Miracle-dz/UniFAR-FTUs huggingface dataset:
ACE-HetEM for ab initio Heterogenous Cryo-EM 3D Reconstruction

Due to the extremely low signal-to-noise ratio (SNR) and unknown poses (projection angles and image translation) in cryo-EM experiments, reconstructing 3D structures from 2D images is very challenging. On top of these challenges, heterogeneous cryo-EM reconstruction also has an additional requirement: conformation classification. An emerging solution to this problem is called amortized inference, implemented using the autoencoder architecture or its variants. Instead of searching for the correct image-to-pose/conformation mapping for every image in the dataset as in non-amortized methods, amortized inference only needs to train an encoder that maps images to appropriate latent spaces representing poses or conformations. Unfortunately, standard amortized-inference-based methods with entangled latent spaces have difficulty learning the distribution of conformations and poses from cryo-EM images. In this paper, we propose an unsupervised deep learning architecture called"ACE-HetEM"based on amortized inference. To explicitly enforce the disentanglement of conformation classifications and pose estimations, we designed two alternating training tasks in our method: image-to-image task and pose-to-pose task. Results on simulated datasets show that ACE-HetEM has comparable accuracy in pose estimation and produces even better reconstruction resolution than non-amortized methods. Furthermore, we show that ACE-HetEM is also applicable to real experimental datasets.
Scalable Hypergraph Visualization

Hypergraph visualization has many applications in network data analysis. Recently, a polygon-based representation for hypergraphs has been proposed with demonstrated benefits. However, the polygon-based layout often suffers from excessive self-intersections when the input dataset is relatively large. In this paper, we propose a framework in which the hypergraph is iteratively simplified through a set of atomic operations. Then, the layout of the simplest hypergraph is optimized and used as the foundation for a reverse process that brings the simplest hypergraph back to the original one, but with an improved layout. At the core of our approach is the set of atomic simplification operations and an operation priority measure to guide the simplification process. In addition, we introduce necessary definitions and conditions for hypergraph planarity within the polygon representation. We extend our approach to handle simultaneous simplification and layout optimization for both the hypergraph and its dual. We demonstrate the utility of our approach with datasets from a number of real-world applications.
Multi-Class Deep SVDD: Anomaly Detection Approach in Astronomy with Distinct Inlier Categories

With the increasing volume of astronomical data generated by modern survey telescopes, automated pipelines and machine learning techniques have become crucial for analyzing and extracting knowledge from these datasets. Anomaly detection, i.e. the task of identifying irregular or unexpected patterns in the data, is a complex challenge in astronomy. In this paper, we propose Multi-Class Deep Support Vector Data Description (MCDSVDD), an extension of the state-of-the-art anomaly detection algorithm One-Class Deep SVDD, specifically designed to handle different inlier categories with distinct data distributions. MCDSVDD uses a neural network to map the data into hyperspheres, where each hypersphere represents a specific inlier category. The distance of each sample from the centers of these hyperspheres determines the anomaly score. We evaluate the effectiveness of MCDSVDD by comparing its performance with several anomaly detection algorithms on a large dataset of astronomical light-curves obtained from the Zwicky Transient Facility. Our results demonstrate the efficacy of MCDSVDD in detecting anomalous sources while leveraging the presence of different inlier categories. The code and the data needed to reproduce our results are publicly available at https://github.com/mperezcarrasco/AnomalyALeRCE.
An Empirical Study on Using Large Language Models to Analyze Software Supply Chain Security Failures

As we increasingly depend on software systems, the consequences of breaches in the software supply chain become more severe. High-profile cyber attacks like SolarWinds and ShadowHammer have resulted in significant financial and data losses, underlining the need for stronger cybersecurity. One way to prevent future breaches is by studying past failures. However, traditional methods of analyzing past failures require manually reading and summarizing reports about them. Automated support could reduce costs and allow analysis of more failures. Natural Language Processing (NLP) techniques such as Large Language Models (LLMs) could be leveraged to assist the analysis of failures. In this study, we assessed the ability of Large Language Models (LLMs) to analyze historical software supply chain breaches. We used LLMs to replicate the manual analysis of 69 software supply chain security failures performed by members of the Cloud Native Computing Foundation (CNCF). We developed prompts for LLMs to categorize these by four dimensions: type of compromise, intent, nature, and impact. GPT 3.5's categorizations had an average accuracy of 68% and Bard's had an accuracy of 58% over these dimensions. We report that LLMs effectively characterize software supply chain failures when the source articles are detailed enough for consensus among manual analysts, but cannot yet replace human analysts. Future work can improve LLM performance in this context, and study a broader range of articles and failures.
A Comprehensive Empirical Study of Bugs in Open-Source Federated Learning Frameworks

Federated learning (FL) is a distributed machine learning (ML) paradigm, allowing multiple clients to collaboratively train shared machine learning (ML) models without exposing clients' data privacy. It has gained substantial popularity in recent years, especially since the enforcement of data protection laws and regulations in many countries. To foster the application of FL, a variety of FL frameworks have been proposed, allowing non-experts to easily train ML models. As a result, understanding bugs in FL frameworks is critical for facilitating the development of better FL frameworks and potentially encouraging the development of bug detection, localization and repair tools. Thus, we conduct the first empirical study to comprehensively collect, taxonomize, and characterize bugs in FL frameworks. Specifically, we manually collect and classify 1,119 bugs from all the 676 closed issues and 514 merged pull requests in 17 popular and representative open-source FL frameworks on GitHub. We propose a classification of those bugs into 12 bug symptoms, 12 root causes, and 18 fix patterns. We also study their correlations and distributions on 23 functionalities. We identify nine major findings from our study, discuss their implications and future research directions based on our findings.
Dual Intents Graph Modeling for User-centric Group Discovery

Online groups have become increasingly prevalent, providing users with space to share experiences and explore interests. Therefore, user-centric group discovery task, i.e., recommending groups to users can help both users' online experiences and platforms' long-term developments. Existing recommender methods can not deal with this task as modeling user-group participation into a bipartite graph overlooks their item-side interests. Although there exist a few works attempting to address this task, they still fall short in fully preserving the social context and ensuring effective interest representation learning. In this paper, we focus on exploring the intents that motivate users to participate in groups, which can be categorized into different types, like the social-intent and the personal interest-intent. The former refers to users joining a group affected by their social links, while the latter relates to users joining groups with like-minded people for interest-oriented self-enjoyment. To comprehend different intents, we propose a novel model, DiRec, that first models each intent separately and then fuses them together for predictions. Specifically, for social-intent, we introduce the hypergraph structure to model the relationship between groups and members. This allows for more comprehensive group information preservation, leading to a richer understanding of the social context. As for interest-intent, we employ novel structural refinement on the interactive graph to uncover more intricate user behaviors, item characteristics, and group interests, realizing better representation learning of interests. Furthermore, we also observe the intent overlapping in real-world scenarios and devise a novel self-supervised learning loss that encourages such alignment for final recommendations. Extensive experiments on three public datasets show the significant improvement of DiRec over the state-of-the-art methods.
A Guide to Impact Evaluation under Sample Selection and Missing Data: Teacher's Aides and Adolescent Mental Health

This paper is concerned with identification, estimation, and specification testing in causal evaluation problems when data is selective and/or missing. We leverage recent advances in the literature on graphical methods to provide a unifying framework for guiding empirical practice. The approach integrates and connects to prominent identification and testing strategies in the literature on missing data, causal machine learning, panel data analysis, and more. We demonstrate its utility in the context of identification and specification testing in sample selection models and field experiments with attrition. We provide a novel analysis of a large-scale cluster-randomized controlled teacher's aide trial in Danish schools at grade 6. Even with detailed administrative data, the handling of missing data crucially affects broader conclusions about effects on mental health. Results suggest that teaching assistants provide an effective way of improving internalizing behavior for large parts of the student population.
Explainable AI in Orthopedics: Challenges, Opportunities, and Prospects

While artificial intelligence (AI) has made many successful applications in various domains, its adoption in healthcare lags a little bit behind other high-stakes settings. Several factors contribute to this slower uptake, including regulatory frameworks, patient privacy concerns, and data heterogeneity. However, one significant challenge that impedes the implementation of AI in healthcare, particularly in orthopedics, is the lack of explainability and interpretability around AI models. Addressing the challenge of explainable AI (XAI) in orthopedics requires developing AI models and algorithms that prioritize transparency and interpretability, allowing clinicians, surgeons, and patients to understand the contributing factors behind any AI-powered predictive or descriptive models. The current contribution outlines several key challenges and opportunities that manifest in XAI in orthopedic practice. This work emphasizes the need for interdisciplinary collaborations between AI practitioners, orthopedic specialists, and regulatory entities to establish standards and guidelines for the adoption of XAI in orthopedics.
Free algebras of topologically enriched multi-sorted equational theories

Classical multi-sorted equational theories and their free algebras have been fundamental in mathematics and computer science. In this paper, we present a generalization of multi-sorted equational theories from the classical ($Set$-enriched) context to the context of enrichment in a symmetric monoidal category $V$ that is topological over $Set$. Prominent examples of such categories include: various categories of topological and measurable spaces; the categories of models of relational Horn theories without equality, including the categories of preordered sets and (extended) pseudo-metric spaces; and the categories of quasispaces (a.k.a. concrete sheaves) on concrete sites, which have recently attracted interest in the study of programming language semantics. Given such a category $V$, we define a notion of $V$-enriched multi-sorted equational theory. We show that every $V$-enriched multi-sorted equational theory $T$ has an underlying classical multi-sorted equational theory $|T|$, and that free $T$-algebras may be obtained as suitable liftings of free $|T|$-algebras. We establish explicit and concrete descriptions of free $T$-algebras, which have a convenient inductive character when $V$ is cartesian closed. We provide several examples of $V$-enriched multi-sorted equational theories, and we also discuss the close connection between these theories and the presentations of $V$-enriched algebraic theories and monads studied in recent papers by the author and Lucyshyn-Wright.
A Comparative Study of Sentence Embedding Models for Assessing Semantic Variation

Analyzing the pattern of semantic variation in long real-world texts such as books or transcripts is interesting from the stylistic, cognitive, and linguistic perspectives. It is also useful for applications such as text segmentation, document summarization, and detection of semantic novelty. The recent emergence of several vector-space methods for sentence embedding has made such analysis feasible. However, this raises the issue of how consistent and meaningful the semantic representations produced by various methods are in themselves. In this paper, we compare several recent sentence embedding methods via time-series of semantic similarity between successive sentences and matrices of pairwise sentence similarity for multiple books of literature. In contrast to previous work using target tasks and curated datasets to compare sentence embedding methods, our approach provides an evaluation of the methods 'in the wild'. We find that most of the sentence embedding methods considered do infer highly correlated patterns of semantic similarity in a given document, but show interesting differences.
Why Data Science Projects Fail

Data Science is a modern Data Intelligence practice, which is the core of many businesses and helps businesses build smart strategies around to deal with businesses challenges more efficiently. Data Science practice also helps in automating business processes using the algorithm, and it has several other benefits, which also deliver in a non-profitable framework. In regards to data science, three key components primarily influence the effective outcome of a data science project. Those are 1.Availability of Data 2.Algorithm 3.Processing power or infrastructure
Capturing Spectral and Long-term Contextual Information for Speech Emotion Recognition Using Deep Learning Techniques

Traditional approaches in speech emotion recognition, such as LSTM, CNN, RNN, SVM, and MLP, have limitations such as difficulty capturing long-term dependencies in sequential data, capturing the temporal dynamics, and struggling to capture complex patterns and relationships in multimodal data. This research addresses these shortcomings by proposing an ensemble model that combines Graph Convolutional Networks (GCN) for processing textual data and the HuBERT transformer for analyzing audio signals. We found that GCNs excel at capturing Long-term contextual dependencies and relationships within textual data by leveraging graph-based representations of text and thus detecting the contextual meaning and semantic relationships between words. On the other hand, HuBERT utilizes self-attention mechanisms to capture long-range dependencies, enabling the modeling of temporal dynamics present in speech and capturing subtle nuances and variations that contribute to emotion recognition. By combining GCN and HuBERT, our ensemble model can leverage the strengths of both approaches. This allows for the simultaneous analysis of multimodal data, and the fusion of these modalities enables the extraction of complementary information, enhancing the discriminative power of the emotion recognition system. The results indicate that the combined model can overcome the limitations of traditional methods, leading to enhanced accuracy in recognizing emotions from speech.
A Survey on Decentralized Federated Learning

In recent years, federated learning (FL) has become a very popular paradigm for training distributed, large-scale, and privacy-preserving machine learning (ML) systems. In contrast to standard ML, where data must be collected at the exact location where training is performed, FL takes advantage of the computational capabilities of millions of edge devices to collaboratively train a shared, global model without disclosing their local private data. Specifically, in a typical FL system, the central server acts only as an orchestrator; it iteratively gathers and aggregates all the local models trained by each client on its private data until convergence. Although FL undoubtedly has several benefits over traditional ML (e.g., it protects private data ownership by design), it suffers from several weaknesses. One of the most critical challenges is to overcome the centralized orchestration of the classical FL client-server architecture, which is known to be vulnerable to single-point-of-failure risks and man-in-the-middle attacks, among others. To mitigate such exposure, decentralized FL solutions have emerged where all FL clients cooperate and communicate without a central server. This survey comprehensively summarizes and reviews existing decentralized FL approaches proposed in the literature. Furthermore, it identifies emerging challenges and suggests promising research directions in this under-explored domain.
Evaluating SZZ Implementations: An Empirical Study on the Linux Kernel

The SZZ algorithm is used to connect bug-fixing commits to the earlier commits that introduced bugs. This algorithm has many applications and many variants have been devised. However, there are some types of commits that cannot be traced by the SZZ algorithm, referred to as"ghost commits". The evaluation of how these ghost commits impact the SZZ algorithm remains limited. Moreover, these algorithms have been evaluated on datasets created by software engineering researchers from information in bug trackers and version controlled histories. Since Oct 2013, the Linux kernel developers have started labelling bug-fixing patches with the commit identifiers of the corresponding bug-inducing commit(s) as a standard practice. As of v6.1-rc5, 76,046 pairs of bug-fixing patches and bug-inducing commits are available. This provides a unique opportunity to evaluate the SZZ algorithm on a large dataset that has been created and reviewed by project developers, entirely independently of the biases of software engineering researchers. In this paper, we apply six SZZ algorithms to 76,046 pairs of bug-fixing patches and bug-introducing commits from the Linux kernel. Our findings reveal that SZZ algorithms experience a more significant decline in recall on our dataset (13.8%) as compared to prior findings reported by Rosa et al., and the disparities between the individual SZZ algorithms diminish. Moreover, we find that 17.47% of bug-fixing commits are ghost commits. Finally, we propose Tracing-Commit SZZ (TC-SZZ), that traces all commits in the change history of lines modified or deleted in bug-fixing commits. Applying TC-SZZ to all failure cases, excluding ghost commits, we found that TC-SZZ could identify 17.7% of them. Our further analysis found that 34.6% of bug-inducing commits were in the function history, 27.5% in the file history (but not in the function history), and.
Blockchain-based Optimized Client Selection and Privacy Preserved Framework for Federated Learning

Federated learning is a distributed mechanism that trained large-scale neural network models with the participation of multiple clients and data remains on their devices, only sharing the local model updates. With this feature, federated learning is considered a secure solution for data privacy issues. However, the typical FL structure relies on the client-server, which leads to the single-point-of-failure (SPoF) attack, and the random selection of clients for model training compromised the model accuracy. Furthermore, adversaries try for inference attacks i.e., attack on privacy leads to gradient leakage attacks. We proposed the blockchain-based optimized client selection and privacy-preserved framework in this context. We designed the three kinds of smart contracts such as 1) registration of clients 2) forward bidding to select optimized clients for FL model training 3) payment settlement and reward smart contracts. Moreover, fully homomorphic encryption with Cheon, Kim, Kim, and Song (CKKS) method is implemented before transmitting the local model updates to the server. Finally, we evaluated our proposed method on the benchmark dataset and compared it with state-of-the-art studies. Consequently, we achieved a higher accuracy rate and privacy-preserved FL framework with decentralized nature.
Ahead of the Text: Leveraging Entity Preposition for Financial Relation Extraction

In the context of the ACM KDF-SIGIR 2023 competition, we undertook an entity relation task on a dataset of financial entity relations called REFind. Our top-performing solution involved a multi-step approach. Initially, we inserted the provided entities at their corresponding locations within the text. Subsequently, we fine-tuned the transformer-based language model roberta-large for text classification by utilizing a labeled training set to predict the entity relations. Lastly, we implemented a post-processing phase to identify and handle improbable predictions generated by the model. As a result of our methodology, we achieved the 1st place ranking on the competition's public leaderboard.
BOPIM: Bayesian Optimization for influence maximization on temporal networks

The goal of influence maximization (IM) is to select a small set of seed nodes which maximize the spread of influence on a network. In this work, we propose BOPIM, a Bayesian Optimization (BO) algorithm for IM on temporal networks. The IM task is well-suited for a BO solution due to its expensive and complicated objective function. We propose a simple surrogate function to model the objective function and leverage Gaussian Process regression with shrinkage priors to fit the model. An acquisition function based on the median of the posterior distribution leads to a straightforward procedure to select the next sampling point. In numerical experiments on real-world networks, we find that, on average, the surrogate function estimates the true influence spread within a few nodes. Additionally, we show that BOPIM yields comparable influence spreads to a gold-standard greedy algorithm while being as much as seventeen times faster. We also use these experiments to demonstrate the proposed method's ability to quantify uncertainty in optimal seed sets. To the knowledge of the author, this is the first attempt to look at uncertainty in the seed sets for IM, as well as the first application of BO to a constrained, combinatorial optimization problem.
Vulnerabilities in AI Code Generators: Exploring Targeted Data Poisoning Attacks

In this work, we assess the security of AI code generators via data poisoning, i.e., an attack that injects malicious samples into the training data to generate vulnerable code. We poison the training data by injecting increasing amounts of code containing security vulnerabilities and assess the attack's success on different state-of-the-art models for code generation. Our analysis shows that AI code generators are vulnerable to even a small amount of data poisoning. Moreover, the attack does not impact the correctness of code generated by pre-trained models, making it hard to detect.