression with an explicit and crucial prompt, which complements the expression in a unified context, facilitating target capturing in the presence of linguistic style changes. Furthermore, we introduce a multi-modal fusion aggregation module with visual guidance from a powerful pretrained model to leverage spatial relations and pixel coherences to handle the incomplete target masks and false positive irregular clumps which often appear on unseen visual entities. Extensive experiments are conducted in the zero-shot cross-dataset settings and the proposed approach achieves consistent gains compared to the state-of-the-art, e.g., 4.15\%, 5.45\%, and 4.64\% mIoU increase on RefCOCO, RefCOCO+ and ReferIt respectively, demonstrating its effectiveness. Additionally, the results on GraspNet-RIS show that our approach also generalizes well to new scenarios with large domain shifts.
SurreyAI 2023 Submission for the Quality Estimation Shared Task
Venue: arXiv cs.CL 2023
Year: 2023

Quality Estimation (QE) systems are important in situations where it is necessary to assess the quality of translations, but there is no reference available. This paper describes the approach adopted by the SurreyAI team for addressing the Sentence-Level Direct Assessment shared task in WMT23. The proposed approach builds upon the TransQuest framework, exploring various autoencoder pre-trained language models within the MonoTransQuest architecture using single and ensemble settings. The autoencoder pre-trained language models employed in the proposed systems are XLMV, InfoXLM-large, and XLMR-large. The evaluation utilizes Spearman and Pearson correlation coefficients, assessing the relationship between machine-predicted quality scores and human judgments for 5 language pairs (English-Gujarati, English-Hindi, English-Marathi, English-Tamil and English-Telugu). The MonoTQ-InfoXLM-large approach emerges as a robust strategy, surpassing all other individual models proposed in this study by significantly improving over the baseline for the majority of the language pairs.
Trained MT Metrics Learn to Cope with Machine-translated References
Venue: arXiv cs.CL 2023
Year: 2023

Neural metrics trained on human evaluations of MT tend to correlate well with human judgments, but their behavior is not fully understood. In this paper, we perform a controlled experiment and compare a baseline metric that has not been trained on human evaluations (Prism) to a trained version of the same metric (Prism+FT). Surprisingly, we find that Prism+FT becomes more robust to machine-translated references, which are a notorious problem in MT evaluation. This suggests that the effects of metric training go beyond the intended effect of improving overall correlation with human judgments.
Pathway to a fully data-driven geotechnics: lessons from materials informatics
Venue: arXiv cs.LG 2023
Year: 2023

This paper elucidates the challenges and opportunities inherent in integrating data-driven methodologies into geotechnics, drawing inspiration from the success of materials informatics. Highlighting the intricacies of soil complexity, heterogeneity, and the lack of comprehensive data, the discussion underscores the pressing need for community-driven database initiatives and open science movements. By leveraging the transformative power of deep learning, particularly in feature extraction from high-dimensional data and the potential of transfer learning, we envision a paradigm shift towards a more collaborative and innovative geotechnics field. The paper concludes with a forward-looking stance, emphasizing the revolutionary potential brought about by advanced computational tools like large language models in reshaping geotechnics informatics.
Rethinking the Domain Gap in Near-infrared Face Recognition
Venue: arXiv cs.CV 2023
Year: 2023

Heterogeneous face recognition (HFR) involves the intricate task of matching face images across the visual domains of visible (VIS) and near-infrared (NIR). While much of the existing literature on HFR identifies the domain gap as a primary challenge and directs efforts towards bridging it at either the input or feature level, our work deviates from this trend. We observe that large neural networks, unlike their smaller counterparts, when pre-trained on large scale homogeneous VIS data, demonstrate exceptional zero-shot performance in HFR, suggesting that the domain gap might be less pronounced than previously believed. By approaching the HFR problem as one of low-data fine-tuning, we introduce a straightforward framework: comprehensive pre-training, succeeded by a regularized fine-tuning strategy, that matches or surpasses the current state-of-the-art on four publicly available benchmarks. Corresponding codes can be found at https://github.com/michaeltrs/RethinkNIRVIS.
What if an SQL Statement Returned a Database?
Venue: arXiv cs.DB 2023
Year: 2023

Every SQL statement is limited to return a single, possibly denormalized, table. This design decision has far reaching consequences. (1.) for databases users in terms of slow query performance, long query result transfer times, usability-issues of SQL in web applications and object-relational mappers. In addition, (2.) for database architects it has consequences when designing query optimizers leading to logical (algebraic) join enumeration effort, memory consumption for intermediate result materialization, and physical operator selection effort. So basically, the entire query optimization stack is shaped by that design decision. In this paper, we argue that the single-table limitation should be dropped. We extend the SELECT-clause of SQL by a keyword 'RESULTDB' to support returning a result database. Our approach has clear semantics, i.e. our extended SQL returns subsets of all tables with only those tuples that would be part of the traditional (single-table) query result set, however without performing any denormalization through joins. Our SQL-extension is downward compatible. Moreover, we discuss the surprisingly long list of benefits of our approach. First, for database users: far simpler and more readable application code, better query performance, smaller query results, better query result transfer times. Second, for database architects, we present how to leverage existing closed source systems as well as change open source database systems to support our feature. We propose a couple of algorithms to integrate our feature into both closed-source as well as open source database systems. We present an initial experimental study with promising results.
How to Tune Autofocals: A Comparative Study of Advanced Tuning Methods
Venue: arXiv cs.HC 2023
Year: 2023

This study comprehensively evaluates tuning methods for autofocal glasses using virtual reality (VR), addressing the challenge of presbyopia. With aging, presbyopia diminishes the eye's ability to focus on nearby objects, impacting the quality of life for billions. Autofocals, employing focus-tunable lenses, dynamically adjust optical power for each fixation, promising a more natural visual experience than traditional bifocal or multifocal lenses. Our research contrasts the most common tuning methods - manual, gaze-based, and vergence - within a VR setup to mimic real-world scenarios. Utilizing the XTAL VR headset equipped with eye-tracking, the study replicated autofocal scenarios, measuring performance and usability through psychophysical tasks and NASA TLX surveys. Results show varying strengths and weaknesses across methods, with gaze control excelling in precision but not necessarily comfort and manual control providing stability and predictability. The findings guide the selection of tuning methods based on task requirements and user preferences, highlighting a balance between precision and ease of use.