pwc-archive/papers-with-abstracts huggingface dataset:
From superposition to sparse codes: interpretable representations in neural networks
Authors: David Klindt, Charles O'Neill, Patrik Reizinger, Harald Maurer, Nina Miolane
Date: 2025-03-03 00:00:00
Tasks: compressed sensing, Representation Learning

Understanding how information is represented in neural networks is a fundamental challenge in both neuroscience and artificial intelligence. Despite their nonlinear architectures, recent evidence suggests that neural networks encode features in superposition, meaning that input concepts are linearly overlaid within the network's representations. We present a perspective that explains this phenomenon and provides a foundation for extracting interpretable representations from neural activations. Our theoretical framework consists of three steps: (1) Identifiability theory shows that neural networks trained for classification recover latent features up to a linear transformation. (2) Sparse coding methods can extract disentangled features from these representations by leveraging principles from compressed sensing. (3) Quantitative interpretability metrics provide a means to assess the success of these methods, ensuring that extracted features align with human-interpretable concepts. By bridging insights from theoretical neuroscience, representation learning, and interpretability research, we propose an emerging perspective on understanding neural representations in both artificial and biological systems. Our arguments have implications for neural coding theories, AI transparency, and the broader goal of making deep learning models more interpretable.
Open-source framework for detecting bias and overfitting for large pathology images
Authors: Anders Sildnes, Nikita Shvetsov, Masoud Tafavvoghi, Vi Ngoc-Nha Tran, Kajsa Møllersen, Lill-Tove Rasmussen Busund, Thomas K. Kilvær, Lars Ailo Bongo
Date: 2025-03-03 00:00:00
Tasks: GPU, Self-Supervised Learning

Even foundational models that are trained on datasets with billions of data samples may develop shortcuts that lead to overfitting and bias. Shortcuts are non-relevant patterns in data, such as the background color or color intensity. So, to ensure the robustness of deep learning applications, there is a need for methods to detect and remove such shortcuts. Today's model debugging methods are time consuming since they often require customization to fit for a given model architecture in a specific domain. We propose a generalized, model-agnostic framework to debug deep learning models. We focus on the domain of histopathology, which has very large images that require large models - and therefore large computation resources. It can be run on a workstation with a commodity GPU. We demonstrate that our framework can replicate non-image shortcuts that have been found in previous work for self-supervised learning models, and we also identify possible shortcuts in a foundation model. Our easy to use tests contribute to the development of more reliable, accurate, and generalizable models for WSI analysis. Our framework is available as an open-source tool available on github.
GRAIN: Exact Graph Reconstruction from Gradients
Authors: Maria Drencheva, Ivo Petrov, Maximilian Baader, Dimitar I. Dimitrov, Martin Vechev
Date: 2025-03-03 00:00:00
Tasks: Federated Learning, Graph Attention, Graph Reconstruction

Federated learning claims to enable collaborative model training among multiple clients with data privacy by transmitting gradient updates instead of the actual client data. However, recent studies have shown the client privacy is still at risk due to the, so called, gradient inversion attacks which can precisely reconstruct clients' text and image data from the shared gradient updates. While these attacks demonstrate severe privacy risks for certain domains and architectures, the vulnerability of other commonly-used data types, such as graph-structured data, remain under-explored. To bridge this gap, we present GRAIN, the first exact gradient inversion attack on graph data in the honest-but-curious setting that recovers both the structure of the graph and the associated node features. Concretely, we focus on Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT) -- two of the most widely used frameworks for learning on graphs. Our method first utilizes the low-rank structure of GNN gradients to efficiently reconstruct and filter the client subgraphs which are then joined to complete the input graph. We evaluate our approach on molecular, citation, and social network datasets using our novel metric. We show that GRAIN reconstructs up to 80% of all graphs exactly, significantly outperforming the baseline, which achieves up to 20% correctly positioned nodes.
Adaptive Attacks Break Defenses Against Indirect Prompt Injection Attacks on LLM Agents
Authors: Qiusi Zhan, Richard Fang, Henil Shalin Panchal, Daniel Kang
Date: 2025-02-27 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model

Large Language Model (LLM) agents exhibit remarkable performance across diverse applications by using external tools to interact with environments. However, integrating external tools introduces security risks, such as indirect prompt injection (IPI) attacks. Despite defenses designed for IPI attacks, their robustness remains questionable due to insufficient testing against adaptive attacks. In this paper, we evaluate eight different defenses and bypass all of them using adaptive attacks, consistently achieving an attack success rate of over 50%. This reveals critical vulnerabilities in current defenses. Our research underscores the need for adaptive attack evaluation when designing defenses to ensure robustness and reliability. The code is available at https://github.com/uiuc-kang-lab/AdaptiveAttackAgent.
ADAGE: Active Defenses Against GNN Extraction
Authors: Jing Xu, Franziska Boenisch, Adam Dziedzic
Date: 2025-02-27 00:00:00
Tasks: Diversity, Drug Discovery, Recommendation Systems

Graph Neural Networks (GNNs) achieve high performance in various real-world applications, such as drug discovery, traffic states prediction, and recommendation systems. The fact that building powerful GNNs requires a large amount of training data, powerful computing resources, and human expertise turns the models into lucrative targets for model stealing attacks. Prior work has revealed that the threat vector of stealing attacks against GNNs is large and diverse, as an attacker can leverage various heterogeneous signals ranging from node labels to high-dimensional node embeddings to create a local copy of the target GNN at a fraction of the original training costs. This diversity in the threat vector renders the design of effective and general defenses challenging and existing defenses usually focus on one particular stealing setup. Additionally, they solely provide means to identify stolen model copies rather than preventing the attack. To close this gap, we propose the first and general Active Defense Against GNN Extraction (ADAGE). By analyzing the queries to the GNN, tracking their diversity in terms of proximity to different communities identified in the underlying graph, and increasing the defense strength with the growing fraction of communities that have been queried, ADAGE can prevent stealing in all common attack setups. Our extensive experimental evaluation using six benchmark datasets, four GNN models, and three types of adaptive attackers shows that ADAGE penalizes attackers to the degree of rendering stealing impossible, whilst not harming predictive performance for legitimate users. ADAGE, thereby, contributes towards securely sharing valuable GNNs in the future.
Exploring the Potential of QEEGNet for Cross-Task and Cross-Dataset Electroencephalography Encoding with Quantum Machine Learning
Authors: Chi-Sheng Chen, Samuel Yen-Chi Chen, Huan-Hsin Tseng
Date: 2025-02-28 00:00:00
Tasks: EEG, Quantum Machine Learning

Electroencephalography (EEG) is widely used in neuroscience and clinical research for analyzing brain activity. While deep learning models such as EEGNet have shown success in decoding EEG signals, they often struggle with data complexity, inter-subject variability, and noise robustness. Recent advancements in quantum machine learning (QML) offer new opportunities to enhance EEG analysis by leveraging quantum computing's unique properties. In this study, we extend the previously proposed Quantum-EEGNet (QEEGNet), a hybrid neural network incorporating quantum layers into EEGNet, to investigate its generalization ability across multiple EEG datasets. Our evaluation spans a diverse set of cognitive and motor task datasets, assessing QEEGNet's performance in different learning scenarios. Experimental results reveal that while QEEGNet demonstrates competitive performance and maintains robustness in certain datasets, its improvements over traditional deep learning methods remain inconsistent. These findings suggest that hybrid quantum-classical architectures require further optimization to fully leverage quantum advantages in EEG processing. Despite these limitations, our study provides new insights into the applicability of QML in EEG research and highlights challenges that must be addressed for future advancements.
Fine-tuning machine-learned particle-flow reconstruction for new detector geometries in future colliders
Authors: Farouk Mokhtar, Joosep Pata, Dolores Garcia, Eric Wulff, Mengke Zhang, Michael Kagan, Javier Duarte
Date: 2025-02-28 00:00:00
Tasks: Transfer Learning

We demonstrate transfer learning capabilities in a machine-learned algorithm trained for particle-flow reconstruction in high energy particle colliders. This paper presents a cross-detector fine-tuning study, where we initially pretrain the model on a large full simulation dataset from one detector design, and subsequently fine-tune the model on a sample with a different collider and detector design. Specifically, we use the Compact Linear Collider detector (CLICdet) model for the initial training set and demonstrate successful knowledge transfer to the CLIC-like detector (CLD) proposed for the Future Circular Collider in electron-positron mode. We show that with an order of magnitude less samples from the second dataset, we can achieve the same performance as a costly training from scratch, across particle-level and event-level performance metrics, including jet and missing transverse momentum resolution. Furthermore, we find that the fine-tuned model achieves comparable performance to the traditional rule-based particle-flow approach on event-level metrics after training on 100,000 CLD events, whereas a model trained from scratch requires at least 1 million CLD events to achieve similar reconstruction performance. To our knowledge, this represents the first full-simulation cross-detector transfer learning study for particle-flow reconstruction. These findings offer valuable insights towards building large foundation models that can be fine-tuned across different detector designs and geometries, helping to accelerate the development cycle for new detectors and opening the door to rapid detector design and optimization using machine learning.
RecCrysFormer: Refined Protein Structural Prediction from 3D Patterson Maps via Recycling Training Runs
Authors: Tom Pan, Evan Dramko, Mitchell D. Miller, George N. Phillips Jr., Anastasios Kyrillidis
Date: 2025-02-28 00:00:00

Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating experimental and ML approaches to protein structure determination from crystallographic data. $\texttt{RecCrysFormer}$ leverages Patterson maps and incorporates known standardized partial structures of amino acid residues to directly predict electron density maps, which are essential for constructing detailed atomic models through crystallographic refinement processes. $\texttt{RecCrysFormer}$ benefits from a ``recycling'' training regimen that iteratively incorporates results from crystallographic refinements and previous training runs as additional inputs in the form of template maps. Using a preliminary dataset of synthetic peptide fragments based on Protein Data Bank, $\texttt{RecCrysFormer}$ achieves good accuracy in structural predictions and shows robustness against variations in crystal parameters, such as unit cell dimensions and angles.
ProDapt: Proprioceptive Adaptation using Long-term Memory Diffusion
Authors: Federico Pizarro Bejarano, Bryson Jones, Daniel Pastor Moreno, Joseph Bowkett, Paul G. Backes, Angela P. Schoellig
Date: 2025-02-28 00:00:00
Tasks: Imitation Learning

Diffusion models have revolutionized imitation learning, allowing robots to replicate complex behaviours. However, diffusion often relies on cameras and other exteroceptive sensors to observe the environment and lacks long-term memory. In space, military, and underwater applications, robots must be highly robust to failures in exteroceptive sensors, operating using only proprioceptive information. In this paper, we propose ProDapt, a method of incorporating long-term memory of previous contacts between the robot and the environment in the diffusion process, allowing it to complete tasks using only proprioceptive data. This is achieved by identifying "keypoints", essential past observations maintained as inputs to the policy. We test our approach using a UR10e robotic arm in both simulation and real experiments and demonstrate the necessity of this long-term memory for task completion.
Seeing Eye to AI? Applying Deep-Feature-Based Similarity Metrics to Information Visualization
Authors: Sheng Long, Angelos Chatzimparmpas, Emma Alexander, Matthew Kay, Jessica Hullman
Date: 2025-02-28 00:00:00
Tasks: Image Super-Resolution, MS-SSIM, Recommendation Systems, SSIM, Style Transfer, Super-Resolution

Judging the similarity of visualizations is crucial to various applications, such as visualization-based search and visualization recommendation systems. Recent studies show deep-feature-based similarity metrics correlate well with perceptual judgments of image similarity and serve as effective loss functions for tasks like image super-resolution and style transfer. We explore the application of such metrics to judgments of visualization similarity. We extend a similarity metric using five ML architectures and three pre-trained weight sets. We replicate results from previous crowd-sourced studies on scatterplot and visual channel similarity perception. Notably, our metric using pre-trained ImageNet weights outperformed gradient-descent tuned MS-SSIM, a multi-scale similarity metric based on luminance, contrast, and structure. Our work contributes to understanding how deep-feature-based metrics can enhance similarity assessments in visualization, potentially improving visual analysis tools and techniques. Supplementary materials are available at https://osf.io/dj2ms.
Synthetic data enables context-aware bioacoustic sound event detection
Authors: Benjamin Hoffman, David Robinson, Marius Miron, Vittorio Baglione, Daniela Canestrari, Damian Elias, Eva Trapote, Olivier Pietquin
Date: 2025-03-01 00:00:00
Tasks: Event Detection, In-Context Learning, Sound Event Detection

We propose a methodology for training foundation models that enhances their in-context learning capabilities within the domain of bioacoustic signal processing. We use synthetically generated training data, introducing a domain-randomization-based pipeline that constructs diverse acoustic scenes with temporally strong labels. We generate over 8.8 thousand hours of strongly-labeled audio and train a query-by-example, transformer-based model to perform few-shot bioacoustic sound event detection. Our second contribution is a public benchmark of 13 diverse few-shot bioacoustics tasks. Our model outperforms previously published methods by 49%, and we demonstrate that this is due to both model design and data scale. We make our trained model available via an API, to provide ecologists and ethologists with a training-free tool for bioacoustic sound event detection.
Stable and Accurate Orbital-Free DFT Powered by Machine Learning
Authors: Roman Remme, Tobias Kaczun, Tim Ebert, Christof A. Gehrig, Dominik Geng, Gerrit Gerhartz, Marc K. Ickler, Manuel V. Klockow, Peter Lippmann, Johannes S. Schmidt, Simon Wagner, Andreas Dreuw, Fred A. Hamprecht
Date: 2025-03-01 00:00:00

Hohenberg and Kohn have proven that the electronic energy and the one-particle electron density can, in principle, be obtained by minimizing an energy functional with respect to the density. Given that decades of theoretical work have so far failed to produce this elusive exact energy functional promising great computational savings, it is reasonable to try and learn it empirically. Using rotationally equivariant atomistic machine learning, we obtain for the first time a density functional that, when applied to the organic molecules in QM9, yields energies with chemical accuracy while also converging to meaningful electron densities. Augmenting the training data with densities obtained from perturbed potentials proved key to these advances. Altogether, we are now closer than ever to fulfilling Hohenberg and Kohn's promise, paving the way for more efficient calculations in large molecular systems.
Polyconvex Physics-Augmented Neural Network Constitutive Models in Principal Stretches
Authors: Adrian Buganza Tepole, Asghar Jadoon, Manuel Rausch, Jan N. Fuhg
Date: 2025-03-01 00:00:00

Accurate constitutive models of soft materials are crucial for understanding their mechanical behavior and ensuring reliable predictions in the design process. To this end, scientific machine learning research has produced flexible and general material model architectures that can capture the behavior of a wide range of materials, reducing the need for expert-constructed closed-form models. The focus has gradually shifted towards embedding physical constraints in the network architecture to regularize these over-parameterized models. Two popular approaches are input convex neural networks (ICNN) and neural ordinary differential equations (NODE). A related alternative has been the generalization of closed-form models, such as sparse regression from a large library. Remarkably, all prior work using ICNN or NODE uses the invariants of the Cauchy-Green tensor and none uses the principal stretches. In this work, we construct general polyconvex functions of the principal stretches in a physics-aware deep-learning framework and offer insights and comparisons to invariant-based formulations. The framework is based on recent developments to characterize polyconvex functions in terms of convex functions of the right stretch tensor $\mathbf{U}$, its cofactor $\text{cof}\mathbf{U}$, and its determinant $J$. Any convex function of a symmetric second-order tensor can be described with a convex and symmetric function of its eigenvalues. Thus, we first describe convex functions of $\mathbf{U}$ and $\text{cof}\mathbf{U}$ in terms of their respective eigenvalues using deep Holder sets composed with ICNN functions. A third ICNN takes as input $J$ and the two convex functions of $\mathbf{U}$ and $\text{cof}\mathbf{U}$, and returns the strain energy as output. The ability of the model to capture arbitrary materials is demonstrated using synthetic and experimental data.
Large Engagement Networks for Classifying Coordinated Campaigns and Organic Twitter Trends
Authors: Atul Anand Gopalakrishnan, Jakir Hossain, Tugrulcan Elmas, Ahmet Erdem Sariyuce
Date: 2025-03-01 00:00:00
Tasks: Classification, Graph Classification

Social media users and inauthentic accounts, such as bots, may coordinate in promoting their topics. Such topics may give the impression that they are organically popular among the public, even though they are astroturfing campaigns that are centrally managed. It is challenging to predict if a topic is organic or a coordinated campaign due to the lack of reliable ground truth. In this paper, we create such ground truth by detecting the campaigns promoted by ephemeral astroturfing attacks. These attacks push any topic to Twitter's (X) trends list by employing bots that tweet in a coordinated manner in a short period and then immediately delete their tweets. We manually curate a dataset of organic Twitter trends. We then create engagement networks out of these datasets which can serve as a challenging testbed for graph classification task to distinguish between campaigns and organic trends. Engagement networks consist of users as nodes and engagements as edges (retweets, replies, and quotes) between users. We release the engagement networks for 179 campaigns and 135 non-campaigns, and also provide finer-grain labels to characterize the type of the campaigns and non-campaigns. Our dataset, LEN (Large Engagement Networks), is available in the URL below. In comparison to traditional graph classification datasets, which are small with tens of nodes and hundreds of edges at most, graphs in LEN are larger. The average graph in LEN has ~11K nodes and ~23K edges. We show that state-of-the-art GNN methods give only mediocre results for campaign vs. non-campaign and campaign type classification on LEN. LEN offers a unique and challenging playfield for the graph classification problem. We believe that LEN will help advance the frontiers of graph classification techniques on large networks and also provide an interesting use case in terms of distinguishing coordinated campaigns and organic trends.
Real-Time Personalization with Simple Transformers
Authors: Lin An, Andrew A. Li, Vaisnavi Nemala, Gabriel Visotsky
Date: 2025-03-01 00:00:00

Real-time personalization has advanced significantly in recent years, with platforms utilizing machine learning models to predict user preferences based on rich behavioral data on each individual user. Traditional approaches usually rely on embedding-based machine learning models to capture user preferences, and then reduce the final optimization task to nearest-neighbors, which can be performed extremely fast. However, these models struggle to capture complex user behaviors, which are essential for making accurate recommendations. Transformer-based models, on the other hand, are known for their practical ability to model sequential behaviors, and hence have been intensively used in personalization recently to overcome these limitations. However, optimizing recommendations under transformer-based models is challenging due to their complicated architectures. In this paper, we address this challenge by considering a specific class of transformers, showing its ability to represent complex user preferences, and developing efficient algorithms for real-time personalization. We focus on a particular set of transformers, called simple transformers, which contain a single self-attention layer. We show that simple transformers are capable of capturing complex user preferences. We then develop an algorithm that enables fast optimization of recommendation tasks based on simple transformers. Our algorithm achieves near-optimal performance in sub-linear time. Finally, we demonstrate the effectiveness of our approach through an empirical study on datasets from Spotify and Trivago. Our experiment results show that (1) simple transformers can model/predict user preferences substantially more accurately than non-transformer models and nearly as accurately as more complex transformers, and (2) our algorithm completes simple-transformer-based recommendation tasks quickly and effectively.