OpenRaiser/Intern-Atlas huggingface dataset:
An experimental sorting method for improving metagenomic data encoding
Venue: arXiv cs.IT 2024
Year: 2024

Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates metagenomic classification followed by a recursive filter for clustering reads by DNA sequence similarity to improve the overall reference-free compression. In the results, we show an overall improvement in the compression of several datasets. As hypothesized, we show a progressive compression gain for higher coverage depth and number of identified species. Additionally, we provide an implementation that is freely available at https://github.com/cobilab/mizar and can be customized to work with other FASTQ compression tools.
Many-Objective-Optimized Semi-Automated Robotic Disassembly Sequences
Venue: arXiv cs.RO 2024
Year: 2024

This study tasckles the problem of many-objective sequence optimization for semi-automated robotic disassembly operations. To this end, we employ a many-objective genetic algorithm (MaOGA) algorithm inspired by the Non-dominated Sorting Genetic Algorithm (NSGA)-III, along with robotic-disassembly-oriented constraints and objective functions derived from geometrical and robot simulations using 3-dimensional (3D) geometrical information stored in a 3D Computer-Aided Design (CAD) model of the target product. The MaOGA begins by generating a set of initial chromosomes based on a contact and connection graph (CCG), rather than random chromosomes, to avoid falling into a local minimum and yield repeatable convergence. The optimization imposes constraints on feasibility and stability as well as objective functions regarding difficulty, efficiency, prioritization, and allocability to generate a sequence that satisfies many preferred conditions under mandatory requirements for semi-automated robotic disassembly. The NSGA-III-inspired MaOGA also utilizes non-dominated sorting and niching with reference lines to further encourage steady and stable exploration and uniformly lower the overall evaluation values. Our sequence generation experiments for a complex product (36 parts) demonstrated that the proposed method can consistently produce feasible and stable sequences with a 100% success rate, bringing the multiple preferred conditions closer to the optimal solution required for semi-automated robotic disassembly operations.
Data-Driven Power Modeling and Monitoring via Hardware Performance Counters Tracking
Venue: arXiv cs.PF 2024
Year: 2024

In the current high-performance and embedded computing era, full-stack energy-centric design is paramount. Use cases require increasingly high performance at an affordable power budget, often under real-time constraints. Extreme heterogeneity and parallelism address these issues but greatly complicate online power consumption assessment, which is essential for dynamic hardware and software stack adaptations. We introduce a novel architecture-agnostic power modeling methodology with state-of-the-art accuracy, low overhead, and high responsiveness. Our methodology identifies the best Performance Monitoring Counters (PMCs) to model the power consumption of each hardware sub-system at each Dynamic Voltage and Frequency Scaling (DVFS) state. The individual linear models are combined into a complete model that effectively describes the power consumption of the whole system, achieving high accuracy and low overhead. Our evaluation reports an average estimation error of 7.5 % for power consumption and 1.3 % for energy. Furthermore, we propose Runmeter, an open-source, PMC-based monitoring framework integrated into the Linux kernel. Runmeter manages PMC samples collection and manipulation, efficiently evaluating our power models at runtime. With a time overhead of only 0.7 % in the worst case, Runmeter provides responsive and accurate power measurements directly in the kernel, which can be employed for actuation policies such as Dynamic Power Management (DPM) and power-aware task scheduling.
Multilingual Instruction Tuning With Just a Pinch of Multilinguality
Venue: arXiv cs.CL 2024
Year: 2024

As instruction-tuned large language models (LLMs) gain global adoption, their ability to follow instructions in multiple languages becomes increasingly crucial. In this work, we investigate how multilinguality during instruction tuning of a multilingual LLM affects instruction-following across languages from the pre-training corpus. We first show that many languages transfer some instruction-following capabilities to other languages from even monolingual tuning. Furthermore, we find that only 40 multilingual examples integrated in an English tuning set substantially improve multilingual instruction-following, both in seen and unseen languages during tuning. In general, we observe that models tuned on multilingual mixtures exhibit comparable or superior performance in multiple languages compared to monolingually tuned models, despite training on 10x fewer examples in those languages. Finally, we find that diversifying the instruction tuning set with even just 2-4 languages significantly improves cross-lingual generalization. Our results suggest that building massively multilingual instruction-tuned models can be done with only a very small set of multilingual instruction-responses.
A rewriting-logic-with-SMT-based formal analysis and parameter synthesis framework for parametric time Petri nets
Venue: arXiv cs.LO 2024
Year: 2024

This paper presents a concrete and a symbolic rewriting logic semantics for parametric time Petri nets with inhibitor arcs (PITPNs), a flexible model of timed systems where parameters are allowed in firing bounds. We prove that our semantics is bisimilar to the "standard" semantics of PITPNs. This allows us to use the rewriting logic tool Maude, combined with SMT solving, to provide sound and complete formal analyses for PITPNs. We develop and implement a new general folding approach for symbolic reachability, so that Maude-with-SMT reachability analysis terminates whenever the parametric state-class graph of the PITPN is finite. Our work opens up the possibility of using the many formal analysis capabilities of Maude -- including full LTL model checking, analysis with user-defined analysis strategies, and even statistical model checking -- for such nets. We illustrate this by explaining how almost all formal analysis and parameter synthesis methods supported by the state-of-the-art PITPN tool Romeo can be performed using Maude with SMT. In addition, we also support analysis and parameter synthesis from parametric initial markings, as well as full LTL model checking and analysis with user-defined execution strategies. Experiments show that our methods outperform Romeo in many cases.
Beyond Regrets: Geometric Metrics for Bayesian Optimization
Venue: arXiv cs.LG 2024
Year: 2024

Bayesian optimization is a principled optimization strategy for a black-box objective function. It shows its effectiveness in a wide variety of real-world applications such as scientific discovery and experimental design. In general, the performance of Bayesian optimization is reported through regret-based metrics such as instantaneous, simple, and cumulative regrets. These metrics only rely on function evaluations, so that they do not consider geometric relationships between query points and global solutions, or query points themselves. Notably, they cannot discriminate if multiple global solutions are successfully found. Moreover, they do not evaluate Bayesian optimization's abilities to exploit and explore a search space given. To tackle these issues, we propose four new geometric metrics, i.e., precision, recall, average degree, and average distance. These metrics allow us to compare Bayesian optimization algorithms considering the geometry of both query points and global optima, or query points. However, they are accompanied by an extra parameter, which needs to be carefully determined. We therefore devise the parameter-free forms of the respective metrics by integrating out the additional parameter. Finally, we validate that our proposed metrics can provide more delicate interpretation of Bayesian optimization, on top of assessment via the conventional metrics.
Improving Diffusion-Based Image Synthesis with Context Prediction
Venue: arXiv cs.CV 2024
Year: 2024

Diffusion models are a new class of generative models, and have dramatically promoted image generation with unprecedented quality and diversity. Existing diffusion models mainly try to reconstruct input image from a corrupted one with a pixel-wise or feature-wise constraint along spatial axes. However, such point-based reconstruction may fail to make each predicted pixel/feature fully preserve its neighborhood context, impairing diffusion-based image synthesis. As a powerful source of automatic supervisory signal, context has been well studied for learning representations. Inspired by this, we for the first time propose ConPreDiff to improve diffusion-based image synthesis with context prediction. We explicitly reinforce each point to predict its neighborhood context (i.e., multi-stride features/tokens/pixels) with a context decoder at the end of diffusion denoising blocks in training stage, and remove the decoder for inference. In this way, each point can better reconstruct itself by preserving its semantic connections with neighborhood context. This new paradigm of ConPreDiff can generalize to arbitrary discrete and continuous diffusion backbones without introducing extra parameters in sampling procedure. Extensive experiments are conducted on unconditional image generation, text-to-image generation and image inpainting tasks. Our ConPreDiff consistently outperforms previous methods and achieves a new SOTA text-to-image generation results on MS-COCO, with a zero-shot FID score of 6.21.
From Function to Distribution Modeling: A PAC-Generative Approach to Offline Optimization
Venue: arXiv cs.LG 2024
Year: 2024

This paper considers the problem of offline optimization, where the objective function is unknown except for a collection of ``offline" data examples. While recent years have seen a flurry of work on applying various machine learning techniques to the offline optimization problem, the majority of these work focused on learning a surrogate of the unknown objective function and then applying existing optimization algorithms. While the idea of modeling the unknown objective function is intuitive and appealing, from the learning point of view it also makes it very difficult to tune the objective of the learner according to the objective of optimization. Instead of learning and then optimizing the unknown objective function, in this paper we take on a less intuitive but more direct view that optimization can be thought of as a process of sampling from a generative model. To learn an effective generative model from the offline data examples, we consider the standard technique of ``re-weighting", and our main technical contribution is a probably approximately correct (PAC) lower bound on the natural optimization objective, which allows us to jointly learn a weight function and a score-based generative model. The robustly competitive performance of the proposed approach is demonstrated via empirical studies using the standard offline optimization benchmarks.
Signal Detection for Ultra-Massive MIMO: An Information Geometry Approach
Venue: arXiv cs.IT 2024
Year: 2024

In this paper, we propose an information geometry approach (IGA) for signal detection (SD) in ultra-massive multiple-input multiple-output (MIMO) systems. We formulate the signal detection as obtaining the marginals of the a posteriori probability distribution of the transmitted symbol vector. Then, a maximization of the a posteriori marginals (MPM) for signal detection can be performed. With the information geometry theory, we calculate the approximations of the a posteriori marginals. It is formulated as an iterative m-projection process between submanifolds with different constraints. We then apply the central-limit-theorem (CLT) to simplify the calculation of the m-projection since the direct calculation of the m-projection is of exponential-complexity. With the CLT, we obtain an approximate solution of the m-projection, which is asymptotically accurate. Simulation results demonstrate that the proposed IGA-SD emerges as a promising and efficient method to implement the signal detector in ultra-massive MIMO systems.
View-based Explanations for Graph Neural Networks
Venue: arXiv cs.LG 2024
Year: 2024

Generating explanations for graph neural networks (GNNs) has been studied to understand their behavior in analytical tasks such as graph classification. Existing approaches aim to understand the overall results of GNNs rather than providing explanations for specific class labels of interest, and may return explanation structures that are hard to access, nor directly queryable.We propose GVEX, a novel paradigm that generates Graph Views for EXplanation. (1) We design a two-tier explanation structure called explanation views. An explanation view consists of a set of graph patterns and a set of induced explanation subgraphs. Given a database G of multiple graphs and a specific class label l assigned by a GNN-based classifier M, it concisely describes the fraction of G that best explains why l is assigned by M. (2) We propose quality measures and formulate an optimization problem to compute optimal explanation views for GNN explanation. We show that the problem is $Σ^2_P$-hard. (3) We present two algorithms. The first one follows an explain-and-summarize strategy that first generates high-quality explanation subgraphs which best explain GNNs in terms of feature influence maximization, and then performs a summarization step to generate patterns. We show that this strategy provides an approximation ratio of 1/2. Our second algorithm performs a single-pass to an input node stream in batches to incrementally maintain explanation views, having an anytime quality guarantee of 1/4 approximation. Using real-world benchmark data, we experimentally demonstrate the effectiveness, efficiency, and scalability of GVEX. Through case studies, we showcase the practical applications of GVEX.
ModuleGuard:Understanding and Detecting Module Conflicts in Python Ecosystem
Venue: arXiv cs.SE 2024
Year: 2024

Python has become one of the most popular programming languages for software development due to its simplicity, readability, and versatility. As the Python ecosystem grows, developers face increasing challenges in avoiding module conflicts, which occur when different packages have the same namespace modules. Unfortunately, existing work has neither investigated the module conflict comprehensively nor provided tools to detect the conflict. Therefore, this paper systematically investigates the module conflict problem and its impact on the Python ecosystem. We propose a novel technique called InstSimulator, which leverages semantics and installation simulation to achieve accurate and efficient module extraction. Based on this, we implement a tool called ModuleGuard to detect module conflicts for the Python ecosystem. For the study, we first collect 97 MC issues, classify the characteristics and causes of these MC issues, summarize three different conflict patterns, and analyze their potential threats. Then, we conducted a large-scale analysis of the whole PyPI ecosystem (4.2 million packages) and GitHub popular projects (3,711 projects) to detect each MC pattern and analyze their potential impact. We discovered that module conflicts still impact numerous TPLs and GitHub projects. This is primarily due to developers' lack of understanding of the modules within their direct dependencies, not to mention the modules of the transitive dependencies. Our work reveals Python's shortcomings in handling naming conflicts and provides a tool and guidelines for developers to detect conflicts.
Oceanship: A Large-Scale Dataset for Underwater Audio Target Recognition
Venue: arXiv cs.CV 2024
Year: 2024

The recognition of underwater audio plays a significant role in identifying a vessel while it is in motion. Underwater target recognition tasks have a wide range of applications in areas such as marine environmental protection, detection of ship radiated noise, underwater noise control, and coastal vessel dispatch. The traditional UATR task involves training a network to extract features from audio data and predict the vessel type. The current UATR dataset exhibits shortcomings in both duration and sample quantity. In this paper, we propose Oceanship, a large-scale and diverse underwater audio dataset. This dataset comprises 15 categories, spans a total duration of 121 hours, and includes comprehensive annotation information such as coordinates, velocity, vessel types, and timestamps. We compiled the dataset by crawling and organizing original communication data from the Ocean Communication Network (ONC) database between 2021 and 2022. While audio retrieval tasks are well-established in general audio classification, they have not been explored in the context of underwater audio recognition. Leveraging the Oceanship dataset, we introduce a baseline model named Oceannet for underwater audio retrieval. This model achieves a recall at 1 (R@1) accuracy of 67.11% and a recall at 5 (R@5) accuracy of 99.13% on the Deepship dataset.
Using LLM to select the right SQL Query from candidates
Venue: arXiv cs.CL 2024
Year: 2024

Text-to-SQL models can generate a list of candidate SQL queries, and the best query is often in the candidate list, but not at the top of the list. An effective re-rank method can select the right SQL query from the candidate list and improve the model's performance. Previous studies on code generation automatically generate test cases and use them to re-rank candidate codes. However, automatic test case generation for text-to-SQL is an understudied field. We propose an automatic test case generation method that first generates a database and then uses LLMs to predict the ground truth, which is the expected execution results of the ground truth SQL query on this database. To reduce the difficulty for LLMs to predict, we conduct experiments to search for ways to generate easy databases for LLMs and design easy-to-understand prompts. Based on our test case generation method, we propose a re-rank method to select the right SQL query from the candidate list. Given a candidate list, our method can generate test cases and re-rank the candidate list according to their pass numbers on these test cases and their generation probabilities. The experiment results on the validation dataset of Spider show that the performance of some state-of-the-art models can get a 3.6\% improvement after applying our re-rank method.
Starling: An I/O-Efficient Disk-Resident Graph Index Framework for High-Dimensional Vector Similarity Search on Data Segment
Venue: arXiv cs.DB 2024
Year: 2024

High-dimensional vector similarity search (HVSS) is gaining prominence as a powerful tool for various data science and AI applications. As vector data scales up, in-memory indexes pose a significant challenge due to the substantial increase in main memory requirements. A potential solution involves leveraging disk-based implementation, which stores and searches vector data on high-performance devices like NVMe SSDs. However, implementing HVSS for data segments proves to be intricate in vector databases where a single machine comprises multiple segments for system scalability. In this context, each segment operates with limited memory and disk space, necessitating a delicate balance between accuracy, efficiency, and space cost. Existing disk-based methods fall short as they do not holistically address all these requirements simultaneously. In this paper, we present Starling, an I/O-efficient disk-resident graph index framework that optimizes data layout and search strategy within the segment. It has two primary components: (1) a data layout incorporating an in-memory navigation graph and a reordered disk-based graph with enhanced locality, reducing the search path length and minimizing disk bandwidth wastage; and (2) a block search strategy designed to minimize costly disk I/O operations during vector query execution. Through extensive experiments, we validate the effectiveness, efficiency, and scalability of Starling. On a data segment with 2GB memory and 10GB disk capacity, Starling can accommodate up to 33 million vectors in 128 dimensions, offering HVSS with over 0.9 average precision and top-10 recall rate, and latency under 1 millisecond. The results showcase Starling's superior performance, exhibiting 43.9$\times$ higher throughput with 98% lower query latency compared to state-of-the-art methods while maintaining the same level of accuracy.
Unit Testing in ASP Revisited: Language and Test-Driven Development Environment
Venue: arXiv cs.SE 2024
Year: 2024

Unit testing frameworks are nowadays considered a best practice, included in almost all modern software development processes, to achieve rapid development of correct specifications. Knowledge representation and reasoning paradigms such as Answer Set Programming (ASP), that have been used in industry-level applications, are not an exception. Indeed, the first unit testing specification language for ASP was proposed in 2011 as a feature of the ASPIDE development environment. Later, a more portable unit testing language was included in the LANA annotation language. In this paper we revisit both languages and tools for unit testing in ASP. We propose a new unit test specification language that allows one to inline tests within ASP programs, and we identify the computational complexity of the tasks associated with checking the various program-correctness assertions. Test-case specifications are transparent to the traditional evaluation, but can be interpreted by a specific testing tool. Thus, we present a novel environment supporting test driven development of ASP programs.
Shayona@SMM4H23: COVID-19 Self diagnosis classification using BERT and LightGBM models
Venue: arXiv cs.CL 2024
Year: 2024

This paper describes approaches and results for shared Task 1 and 4 of SMMH4-23 by Team Shayona. Shared Task-1 was binary classification of english tweets self-reporting a COVID-19 diagnosis, and Shared Task-4 was Binary classification of English Reddit posts self-reporting a social anxiety disorder diagnosis. Our team has achieved the highest f1-score 0.94 in Task-1 among all participants. We have leveraged the Transformer model (BERT) in combination with the LightGBM model for both tasks.
Human-in-the-Loop Policy Optimization for Preference-Based Multi-Objective Reinforcement Learning
Venue: arXiv cs.NE 2024
Year: 2024

Multi-objective reinforcement learning (MORL) aims to find a set of high-performing and diverse policies that address trade-offs between multiple conflicting objectives. However, in practice, decision makers (DMs) often deploy only one or a limited number of trade-off policies. Providing too many diversified trade-off policies to the DM not only significantly increases their workload but also introduces noise in multi-criterion decision-making. With this in mind, we propose a human-in-the-loop policy optimization framework for preference-based MORL that interactively identifies policies of interest. Our method proactively learns the DM's implicit preference information without requiring any a priori knowledge, which is often unavailable in real-world black-box decision scenarios. The learned preference information is used to progressively guide policy optimization towards policies of interest. We evaluate our approach against three conventional MORL algorithms that do not consider preference information and four state-of-the-art preference-based MORL algorithms on two MORL environments for robot control and smart grid management. Experimental results fully demonstrate the effectiveness of our proposed method in comparison to the other peer algorithms.