pwc-archive/papers-with-abstracts huggingface dataset:
Multi-Modality Conditioned Variational U-Net for Field-of-View Extension in Brain Diffusion MRI
Authors: Zhiyuan Li, Tianyuan Yao, Praitayini Kanakaraj, Chenyu Gao, Shunxing Bao, Lianrui Zuo, Michael E. Kim, Nancy R. Newlin, Gaurav Rudravaram, Nazirah M. Khairi, Yuankai Huo, Kurt G. Schilling, Walter A. Kukull, Arthur W. Toga, Derek B. Archer, Timothy J. Hohman, Bennett A. Landman
Date: 2024-09-20 00:00:00
Tasks: Diffusion  MRI, Imputation

An incomplete field-of-view (FOV) in diffusion magnetic resonance imaging (dMRI) can severely hinder the volumetric and bundle analyses of whole-brain white matter connectivity. Although existing works have investigated imputing the missing regions using deep generative models, it remains unclear how to specifically utilize additional information from paired multi-modality data and whether this can enhance the imputation quality and be useful for downstream tractography. To fill this gap, we propose a novel framework for imputing dMRI scans in the incomplete part of the FOV by integrating the learned diffusion features in the acquired part of the FOV to the complete brain anatomical structure. We hypothesize that by this design the proposed framework can enhance the imputation performance of the dMRI scans and therefore be useful for repairing whole-brain tractography in corrupted dMRI scans with incomplete FOV. We tested our framework on two cohorts from different sites with a total of 96 subjects and compared it with a baseline imputation method that treats the information from T1w and dMRI scans equally. The proposed framework achieved significant improvements in imputation performance, as demonstrated by angular correlation coefficient (p < 1E-5), and in downstream tractography accuracy, as demonstrated by Dice score (p < 0.01). Results suggest that the proposed framework improved imputation performance in dMRI scans by specifically utilizing additional information from paired multi-modality data, compared with the baseline method. The imputation achieved by the proposed framework enhances whole brain tractography, and therefore reduces the uncertainty when analyzing bundles associated with neurodegenerative.
Learning Ordering in Crystalline Materials with Symmetry-Aware Graph Neural Networks
Authors: Jiayu Peng, James Damewood, Jessica Karaguesian, Jaclyn R. Lunger, Rafael Gómez-Bombarelli
Date: 2024-09-20 00:00:00

Graph convolutional neural networks (GCNNs) have become a machine learning workhorse for screening the chemical space of crystalline materials in fields such as catalysis and energy storage, by predicting properties from structures. Multicomponent materials, however, present a unique challenge since they can exhibit chemical (dis)order, where a given lattice structure can encompass a variety of elemental arrangements ranging from highly ordered structures to fully disordered solid solutions. Critically, properties like stability, strength, and catalytic performance depend not only on structures but also on orderings. To enable rigorous materials design, it is thus critical to ensure GCNNs are capable of distinguishing among atomic orderings. However, the ordering-aware capability of GCNNs has been poorly understood. Here, we benchmark various neural network architectures for capturing the ordering-dependent energetics of multicomponent materials in a custom-made dataset generated with high-throughput atomistic simulations. Conventional symmetry-invariant GCNNs were found unable to discern the structural difference between the diverse symmetrically inequivalent atomic orderings of the same material, while symmetry-equivariant model architectures could inherently preserve and differentiate the distinct crystallographic symmetries of various orderings.
Learning to Simulate Aerosol Dynamics with Graph Neural Networks
Authors: Fabiana Ferracina, Payton Beeler, Mahantesh Halappanavar, Bala Krishnamoorthy, Marco Minutoli, Laura Fierce
Date: 2024-09-20 00:00:00
Tasks: Graph Neural Network

Aerosol effects on climate, weather, and air quality depend on characteristics of individual particles, which are tremendously diverse and change in time. Particle-resolved models are the only models able to capture this diversity in particle physiochemical properties, and these models are computationally expensive. As a strategy for accelerating particle-resolved microphysics models, we introduce Graph-based Learning of Aerosol Dynamics (GLAD) and use this model to train a surrogate of the particle-resolved model PartMC-MOSAIC. GLAD implements a Graph Network-based Simulator (GNS), a machine learning framework that has been used to simulate particle-based fluid dynamics models. In GLAD, each particle is represented as a node in a graph, and the evolution of the particle population over time is simulated through learned message passing. We demonstrate our GNS approach on a simple aerosol system that includes condensation of sulfuric acid onto particles composed of sulfate, black carbon, organic carbon, and water. A graph with particles as nodes is constructed, and a graph neural network (GNN) is then trained using the model output from PartMC-MOSAIC. The trained GNN can then be used for simulating and predicting aerosol dynamics over time. Results demonstrate the framework's ability to accurately learn chemical dynamics and generalize across different scenarios, achieving efficient training and prediction times. We evaluate the performance across three scenarios, highlighting the framework's robustness and adaptability in modeling aerosol microphysics and chemistry.
Deep Learning-Based Channel Squeeze U-Structure for Lung Nodule Detection and Segmentation
Authors: Mingxiu Sui, Jiacheng Hu, Tong Zhou, Zibo Liu, Likang Wen, Junliang Du
Date: 2024-09-20 00:00:00
Tasks: Lung Cancer Diagnosis, Lung Nodule Detection

This paper introduces a novel deep-learning method for the automatic detection and segmentation of lung nodules, aimed at advancing the accuracy of early-stage lung cancer diagnosis. The proposed approach leverages a unique "Channel Squeeze U-Structure" that optimizes feature extraction and information integration across multiple semantic levels of the network. This architecture includes three key modules: shallow information processing, channel residual structure, and channel squeeze integration. These modules enhance the model's ability to detect and segment small, imperceptible, or ground-glass nodules, which are critical for early diagnosis. The method demonstrates superior performance in terms of sensitivity, Dice similarity coefficient, precision, and mean Intersection over Union (IoU). Extensive experiments were conducted on the Lung Image Database Consortium (LIDC) dataset using five-fold cross-validation, showing excellent stability and robustness. The results indicate that this approach holds significant potential for improving computer-aided diagnosis systems, providing reliable support for radiologists in clinical practice and aiding in the early detection of lung cancer, especially in resource-limited settings
Cross-Domain Knowledge Transfer for Underwater Acoustic Classification Using Pre-trained Models
Authors: Amirmohammad Mohammadi, Tejashri Kelhe, Davelle Carreiro, Alexandra Van Dine, Joshua Peeples
Date: 2024-09-20 00:00:00
Tasks: Transfer Learning, Underwater Acoustic Classification

Transfer learning is commonly employed to leverage large, pre-trained models and perform fine-tuning for downstream tasks. The most prevalent pre-trained models are initially trained using ImageNet. However, their ability to generalize can vary across different data modalities. This study compares pre-trained Audio Neural Networks (PANNs) and ImageNet pre-trained models within the context of underwater acoustic target recognition (UATR). It was observed that the ImageNet pre-trained models slightly out-perform pre-trained audio models in passive sonar classification. We also analyzed the impact of audio sampling rates for model pre-training and fine-tuning. This study contributes to transfer learning applications of UATR, illustrating the potential of pre-trained models to address limitations caused by scarce, labeled data in the UATR domain.
Investigation of Time-Frequency Feature Combinations with Histogram Layer Time Delay Neural Networks
Authors: Amirmohammad Mohammadi, Iren'e Masabarakiza, Ethan Barnes, Davelle Carreiro, Alexandra Van Dine, Joshua Peeples
Date: 2024-09-20 00:00:00
Tasks: Feature Engineering

While deep learning has reduced the prevalence of manual feature extraction, transformation of data via feature engineering remains essential for improving model performance, particularly for underwater acoustic signals. The methods by which audio signals are converted into time-frequency representations and the subsequent handling of these spectrograms can significantly impact performance. This work demonstrates the performance impact of using different combinations of time-frequency features in a histogram layer time delay neural network. An optimal set of features is identified with results indicating that specific feature combinations outperform single data features.
PTQ4ADM: Post-Training Quantization for Efficient Text Conditional Audio Diffusion Models
Authors: Jayneel Vora, Aditya Krishnan, Nader Bouacida, Prabhu RV Shankar, Prasant Mohapatra
Date: 2024-09-20 00:00:00
Tasks: Audio Generation, Audio Synthesis, Denoising, Quantization

Denoising diffusion models have emerged as state-of-the-art in generative tasks across image, audio, and video domains, producing high-quality, diverse, and contextually relevant data. However, their broader adoption is limited by high computational costs and large memory footprints. Post-training quantization (PTQ) offers a promising approach to mitigate these challenges by reducing model complexity through low-bandwidth parameters. Yet, direct application of PTQ to diffusion models can degrade synthesis quality due to accumulated quantization noise across multiple denoising steps, particularly in conditional tasks like text-to-audio synthesis. This work introduces PTQ4ADM, a novel framework for quantizing audio diffusion models(ADMs). Our key contributions include (1) a coverage-driven prompt augmentation method and (2) an activation-aware calibration set generation algorithm for text-conditional ADMs. These techniques ensure comprehensive coverage of audio aspects and modalities while preserving synthesis fidelity. We validate our approach on TANGO, Make-An-Audio, and AudioLDM models for text-conditional audio generation. Extensive experiments demonstrate PTQ4ADM's capability to reduce the model size by up to 70\% while achieving synthesis quality metrics comparable to full-precision models($<$5\% increase in FD scores). We show that specific layers in the backbone network can be quantized to 4-bit weights and 8-bit activations without significant quality loss. This work paves the way for more efficient deployment of ADMs in resource-constrained environments.
High-dimensional learning of narrow neural networks
Authors: Hugo Cui
Date: 2024-09-20 00:00:00
Tasks: Contrastive Learning, Denoising

Recent years have been marked with the fast-pace diversification and increasing ubiquity of machine learning applications. Yet, a firm theoretical understanding of the surprising efficiency of neural networks to learn from high-dimensional data still proves largely elusive. In this endeavour, analyses inspired by statistical physics have proven instrumental, enabling the tight asymptotic characterization of the learning of neural networks in high dimensions, for a broad class of solvable models. This manuscript reviews the tools and ideas underlying recent progress in this line of work. We introduce a generic model -- the sequence multi-index model -- which encompasses numerous previously studied models as special instances. This unified framework covers a broad class of machine learning architectures with a finite number of hidden units, including multi-layer perceptrons, autoencoders, attention mechanisms; and tasks, including (un)supervised learning, denoising, contrastive learning, in the limit of large data dimension, and comparably large number of samples. We explicate in full detail the analysis of the learning of sequence multi-index models, using statistical physics techniques such as the replica method and approximate message-passing algorithms. This manuscript thus provides a unified presentation of analyses reported in several previous works, and a detailed overview of central techniques in the field of statistical physics of machine learning. This review should be a useful primer for machine learning theoreticians curious of statistical physics approaches; it should also be of value to statistical physicists interested in the transfer of such ideas to the study of neural networks.
Deep learning for fast segmentation and critical dimension metrology & characterization enabling AR/VR design and fabrication
Authors: Kundan Chaudhary, Subhei Shaar, Raja Muthinti
Date: 2024-09-20 00:00:00
Tasks: Zero-Shot Learning

Quantitative analysis of microscopy images is essential in the design and fabrication of components used in augmented reality/virtual reality (AR/VR) modules. However, segmenting regions of interest (ROIs) from these complex images and extracting critical dimensions (CDs) requires novel techniques, such as deep learning models which are key for actionable decisions on process, material and device optimization. In this study, we report on the fine-tuning of a pre-trained Segment Anything Model (SAM) using a diverse dataset of electron microscopy images. We employed methods such as low-rank adaptation (LoRA) to reduce training time and enhance the accuracy of ROI extraction. The model's ability to generalize to unseen images facilitates zero-shot learning and supports a CD extraction model that precisely extracts CDs from the segmented ROIs. We demonstrate the accurate extraction of binary images from cross-sectional images of surface relief gratings (SRGs) and Fresnel lenses in both single and multiclass modes. Furthermore, these binary images are used to identify transition points, aiding in the extraction of relevant CDs. The combined use of the fine-tuned segmentation model and the CD extraction model offers substantial advantages to various industrial applications by enhancing analytical capabilities, time to data and insights, and optimizing manufacturing processes.
Training Large ASR Encoders with Differential Privacy
Authors: Geeticka Chauhan, Steve Chien, Om Thakkar, Abhradeep Thakurta, Arun Narayanan
Date: 2024-09-21 00:00:00
Tasks: Memorization, Self-Supervised Learning

Self-supervised learning (SSL) methods for large speech models have proven to be highly effective at ASR. With the interest in public deployment of large pre-trained models, there is a rising concern for unintended memorization and leakage of sensitive data points from the training data. In this paper, we apply differentially private (DP) pre-training to a SOTA Conformer-based encoder, and study its performance on a downstream ASR task assuming the fine-tuning data is public. This paper is the first to apply DP to SSL for ASR, investigating the DP noise tolerance of the BEST-RQ pre-training method. Notably, we introduce a novel variant of model pruning called gradient-based layer freezing that provides strong improvements in privacy-utility-compute trade-offs. Our approach yields a LibriSpeech test-clean/other WER (%) of 3.78/ 8.41 with ($10$, 1e^-9)-DP for extrapolation towards low dataset scales, and 2.81/ 5.89 with (10, 7.9e^-11)-DP for extrapolation towards high scales.
AMT-APC: Automatic Piano Cover by Fine-Tuning an Automatic Music Transcription Model
Authors: Kazuma Komiya, Yoshihisa Fukuhara
Date: 2024-09-21 00:00:00
Tasks: Music Transcription

There have been several studies on automatically generating piano covers, and recent advancements in deep learning have enabled the creation of more sophisticated covers. However, existing automatic piano cover models still have room for improvement in terms of expressiveness and fidelity to the original. To address these issues, we propose a learning algorithm called AMT-APC, which leverages the capabilities of automatic music transcription models. By utilizing the strengths of well-established automatic music transcription models, we aim to improve the accuracy of piano cover generation. Our experiments demonstrate that the AMT-APC model reproduces original tracks more accurately than any existing models.
BRep Boundary and Junction Detection for CAD Reverse Engineering
Authors: Sk Aziz Ali, Mohammad Sadil Khan, Didier Stricker
Date: 2024-09-21 00:00:00
Tasks: Junction Detection

In machining process, 3D reverse engineering of the mechanical system is an integral, highly important, and yet time consuming step to obtain parametric CAD models from 3D scans. Therefore, deep learning-based Scan-to-CAD modeling can offer designers enormous editability to quickly modify CAD model, being able to parse all its structural compositions and design steps. In this paper, we propose a supervised boundary representation (BRep) detection network BRepDetNet from 3D scans of CC3D and ABC dataset. We have carefully annotated the 50K and 45K scans of both the datasets with appropriate topological relations (e.g., next, mate, previous) between the geometrical primitives (i.e., boundaries, junctions, loops, faces) of their BRep data structures. The proposed solution decomposes the Scan-to-CAD problem in Scan-to-BRep ensuring the right step towards feature-based modeling, and therefore, leveraging other existing BRep-to-CAD modeling methods. Our proposed Scan-to-BRep neural network learns to detect BRep boundaries and junctions by minimizing focal-loss and non-maximal suppression (NMS) during training time. Experimental results show that our BRepDetNet with NMS-Loss achieves impressive results.
Quantum enhanced stratification of Breast Cancer: exploring quantum expressivity for real omics data
Authors: Valeria Repetto, Elia Giuseppe Ceroni, Giuseppe Buonaiuto, Romina D'Aurizio
Date: 2024-09-21 00:00:00
Tasks: Quantum Machine Learning

Quantum Machine Learning (QML) is considered one of the most promising applications of Quantum Computing in the Noisy Intermediate Scale Quantum (NISQ) era for the impact it is thought to have in the near future. Although promising theoretical assumptions, the exploration of how QML could foster new discoveries in Medicine and Biology fields is still in its infancy with few examples. In this study, we aimed to assess whether Quantum Kernels (QK) could effectively classify subtypes of Breast Cancer (BC) patients on the basis of molecular characteristics. We performed an heuristic exploration of encoding configurations with different entanglement levels to determine a trade-off between kernel expressivity and performances. Our results show that QKs yield comparable clustering results with classical methods while using fewer data points, and are able to fit the data with a higher number of clusters. Additionally, we conducted the experiments on the Quantum Processing Unit (QPU) to evaluate the effect of noise on the outcome. We found that less expressive encodings showed a higher resilience to noise, indicating that the computational pipeline can be reliably implemented on the NISQ devices. Our findings suggest that QK methods show promises for application in Precision Oncology, especially in scenarios where the dataset is limited in size and a granular non-trivial stratification of complex molecular data cannot be achieved classically.
CONGRA: Benchmarking Automatic Conflict Resolution
Authors: Qingyu Zhang, Liangcai Su, Kai Ye, Chenxiong Qian
Date: 2024-09-21 00:00:00
Tasks: Benchmarking

Resolving conflicts from merging different software versions is a challenging task. To reduce the overhead of manual merging, researchers develop various program analysis-based tools which only solve specific types of conflicts and have a limited scope of application. With the development of language models, researchers treat conflict code as text, which theoretically allows for addressing almost all types of conflicts. However, the absence of effective conflict difficulty grading methods hinders a comprehensive evaluation of large language models (LLMs), making it difficult to gain a deeper understanding of their limitations. Furthermore, there is a notable lack of large-scale open benchmarks for evaluating the performance of LLMs in automatic conflict resolution. To address these issues, we introduce ConGra, a CONflict-GRAded benchmarking scheme designed to evaluate the performance of software merging tools under varying complexity conflict scenarios. We propose a novel approach to classify conflicts based on code operations and use it to build a large-scale evaluation dataset based on 44,948 conflicts from 34 real-world projects. We evaluate state-of-the-art LLMs on conflict resolution tasks using this dataset. By employing the dataset, we assess the performance of multiple state-of-the-art LLMs and code LLMs, ultimately uncovering two counterintuitive yet insightful phenomena. ConGra will be released at https://github.com/HKU-System-Security-Lab/ConGra.
Efficient and Effective Model Extraction
Authors: Hongyu Zhu, Wentao Hu, Sichu Liang, Fangqi Li, Wenwen Wang, Shilin Wang
Date: 2024-09-21 00:00:00
Tasks: Benchmarking, model, Model extraction

Model extraction aims to create a functionally similar copy from a machine learning as a service (MLaaS) API with minimal overhead, typically for illicit profit or as a precursor to further attacks, posing a significant threat to the MLaaS ecosystem. However, recent studies have shown that model extraction is highly inefficient, particularly when the target task distribution is unavailable. In such cases, even substantially increasing the attack budget fails to produce a sufficiently similar replica, reducing the adversary's motivation to pursue extraction attacks. In this paper, we revisit the elementary design choices throughout the extraction lifecycle. We propose an embarrassingly simple yet dramatically effective algorithm, Efficient and Effective Model Extraction (E3), focusing on both query preparation and training routine. E3 achieves superior generalization compared to state-of-the-art methods while minimizing computational costs. For instance, with only 0.005 times the query budget and less than 0.2 times the runtime, E3 outperforms classical generative model based data-free model extraction by an absolute accuracy improvement of over 50% on CIFAR-10. Our findings underscore the persistent threat posed by model extraction and suggest that it could serve as a valuable benchmarking algorithm for future security evaluations.
A General Framework of the Consistency for Large Neural Networks
Authors: Haoran Zhan, Yingcun Xia
Date: 2024-09-21 00:00:00

Neural networks have shown remarkable success, especially in overparameterized or "large" models. Despite increasing empirical evidence and intuitive understanding, a formal mathematical justification for the behavior of such models, particularly regarding overfitting, remains incomplete. In this paper, we propose a general regularization framework to study the Mean Integrated Squared Error (MISE) of neural networks. This framework includes many commonly used neural networks and penalties, such as ReLu and Sigmoid activations and $L^1$, $L^2$ penalties. Based on our frameworks, we find the MISE curve has two possible shapes, namely the shape of double descents and monotone decreasing. The latter phenomenon is new in literature and the causes of these two phenomena are also studied in theory. These studies challenge conventional statistical modeling frameworks and broadens recent findings on the double descent phenomenon in neural networks.