pwc-archive/papers-with-abstracts huggingface dataset:
T-cell receptor specificity landscape revealed through de novo peptide design
Authors: Gian Marco Visani, Michael N. Pun, Anastasia A. Minervina, Philip Bradley, Paul Thomas, Armita Nourmohammad
Date: 2025-03-01 00:00:00
Tasks: Specificity

T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs) mediate an immune response. However, predicting these interactions remains challenging due to limited functional data on T-cell reactivities. Here, we introduce a computational approach to predict TCR interactions with peptides presented on MHC class I alleles, and to design novel immunogenic peptides for specified TCR-MHC complexes. Our method leverages HERMES, a structure-based, physics-guided machine learning model trained on the protein universe to predict amino acid preferences based on local structural environments. Despite no direct training on TCR-pMHC data, the implicit physical reasoning in HERMES enables us to make accurate predictions of both TCR-pMHC binding affinities and T-cell activities across diverse viral epitopes and cancer neoantigens, achieving up to 72% correlation with experimental data. Leveraging our TCR recognition model, we develop a computational protocol for de novo design of immunogenic peptides. Through experimental validation in three TCR-MHC systems targeting viral and cancer peptides, we demonstrate that our designs--with up to five substitutions from the native sequence--activate T-cells at success rates of up to 50%. Lastly, we use our generative framework to quantify the diversity of the peptide recognition landscape for various TCR-MHC complexes, offering key insights into T-cell specificity in both humans and mice. Our approach provides a platform for immunogenic peptide and neoantigen design, opening new computational paths for T-cell vaccine development against viruses and cancer.
Towards Refining Developer Questions using LLM-Based Named Entity Recognition for Developer Chatroom Conversations
Authors: Pouya Fathollahzadeh, Mariam El Mezouar, Hao Li, Ying Zou, Ahmed E. Hassan
Date: 2025-03-02 00:00:00
Tasks: Diagnostic, Intent Detection, Large Language Model, named-entity-recognition, Named Entity Recognition

In software engineering chatrooms, communication is often hindered by imprecise questions that cannot be answered. Recognizing key entities can be essential for improving question clarity and facilitating better exchange. However, existing research using natural language processing techniques often overlooks these software-specific nuances. In this paper, we introduce Software-specific Named Entity Recognition, Intent Detection, and Resolution Classification (SENIR), a labeling approach that leverages a Large Language Model to annotate entities, intents, and resolution status in developer chatroom conversations. To offer quantitative guidance for improving question clarity and resolvability, we build a resolution prediction model that leverages SENIR's entity and intent labels along with additional predictive features. We evaluate SENIR on the DISCO dataset using a subset of annotated chatroom dialogues. SENIR achieves an 86% F-score for entity recognition, a 71% F-score for intent detection, and an 89% F-score for resolution status classification. Furthermore, our resolution prediction model, tested with various sampling strategies (random undersampling and oversampling with SMOTE) and evaluation methods (5-fold cross-validation, 10-fold cross-validation, and bootstrapping), demonstrates AUC values ranging from 0.7 to 0.8. Key factors influencing resolution include positive sentiment and entities such as Programming Language and User Variable across multiple intents, while diagnostic entities are more relevant in error-related questions. Moreover, resolution rates vary significantly by intent: questions about API Usage and API Change achieve higher resolution rates, whereas Discrepancy and Review have lower resolution rates. A Chi-Square analysis confirms the statistical significance of these differences.
Insights into dendritic growth mechanisms in batteries: A combined machine learning and computational study
Authors: Zirui Zhao, Junchao Xia, Si Wu, Xiaoke Wang, Guanping Xu, Yinghao Zhu, Jing Sun, Hai-Feng Li
Date: 2025-03-02 00:00:00

In recent years, researchers have increasingly sought batteries as an efficient and cost-effective solution for energy storage and supply, owing to their high energy density, low cost, and environmental resilience. However, the issue of dendrite growth has emerged as a significant obstacle in battery development. Excessive dendrite growth during charging and discharging processes can lead to battery short-circuiting, degradation of electrochemical performance, reduced cycle life, and abnormal exothermic events. Consequently, understanding the dendrite growth process has become a key challenge for researchers. In this study, we investigated dendrite growth mechanisms in batteries using a combined machine learning approach, specifically a two-dimensional artificial convolutional neural network (CNN) model, along with computational methods. We developed two distinct computer models to predict dendrite growth in batteries. The CNN-1 model employs standard convolutional neural network techniques for dendritic growth prediction, while CNN-2 integrates additional physical parameters to enhance model robustness. Our results demonstrate that CNN-2 significantly enhances prediction accuracy, offering deeper insights into the impact of physical factors on dendritic growth. This improved model effectively captures the dynamic nature of dendrite formation, exhibiting high accuracy and sensitivity. These findings contribute to the advancement of safer and more reliable energy storage systems.
Impact of Fasteners on the Radar Cross-Section performance of Radar Absorbing Air Intake Duct
Authors: Vijay Kumar Sutrakar, Anjana P K
Date: 2025-03-02 00:00:00

An aircraft consists of various cavities including air intake ducts, cockpit, radome, inlet and exhaust of heat exchangers, passage for engine bay/other bay cooling etc. These cavities are prime radar cross-section (RCS) contributors of aircraft. The major such cavity is air intake duct, and it contributes significantly to frontal sector RCS of an aircraft. The RCS reductions of air intake duct is very important to achieve a low RCS (or stealthy) aircraft configuration. In general, radar absorbing materials (RAM) are getting utilized for RCS reduction of air intake duct. It can also be noticed that a large number of fasteners are used for integration of air intake duct with the aircraft structures. The installation of fasteners on RAS may lead to degradation of RCS performance of air intake. However, no such studies are reported in the literature on the impact of rivets on the RCS performance of RAS air intake duct. In this paper, radar absorbing material of thickness 6.25 mm is designed which givens more than -10 dB reflection loss from 4 to 18GHz of frequencies. Next, the effect of rivet installation on these RAS is carried out using three different rivet configurations. The RCS performance of RAS is evaluated for duct of different lengths from 1 to 18GHz of frequencies. In order to see the RCS performance, five different air intake cases are considered The RCS performance with increase in percentage surface area of rivet heads to RAS is reported in detail. At the last, an open-source aircraft CAD model is considered and the RCS performance of RAS air intake with and without rivets is evaluated.
Large AI Model for Delay-Doppler Domain Channel Prediction in 6G OTFS-Based Vehicular Networks
Authors: Jianzhe Xue, Dongcheng Yuan, Zhanxi Ma, Tiankai Jiang, Yu Sun, Haibo Zhou, Xuemin Shen
Date: 2025-03-03 00:00:00
Tasks: Prediction, Time Series

Channel prediction is crucial for high-mobility vehicular networks, as it enables the anticipation of future channel conditions and the proactive adjustment of communication strategies. However, achieving accurate vehicular channel prediction is challenging due to significant Doppler effects and rapid channel variations resulting from high-speed vehicle movement and complex propagation environments. In this paper, we propose a novel delay-Doppler (DD) domain channel prediction framework tailored for high-mobility vehicular networks. By transforming the channel representation into the DD domain, we obtain an intuitive, sparse, and stable depiction that closely aligns with the underlying physical propagation processes, effectively reducing the complex vehicular channel to a set of time-series parameters with enhanced predictability. Furthermore, we leverage the large artificial intelligence (AI) model to predict these DD-domain time-series parameters, capitalizing on their advanced ability to model temporal correlations. The zero-shot capability of the pre-trained large AI model facilitates accurate channel predictions without requiring task-specific training, while subsequent fine-tuning on specific vehicular channel data further improves prediction accuracy. Extensive simulation results demonstrate the effectiveness of our DD-domain channel prediction framework and the superior accuracy of the large AI model in predicting time-series channel parameters, thereby highlighting the potential of our approach for robust vehicular communication systems.
Dementia Insights: A Context-Based MultiModal Approach
Authors: Sahar Sinene Mehdoui, Abdelhamid Bouzid, Daniel Sierra-Sosa, Adel Elmaghraby
Date: 2025-03-03 00:00:00
Tasks: Diagnostic, In-Context Learning

Dementia, a progressive neurodegenerative disorder, affects memory, reasoning, and daily functioning, creating challenges for individuals and healthcare systems. Early detection is crucial for timely interventions that may slow disease progression. Large pre-trained models (LPMs) for text and audio, such as Generative Pre-trained Transformer (GPT), Bidirectional Encoder Representations from Transformers (BERT), and Contrastive Language-Audio Pretraining (CLAP), have shown promise in identifying cognitive impairments. However, existing studies generally rely heavily on expert-annotated datasets and unimodal approaches, limiting robustness and scalability. This study proposes a context-based multimodal method, integrating both text and audio data using the best-performing LPMs in each modality. By incorporating contextual embeddings, our method improves dementia detection performance. Additionally, motivated by the effectiveness of contextual embeddings, we further experimented with a context-based In-Context Learning (ICL) as a complementary technique. Results show that GPT-based embeddings, particularly when fused with CLAP audio features, achieve an F1-score of $83.33\%$, surpassing state-of-the-art dementia detection models. Furthermore, raw text data outperforms expert-annotated datasets, demonstrating that LPMs can extract meaningful linguistic and acoustic patterns without extensive manual labeling. These findings highlight the potential for scalable, non-invasive diagnostic tools that reduce reliance on costly annotations while maintaining high accuracy. By integrating multimodal learning with contextual embeddings, this work lays the foundation for future advancements in personalized dementia detection and cognitive health research.
Pre-training Graph Neural Networks with Structural Fingerprints for Materials Discovery
Authors: Shuyi Jia, Shitij Govil, Manav Ramprasad, Victor Fung
Date: 2025-03-03 00:00:00
Tasks: Denoising

In recent years, pre-trained graph neural networks (GNNs) have been developed as general models which can be effectively fine-tuned for various potential downstream tasks in materials science, and have shown significant improvements in accuracy and data efficiency. The most widely used pre-training methods currently involve either supervised training to fit a general force field or self-supervised training by denoising atomic structures equilibrium. Both methods require datasets generated from quantum mechanical calculations, which quickly become intractable when scaling to larger datasets. Here we propose a novel pre-training objective which instead uses cheaply-computed structural fingerprints as targets while maintaining comparable performance across a range of different structural descriptors. Our experiments show this approach can act as a general strategy for pre-training GNNs with application towards large scale foundational models for atomistic data.
Large Language Models for Code Generation: A Comprehensive Survey of Challenges, Techniques, Evaluation, and Applications
Authors: Nam Huynh, Beiyu Lin
Date: 2025-03-03 00:00:00
Tasks: Code Generation, Survey

Large Language Models (LLMs) have demonstrated their remarkable capabilities in numerous fields. This survey focuses on how LLMs empower users, regardless of their technical background, to use human languages to automatically generate executable code. We begin with understanding LLMs' limitations and challenges in automated code generation. Subsequently, we review various fine-tuning techniques designed to enhance both the performance and adaptability of LLMs in code generation tasks. We then review the existing metrics and benchmarks for evaluations to assess model performance based on fine-tuning techniques. Finally, we explore the applications of LLMs (e.g. CodeLlama, GitHub Copilot, ToolGen) in code generation tasks to illustrate their roles and functionalities. This survey provides a comprehensive overview of LLMs for code generation, helps researchers in diverse fields better understand the current state-of-the-art technologies, and offers the potential of effectively leveraging LLMs for code generation tasks.
Stone Soup Multi-Target Tracking Feature Extraction For Autonomous Search And Track In Deep Reinforcement Learning Environment
Authors: Jan-Hendrik Ewers, Joe Gibbs, David Anderson
Date: 2025-03-03 00:00:00
Tasks: Deep Reinforcement Learning, Management, reinforcement-learning, Reinforcement Learning

Management of sensing resources is a non-trivial problem for future military air assets with future systems deploying heterogeneous sensors to generate information of the battlespace. Machine learning techniques including deep reinforcement learning (DRL) have been identified as promising approaches, but require high-fidelity training environments and feature extractors to generate information for the agent. This paper presents a deep reinforcement learning training approach, utilising the Stone Soup tracking framework as a feature extractor to train an agent for a sensor management task. A general framework for embedding Stone Soup tracker components within a Gymnasium environment is presented, enabling fast and configurable tracker deployments for RL training using Stable Baselines3. The approach is demonstrated in a sensor management task where an agent is trained to search and track a region of airspace utilising track lists generated from Stone Soup trackers. A sample implementation using three neural network architectures in a search-and-track scenario demonstrates the approach and shows that RL agents can outperform simple sensor search and track policies when trained within the Gymnasium and Stone Soup environment.
Statistical physics analysis of graph neural networks: Approaching optimality in the contextual stochastic block model
Authors: O. Duranthon, L. Zdeborová
Date: 2025-03-03 00:00:00
Tasks: Node Classification, Stochastic Block Model

Graph neural networks (GNNs) are designed to process data associated with graphs. They are finding an increasing range of applications; however, as with other modern machine learning techniques, their theoretical understanding is limited. GNNs can encounter difficulties in gathering information from nodes that are far apart by iterated aggregation steps. This situation is partly caused by so-called oversmoothing; and overcoming it is one of the practically motivated challenges. We consider the situation where information is aggregated by multiple steps of convolution, leading to graph convolutional networks (GCNs). We analyze the generalization performance of a basic GCN, trained for node classification on data generated by the contextual stochastic block model. We predict its asymptotic performance by deriving the free energy of the problem, using the replica method, in the high-dimensional limit. Calling depth the number of convolutional steps, we show the importance of going to large depth to approach the Bayes-optimality. We detail how the architecture of the GCN has to scale with the depth to avoid oversmoothing. The resulting large depth limit can be close to the Bayes-optimality and leads to a continuous GCN. Technically, we tackle this continuous limit via an approach that resembles dynamical mean-field theory (DMFT) with constraints at the initial and final times. An expansion around large regularization allows us to solve the corresponding equations for the performance of the deep GCN. This promising tool may contribute to the analysis of further deep neural networks.
Reconstruction of muon bundles in KM3NeT detectors using machine learning methods
Authors: Piotr Kalaczyński
Date: 2025-03-03 00:00:00
Tasks: Astronomy

The KM3NeT Collaboration is installing the ARCA and ORCA neutrino detectors at the bottom of the Mediterranean Sea. The focus of ARCA is neutrino astronomy, while ORCA is optimised for neutrino oscillation studies. Both detectors are already operational in their intermediate states and collect valuable data, including the measurements of the muons produced by cosmic ray interactions in the atmosphere. This work explores the potential of machine learning models for the reconstruction of muon bundles, which are multi-muon events. For this, data collected with intermediate detector configurations of ARCA and ORCA was used in addition to simulated data from the envisaged final configurations of those detectors. Prediction of the total number of muons in a bundle as well as their total energy and even the energy of the primary cosmic ray is presented.
A Linearly Convergent Frank-Wolfe-type Method for Smooth Convex Minimization over the Spectrahedron
Authors: Dan Garber
Date: 2025-03-03 00:00:00

We consider the problem of minimizing a smooth and convex function over the $n$-dimensional spectrahedron -- the set of real symmetric $n\times n$ positive semidefinite matrices with unit trace, which underlies numerous applications in statistics, machine learning and additional domains. Standard first-order methods often require high-rank matrix computations which are prohibitive when the dimension $n$ is large. The well-known Frank-Wolfe method on the other hand, only requires efficient rank-one matrix computations, however suffers from worst-case slow convergence, even under conditions that enable linear convergence rates for standard methods. In this work we present the first Frank-Wolfe-based algorithm that only applies efficient rank-one matrix computations and, assuming quadratic growth and strict complementarity conditions, is guaranteed, after a finite number of iterations, to converges linearly, in expectation, and independently of the ambient dimension.
Primer C-VAE: An interpretable deep learning primer design method to detect emerging virus variants
Authors: Hanyu Wang, Emmanuel K. Tsinda, Anthony J. Dunn, Francis Chikweto, Alain B. Zemkoho
Date: 2025-03-03 00:00:00
Tasks: Epidemiology

Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is challenging. Traditional methods require substantial manual intervention and struggle to ensure effective primer design across different strains. For organisms with large, similar genomes like Escherichia coli and Shigella flexneri, differentiating between species is also difficult but crucial. Results: We developed Primer C-VAE, a model based on a Variational Auto-Encoder framework with Convolutional Neural Networks to identify variants and generate specific primers. Using SARS-CoV-2, our model classified variants (alpha, beta, gamma, delta, omicron) with 98% accuracy and generated variant-specific primers. These primers appeared with >95% frequency in target variants and <5% in others, showing good performance in in-silico PCR tests. For Alpha, Delta, and Omicron, our primer pairs produced fragments <200 bp, suitable for qPCR detection. The model also generated effective primers for organisms with longer gene sequences like E. coli and S. flexneri. Conclusion: Primer C-VAE is an interpretable deep learning approach for developing specific primer pairs for target organisms. This flexible, semi-automated and reliable tool works regardless of sequence completeness and length, allowing for qPCR applications and can be applied to organisms with large and highly similar genomes.
FlowDec: A flow-based full-band general audio codec with high perceptual quality
Authors: Simon Welker, Matthew Le, Ricky T. Q. Chen, Wei-Ning Hsu, Timo Gerkmann, Alexander Richard, Yi-Chiao Wu
Date: 2025-03-03 00:00:00
Tasks: FAD

We propose FlowDec, a neural full-band audio codec for general audio sampled at 48 kHz that combines non-adversarial codec training with a stochastic postfilter based on a novel conditional flow matching method. Compared to the prior work ScoreDec which is based on score matching, we generalize from speech to general audio and move from 24 kbit/s to as low as 4 kbit/s, while improving output quality and reducing the required postfilter DNN evaluations from 60 to 6 without any fine-tuning or distillation techniques. We provide theoretical insights and geometric intuitions for our approach in comparison to ScoreDec as well as another recent work that uses flow matching, and conduct ablation studies on our proposed components. We show that FlowDec is a competitive alternative to the recent GAN-dominated stream of neural codecs, achieving FAD scores better than those of the established GAN-based codec DAC and listening test scores that are on par, and producing qualitatively more natural reconstructions for speech and harmonic structures in music.