OpenRaiser/Intern-Atlas huggingface dataset:
Are Your Epochs Too Epic? Batch Free Can Be Harmful
Venue: arXiv cs.DC 2024
Year: 2024

Epoch based memory reclamation (EBR) is one of the most popular techniques for reclaiming memory in lock-free and optimistic locking data structures, due to its ease of use and good performance in practice. However, EBR is known to be sensitive to thread delays, which can result in performance degradation. Moreover, the exact mechanism for this performance degradation is not well understood. This paper illustrates this performance degradation in a popular data structure benchmark, and does a deep dive to uncover its root cause-a subtle interaction between EBR and state of the art memory allocators. In essence, modern allocators attempt to reduce the overhead of freeing by maintaining bounded thread caches of objects for local reuse, actually freeing them (a very high latency operation) only when thread caches become too large. EBR immediately bypasses these mechanisms whenever a particularly large batch of objects is freed, substantially increasing overheads and latencies. Beyond EBR, many memory reclamation algorithms, and data structures, that reclaim objects in large batches suffer similar deleterious interactions with popular allocators. We propose a simple algorithmic fix for such algorithms to amortize the freeing of large object batches over time, and apply this technique to ten existing memory reclamation algorithms, observing performance improvements for nine out of ten, and over 50% improvement for six out of ten in experiments on a high performance lock-free ABtree. We also present an extremely simple token passing variant of EBR and show that, with our fix, it performs 1.5-2.6x faster than the fastest known memory reclamation algorithm, and 1.2-1.5x faster than not reclaiming at all, on a 192 thread four socket Intel system.
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding
Venue: arXiv cs.LG 2024
Year: 2024

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.
Revolutionizing API Documentation through Summarization
Venue: arXiv cs.SE 2024
Year: 2024

This study tackles the challenges associated with interpreting Application Programming Interface (API) documentation, an integral aspect of software development. Official API documentation, while essential, can be lengthy and challenging to navigate, prompting developers to seek unofficial sources such as Stack Overflow. Leveraging the vast user-generated content on Stack Overflow, including code snippets and discussions, we employ BERTopic and extractive summarization to automatically generate concise and informative API summaries. These summaries encompass key insights like general usage, common developer issues, and potential solutions, sourced from the wealth of knowledge on Stack Overflow. Software developers evaluate these summaries for performance, coherence, and interoperability, providing valuable feedback on the practicality of our approach.
Multi-Agent Generative Adversarial Interactive Self-Imitation Learning for AUV Formation Control and Obstacle Avoidance
Venue: arXiv cs.RO 2024
Year: 2024

Multiple autonomous underwater vehicles (multi-AUV) can cooperatively accomplish tasks that a single AUV cannot complete. Recently, multi-agent reinforcement learning has been introduced to control of multi-AUV. However, designing efficient reward functions for various tasks of multi-AUV control is difficult or even impractical. Multi-agent generative adversarial imitation learning (MAGAIL) allows multi-AUV to learn from expert demonstration instead of pre-defined reward functions, but suffers from the deficiency of requiring optimal demonstrations and not surpassing provided expert demonstrations. This paper builds upon the MAGAIL algorithm by proposing multi-agent generative adversarial interactive self-imitation learning (MAGAISIL), which can facilitate AUVs to learn policies by gradually replacing the provided sub-optimal demonstrations with self-generated good trajectories selected by a human trainer. Our experimental results in a multi-AUV formation control and obstacle avoidance task on the Gazebo platform with AUV simulator of our lab show that AUVs trained via MAGAISIL can surpass the provided sub-optimal expert demonstrations and reach a performance close to or even better than MAGAIL with optimal demonstrations. Further results indicate that AUVs' policies trained via MAGAISIL can adapt to complex and different tasks as well as MAGAIL learning from optimal demonstrations.
MedLM: Exploring Language Models for Medical Question Answering Systems
Venue: arXiv cs.CL 2024
Year: 2024

In the face of rapidly expanding online medical literature, automated systems for aggregating and summarizing information are becoming increasingly crucial for healthcare professionals and patients. Large Language Models (LLMs), with their advanced generative capabilities, have shown promise in various NLP tasks, and their potential in the healthcare domain, particularly for Closed-Book Generative QnA, is significant. However, the performance of these models in domain-specific tasks such as medical Q&A remains largely unexplored. This study aims to fill this gap by comparing the performance of general and medical-specific distilled LMs for medical Q&A. We aim to evaluate the effectiveness of fine-tuning domain-specific LMs and compare the performance of different families of Language Models. The study will address critical questions about these models' reliability, comparative performance, and effectiveness in the context of medical Q&A. The findings will provide valuable insights into the suitability of different LMs for specific applications in the medical domain.
Agricultural Recommendation System based on Deep Learning: A Multivariate Weather Forecasting Approach
Venue: arXiv cs.LG 2024
Year: 2024

Agriculture plays a fundamental role in driving economic growth and ensuring food security for populations around the world. Although labor-intensive agriculture has led to steady increases in food grain production in many developing countries, it is frequently challenged by adverse weather conditions, including heavy rainfall, low temperatures, and drought. These factors substantially hinder food production, posing significant risks to global food security. In order to have a profitable, sustainable, and farmer-friendly agricultural practice, this paper proposes a context-based crop recommendation system powered by a weather forecast model. For implementation purposes, we have considered the whole territory of Bangladesh. With extensive evaluation, the multivariate Stacked Bi-LSTM (three Bi-LSTM layers with a time Distributed layer) Network is employed as the weather forecasting model. The proposed weather model can forecast Rainfall, Temperature, Humidity, and Sunshine for any given location in Bangladesh with an average R-Squared value of 0.9824, and the model outperforms other state-of-the-art LSTM models. These predictions guide our system in generating viable farming decisions. Additionally, our full-fledged system is capable of alerting the farmers about extreme weather conditions so that preventive measures can be undertaken to protect the crops. Finally, the system is also adept at making knowledge-based crop suggestions for flood and drought-prone regions.
Joint Downlink and Uplink Optimization for RIS-Aided FDD MIMO Communication Systems
Venue: arXiv cs.IT 2024
Year: 2024

This paper investigates reconfigurable intelligent surface (RIS)-aided frequency division duplexing (FDD) communication systems. Since the downlink and uplink signals are simultaneously transmitted in FDD, the phase shifts at the RIS should be designed to support both transmissions. Considering a single-user multiple-input multiple-output system, we formulate a weighted sum-rate maximization problem to jointly maximize the downlink and uplink system performance. To tackle the non-convex optimization problem, we adopt an alternating optimization (AO) algorithm, in which two phase shift optimization techniques are developed to handle the unit-modulus constraints induced by the reflection coefficients at the RIS. The first technique exploits the manifold optimization-based algorithm, while the second uses a lower-complexity AO approach. Numerical results verify that the proposed techniques rapidly converge to local optima and significantly improve the overall system performance compared to existing benchmark schemes.
Bimanual Deformable Bag Manipulation Using a Structure-of-Interest Based Neural Dynamics Model
Venue: arXiv cs.RO 2024
Year: 2024

The manipulation of deformable objects by robotic systems presents a significant challenge due to their complex and infinite-dimensional configuration spaces. This paper introduces a novel approach to Deformable Object Manipulation (DOM) by emphasizing the identification and manipulation of Structures of Interest (SOIs) in deformable fabric bags. We propose a bimanual manipulation framework that leverages a Graph Neural Network (GNN)-based latent dynamics model to succinctly represent and predict the behavior of these SOIs. Our approach involves constructing a graph representation from partial point cloud data of the object and learning the latent dynamics model that effectively captures the essential deformations of the fabric bag within a reduced computational space. By integrating this latent dynamics model with Model Predictive Control (MPC), we empower robotic manipulators to perform precise and stable manipulation tasks focused on the SOIs. We have validated our framework through various empirical experiments demonstrating its efficacy in bimanual manipulation of fabric bags. Our contributions not only address the complexities inherent in DOM but also provide new perspectives and methodologies for enhancing robotic interactions with deformable objects by concentrating on their critical structural elements. Experimental videos can be obtained from https://sites.google.com/view/bagbot.
Frost Prediction Using Machine Learning Methods in Fars Province
Venue: arXiv cs.LG 2024
Year: 2024

One of the common hazards and issues in meteorology and agriculture is the problem of frost, chilling or freezing. This event occurs when the minimum ambient temperature falls below a certain value. This phenomenon causes a lot of damage to the country, especially Fars province. Solving this problem requires that, in addition to predicting the minimum temperature, we can provide enough time to implement the necessary measures. Empirical methods have been provided by the Food and Agriculture Organization (FAO), which can predict the minimum temperature, but not in time. In addition to this, we can use machine learning methods to model the minimum temperature. In this study, we have used three methods Gated Recurrent Unit (GRU), Temporal Convolutional Network (TCN) as deep learning methods, and Gradient Boosting (XGBoost). A customized loss function designed for methods based on deep learning, which can be effective in reducing prediction errors. With methods based on deep learning models, not only do we observe a reduction in RMSE error compared to empirical methods but also have more time to predict minimum temperature. Thus, we can model the minimum temperature for the next 24 hours by having the current 24 hours. With the gradient boosting model (XGBoost) we can keep the prediction time as deep learning and RMSE error reduced. Finally, we experimentally concluded that machine learning methods work better than empirical methods and XGBoost model can have better performance in this problem among other implemented.
CheX-GPT: Harnessing Large Language Models for Enhanced Chest X-ray Report Labeling
Venue: arXiv cs.CL 2024
Year: 2024

Free-text radiology reports present a rich data source for various medical tasks, but effectively labeling these texts remains challenging. Traditional rule-based labeling methods fall short of capturing the nuances of diverse free-text patterns. Moreover, models using expert-annotated data are limited by data scarcity and pre-defined classes, impacting their performance, flexibility and scalability. To address these issues, our study offers three main contributions: 1) We demonstrate the potential of GPT as an adept labeler using carefully designed prompts. 2) Utilizing only the data labeled by GPT, we trained a BERT-based labeler, CheX-GPT, which operates faster and more efficiently than its GPT counterpart. 3) To benchmark labeler performance, we introduced a publicly available expert-annotated test set, MIMIC-500, comprising 500 cases from the MIMIC validation set. Our findings demonstrate that CheX-GPT not only excels in labeling accuracy over existing models, but also showcases superior efficiency, flexibility, and scalability, supported by our introduction of the MIMIC-500 dataset for robust benchmarking. Code and models are available at https://github.com/Soombit-ai/CheXGPT.
Is it a Real CD Mismatch in Interdomain Routing?
Venue: arXiv cs.NI 2024
Year: 2024

In inter-domain routing, a packet is not always forwarded along the Autonomous System (AS) level path determined by the BGP routing protocol. This is often called control-plane and data-plane (CD) mismatch, which allows for flexible traffic control, but also leads to operation and security issues. We systematically analyze this phenomenon with path pairs collected from 128 pairs of vantage points over more than 5 years, and use multiple IP-to-AS mapping methods to compare CD paths. What is interesting is that, working at such a large scale in turn helps us design a novel method to fairly evaluate the accuracy of various existing mapping methods, and further develop a new mapping method, i.e., LearnToCorrect, that can correct more than 70\% mapping errors of the state-of-the-art one. Then we devise to identify real mismatches with LearnToCorrect, and estimate that the real-mismatch ratio in the wild is typically less than 6\%. At last, we use our proposed methods to detect routing security issues, which are previously difficult to accurately find out.
Computational predictions of weld structural integrity in hydrogen transport pipelines
Venue: arXiv cs.CE 2024
Year: 2024

We combine welding process modelling with deformation-diffusion-fracture (embrittlement) simulations to predict failures in hydrogen transport pipelines. The focus is on the structural integrity of seam welds, as these are often the locations most susceptible to damage in gas transport infrastructure. Finite element analyses are conducted to showcase the ability of the model to predict cracking in pipeline steels exposed to hydrogen-containing environments. The validated model is then employed to quantify critical H$_2$ fracture pressures. The coupled, phase field-based simulations conducted provide insight into the role of existing defects, microstructural heterogeneity, and residual stresses. We find that under a combination of deleterious yet realistic conditions, the critical pressure at which fracture takes place can be as low as 15 MPa. These results bring new mechanistic insight into the viability of using the existing natural gas pipeline network to transport hydrogen, and the computational framework presented enables mapping the conditions under which this can be achieved safely.
Tempo: Confidentiality Preservation in Cloud-Based Neural Network Training
Venue: arXiv cs.CR 2024
Year: 2024

Cloud deep learning platforms provide cost-effective deep neural network (DNN) training for customers who lack computation resources. However, cloud systems are often untrustworthy and vulnerable to attackers, leading to growing concerns about model privacy. Recently, researchers have sought to protect data privacy in deep learning by leveraging CPU trusted execution environments (TEEs), which minimize the use of cryptography, but existing works failed to simultaneously utilize the computational resources of GPUs to assist in training and prevent model leakage. This paper presents Tempo, the first cloud-based deep learning system that cooperates with TEE and distributed GPUs for efficient DNN training with model confidentiality preserved. To tackle the challenge of preserving privacy while offloading linear algebraic operations from TEE to GPUs for efficient batch computation, we introduce a customized permutation-based obfuscation algorithm to blind both inputs and model parameters. An optimization mechanism that reduces encryption operations is proposed for faster weight updates during backpropagation to speed up training. We implement Tempo and evaluate it with both training and inference for two prevalent DNNs. Empirical results indicate that Tempo outperforms baselines and offers sufficient privacy protection.
Multi-View Neural 3D Reconstruction of Micro-/Nanostructures with Atomic Force Microscopy
Venue: arXiv cs.CV 2024
Year: 2024

Atomic Force Microscopy (AFM) is a widely employed tool for micro-/nanoscale topographic imaging. However, conventional AFM scanning struggles to reconstruct complex 3D micro-/nanostructures precisely due to limitations such as incomplete sample topography capturing and tip-sample convolution artifacts. Here, we propose a multi-view neural-network-based framework with AFM (MVN-AFM), which accurately reconstructs surface models of intricate micro-/nanostructures. Unlike previous works, MVN-AFM does not depend on any specially shaped probes or costly modifications to the AFM system. To achieve this, MVN-AFM uniquely employs an iterative method to align multi-view data and eliminate AFM artifacts simultaneously. Furthermore, we pioneer the application of neural implicit surface reconstruction in nanotechnology and achieve markedly improved results. Extensive experiments show that MVN-AFM effectively eliminates artifacts present in raw AFM images and reconstructs various micro-/nanostructures including complex geometrical microstructures printed via Two-photon Lithography and nanoparticles such as PMMA nanospheres and ZIF-67 nanocrystals. This work presents a cost-effective tool for micro-/nanoscale 3D analysis.
Nigel -- Mechatronic Design and Robust Sim2Real Control of an Over-Actuated Autonomous Vehicle
Venue: arXiv cs.RO 2024
Year: 2024

Simulation to reality (sim2real) transfer from a dynamics and controls perspective usually involves re-tuning or adapting the designed algorithms to suit real-world operating conditions, which often violates the performance guarantees established originally. This work presents a generalizable framework for achieving reliable sim2real transfer of autonomy-oriented control systems using multi-model multi-objective robust optimal control synthesis, which lends well to uncertainty handling and disturbance rejection with theoretical guarantees. Particularly, this work is centered around a novel actuation-redundant scaled autonomous vehicle called Nigel, with independent all-wheel drive and independent all-wheel steering architecture, whose enhanced configuration space bodes well for robust control applications. To this end, we present the mechatronic design, dynamics modeling, parameter identification, and robust stabilizing as well as tracking control of Nigel using the proposed framework, with exhaustive experimentation and benchmarking in simulation as well as real-world settings.
Thermal Image Calibration and Correction using Unpaired Cycle-Consistent Adversarial Networks
Venue: arXiv cs.CV 2024
Year: 2024

Unmanned aerial vehicles (UAVs) offer a flexible and cost-effective solution for wildfire monitoring. However, their widespread deployment during wildfires has been hindered by a lack of operational guidelines and concerns about potential interference with aircraft systems. Consequently, the progress in developing deep-learning models for wildfire detection and characterization using aerial images is constrained by the limited availability, size, and quality of existing datasets. This paper introduces a solution aimed at enhancing the quality of current aerial wildfire datasets to align with advancements in camera technology. The proposed approach offers a solution to create a comprehensive, standardized large-scale image dataset. This paper presents a pipeline based on CycleGAN to enhance wildfire datasets and a novel fusion method that integrates paired RGB images as attribute conditioning in the generators of both directions, improving the accuracy of the generated images.
Small Even Covers, Locally Decodable Codes and Restricted Subgraphs of Edge-Colored Kikuchi Graphs
Venue: arXiv cs.CC 2024
Year: 2024

Given a $k$-uniform hypergraph $H$ on $n$ vertices, an even cover in $H$ is a collection of hyperedges that touch each vertex an even number of times. Even covers are a generalization of cycles in graphs and are equivalent to linearly dependent subsets of a system of linear equations modulo $2$. As a result, they arise naturally in the context of well-studied questions in coding theory and refuting unsatisfiable $k$-SAT formulas. Analogous to the irregular Moore bound of Alon, Hoory, and Linial (2002), in 2008, Feige conjectured an extremal trade-off between the number of hyperedges and the length of the smallest even cover in a $k$-uniform hypergraph. This conjecture was recently settled up to a multiplicative logarithmic factor in the number of hyperedges (Guruswami, Kothari, and Manohar 2022 and Hsieh, Kothari, and Mohanty 2023). These works introduce the new technique that relates hypergraph even covers to cycles in the associated Kikuchi graphs. Their analysis of these Kikuchi graphs, especially for odd $k$, is rather involved and relies on matrix concentration inequalities. In this work, we give a simple and purely combinatorial argument that recovers the best-known bound for Feige's conjecture for even $k$. We also introduce a novel variant of a Kikuchi graph which together with this argument improves the logarithmic factor in the best-known bounds for odd $k$. As an application of our ideas, we also give a purely combinatorial proof of the improved lower bounds (Alrabiah, Guruswami, Kothari and Manohar, 2023) on 3-query binary linear locally decodable codes.