pwc-archive/papers-with-abstracts huggingface dataset:
Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning
Authors: Yin Fang, Qiao Jin, Guangzhi Xiong, Bowen Jin, Xianrui Zhong, Siru Ouyang, Aidong Zhang, Jiawei Han, Zhiyong Lu
Date: 2025-06-03 00:00:00

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.
Enriching Location Representation with Detailed Semantic Information
Authors: Junyuan Liu, Xinglei Wang, Tao Cheng
Date: 2025-06-03 00:00:00
Tasks: Contrastive Learning

Spatial representations that capture both structural and semantic characteristics of urban environments are essential for urban modeling. Traditional spatial embeddings often prioritize spatial proximity while underutilizing fine-grained contextual information from places. To address this limitation, we introduce CaLLiPer+, an extension of the CaLLiPer model that systematically integrates Point-of-Interest (POI) names alongside categorical labels within a multimodal contrastive learning framework. We evaluate its effectiveness on two downstream tasks, land use classification and socioeconomic status distribution mapping, demonstrating consistent performance gains of 4% to 11% over baseline methods. Additionally, we show that incorporating POI names enhances location retrieval, enabling models to capture complex urban concepts with greater precision. Ablation studies further reveal the complementary role of POI names and the advantages of leveraging pretrained text encoders for spatial representations. Overall, our findings highlight the potential of integrating fine-grained semantic attributes and multimodal learning techniques to advance the development of urban foundation models.
TL;DR: Too Long, Do Re-weighting for Efficient LLM Reasoning Compression
Authors: Zhong-Zhi Li, Xiao Liang, Zihao Tang, Lei Ji, Peijie Wang, Haotian Xu, Xing W, Haizhen Huang, Weiwei Deng, Yeyun Gong, Zhijiang Guo, Xiao Liu, Fei Yin, Cheng-Lin Liu
Date: 2025-06-03 00:00:00

Large Language Models (LLMs) have recently achieved remarkable progress by leveraging Reinforcement Learning and extended Chain-of-Thought (CoT) techniques. However, the challenge of performing efficient language reasoning--especially during inference with extremely long outputs--has drawn increasing attention from the research community. In this work, we propose a dynamic ratio-based training pipeline that does not rely on sophisticated data annotations or interpolation between multiple models. We continuously balance the weights between the model's System-1 and System-2 data to eliminate redundant reasoning processes while preserving the model's reasoning capability. We validate our approach across models on DeepSeek-R1-Distill-7B and DeepSeek-R1-Distill-14B and on a diverse set of benchmarks with varying difficulty levels. Our method significantly reduces the number of output tokens by nearly 40% while maintaining the accuracy of the reasoning. Our code and data will be available soon.
Generative AI for Predicting 2D and 3D Wildfire Spread: Beyond Physics-Based Models and Traditional Deep Learning
Authors: Haowen Xu, Sisi Zlatanova, Ruiyu Liang, Ismet Canbulat
Date: 2025-06-03 00:00:00
Tasks: Edge-computing

Wildfires continue to inflict devastating human, environmental, and economic losses globally, as tragically exemplified by the 2025 Los Angeles wildfire and the urgent demand for more effective response strategies. While physics-based and deep learning models have advanced wildfire simulation, they face critical limitations in predicting and visualizing multimodal fire spread in real time, particularly in both 2D and 3D spatial domains using dynamically updated GIS data. These limitations hinder timely emergency response, infrastructure protection, and community safety. Generative AI has recently emerged as a transformative approach across research and industry. Models such as Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), Transformers, and diffusion-based architectures offer distinct advantages over traditional methods, including the integration of multimodal data, generation of diverse scenarios under uncertainty, and improved modeling of wildfire dynamics across spatial and temporal scales. This position paper advocates for the adoption of generative AI as a foundational framework for wildfire prediction. We explore how such models can enhance 2D fire spread forecasting and enable more realistic, scalable 3D simulations. Additionally, we employ a novel human-AI collaboration framework using large language models (LLMs) for automated knowledge extraction, literature synthesis, and bibliometric mapping. Looking ahead, we identify five key visions for integrating generative AI into wildfire management: multimodal approaches, AI foundation models, conversational AI systems, edge-computing-based scenario generation, and cognitive digital twins. We also address three major challenges accompanying these opportunities and propose potential solutions to support their implementation.
Sensitivity-Aware Density Estimation in Multiple Dimensions
Authors: Aleix Boquet-Pujadas, Pol del Aguila Pla, Michael Unser
Date: 2025-06-02 00:00:00
Tasks: Density Estimation, Sensitivity

We formulate an optimization problem to estimate probability densities in the context of multidimensional problems that are sampled with uneven probability. It considers detector sensitivity as an heterogeneous density and takes advantage of the computational speed and flexible boundary conditions offered by splines on a grid. We choose to regularize the Hessian of the spline via the nuclear norm to promote sparsity. As a result, the method is spatially adaptive and stable against the choice of the regularization parameter, which plays the role of the bandwidth. We test our computational pipeline on standard densities and provide software. We also present a new approach to PET rebinning as an application of our framework.
COALESCE: Economic and Security Dynamics of Skill-Based Task Outsourcing Among Team of Autonomous LLM Agents
Authors: Manish Bhatt, Ronald F. Del Rosario, Vineeth Sai Narajala, Idan Habler
Date: 2025-06-02 00:00:00
Tasks: GPU, Large Language Model

The meteoric rise and proliferation of autonomous Large Language Model (LLM) agents promise significant capabilities across various domains. However, their deployment is increasingly constrained by substantial computational demands, specifically for Graphics Processing Unit (GPU) resources. This paper addresses the critical problem of optimizing resource utilization in LLM agent systems. We introduce COALESCE (Cost-Optimized and Secure Agent Labour Exchange via Skill-based Competence Estimation), a novel framework designed to enable autonomous LLM agents to dynamically outsource specific subtasks to specialized, cost-effective third-party LLM agents. The framework integrates mechanisms for hybrid skill representation, dynamic skill discovery, automated task decomposition, a unified cost model comparing internal execution costs against external outsourcing prices, simplified market-based decision-making algorithms, and a standardized communication protocol between LLM agents. Comprehensive validation through 239 theoretical simulations demonstrates 41.8\% cost reduction potential, while large-scale empirical validation across 240 real LLM tasks confirms 20.3\% cost reduction with proper epsilon-greedy exploration, establishing both theoretical viability and practical effectiveness. The emergence of proposed open standards like Google's Agent2Agent (A2A) protocol further underscores the need for frameworks like COALESCE that can leverage such standards for efficient agent interaction. By facilitating a dynamic market for agent capabilities, potentially utilizing protocols like A2A for communication, COALESCE aims to significantly reduce operational costs, enhance system scalability, and foster the emergence of specialized agent economies, making complex LLM agent functionalities more accessible and economically viable.
Regulatory Graphs and GenAI for Real-Time Transaction Monitoring and Compliance Explanation in Banking
Authors: Kunal Khanvilkar, Kranthi Kommuru
Date: 2025-06-01 00:00:00
Tasks: Graph Neural Network, Retrieval-augmented Generation

This paper presents a real-time transaction monitoring framework that integrates graph-based modeling, narrative field embedding, and generative explanation to support automated financial compliance. The system constructs dynamic transaction graphs, extracts structural and contextual features, and classifies suspicious behavior using a graph neural network. A retrieval-augmented generation module generates natural language explanations aligned with regulatory clauses for each flagged transaction. Experiments conducted on a simulated stream of financial data show that the proposed method achieves superior results, with 98.2% F1-score, 97.8% precision, and 97.0% recall. Expert evaluation further confirms the quality and interpretability of generated justifications. The findings demonstrate the potential of combining graph intelligence and generative models to support explainable, audit-ready compliance in high-risk financial environments.
ChemReservoir -- An Open-Source Framework for Chemically-Inspired Reservoir Computing
Authors: Mehmet Aziz Yirik, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle
Date: 2025-05-31 00:00:00

Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the literature, there are various types of reservoirs ranging from in-silico to in-vitro. In cheminformatics, previous studies contributed to the field by developing simulation-based chemically inspired in-silico reservoir models. Yahiro used a DNA-based chemical reaction network as its reservoir and Nguyen developed a DNA chemistry-inspired tool based on Gillespie algorithm. However, these software tools were designed mainly with the focus on DNA chemistry and their maintenance status has limited their current usability. Due to these limitations, there was a need for a proper open-source tool. This study introduces ChemReservoir, an open-source framework for chemically-inspired reservoir computing. In contrast to the former studies focused on DNA-chemistry, ChemReservoir is a general framework for the construction and analysis of chemically-inspired reservoirs, which also addresses the limitations in these previous studies by ensuring enhanced testing, evaluation, and reproducibility. The tool was evaluated using various cycle-based reservoir topologies and demonstrated stable performance across a range of configurations in memory capacity tasks.
Multi-Objective Neural Network Assisted Design Optimization of Soft Fin-Ray Grippers for Enhanced Grasping Performance
Authors: Ali Ghanizadeh, Ali Ahmadi, Arash Bahrami
Date: 2025-05-31 00:00:00

Soft Fin-Ray grippers can perform delicate and careful manipulation, which has caused notable attention in different fields. These grippers can handle objects of various forms and sizes safely. The internal structure of the Fin-Ray finger plays a significant role in its adaptability and grasping performance. However, modeling the non-linear grasp force and deformation behaviors for design purposes is challenging. Moreover, when the Fin-Ray finger becomes more rigid and capable of exerting higher forces, it becomes less delicate in handling objects. The contrast between these two objectives gives rise to a multi-objective optimization problem. In this study, we employ finite element method (FEM) to estimate the deflections and contact forces of the Fin-Ray, grasping cylindrical objects. This dataset is then used to construct a multilayer perception (MLP) for prediction of the contact force and the tip displacement. The FEM dataset consists of three input and four target features. The three input features of the MLP and optimization design variables are the thickness of the front and supporting beams, the thickness of the cross beams, and the equal spacing between the cross beams. In addition, the target features are the maximum contact forces and maximum tip displacements in x- and y-directions. The magnitude of maximum contact force and magnitude of maximum tip displacement are the two objectives, showing the trade-off between force and delicate manipulation in soft Fin-Ray grippers. Furthermore, the optimized set of solutions are found using multi-objective optimal techniques. We use non-dominated sorting genetic algorithm (NSGA-II) method for this purpose. Our findings demonstrate that our methodologies can be used to improve the design and gripping performance of soft robotic grippers, helping us to choose a design not only for delicate grasping but also for high-force applications.
Risks of AI-driven product development and strategies for their mitigation
Authors: Jan Göpfert, Jann M. Weinand, Patrick Kuckertz, Noah Pflugradt, Jochen Linßen
Date: 2025-05-28 00:00:00

Humanity is progressing towards automated product development, a trend that promises faster creation of better products and thus the acceleration of technological progress. However, increasing reliance on non-human agents for this process introduces many risks. This perspective aims to initiate a discussion on these risks and appropriate mitigation strategies. To this end, we outline a set of principles for safer AI-driven product development which emphasize human oversight, accountability, and explainable design, among others. The risk assessment covers both technical risks which affect product quality and safety, and sociotechnical risks which affect society. While AI-driven product development is still in its early stages, this discussion will help balance its opportunities and risks without delaying essential progress in understanding, norm-setting, and regulation.
Benchmark for Antibody Binding Affinity Maturation and Design
Authors: Xinyan Zhao, Yi-Ching Tang, Akshita Singh, Victor J Cantu, KwanHo An, Junseok Lee, Adam E Stogsdill, Ashwin Kumar Ramesh, Zhiqiang An, Xiaoqian Jiang, Yejin Kim
Date: 2025-05-23 00:00:00
Tasks: Benchmarking

We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike existing antibody evaluation strategies that rely on antibody alone and its similarity to natural ones (e.g., amino acid identity rate, structural RMSD), AbBiBench considers an antibody-antigen (Ab-Ag) complex as a functional unit and evaluates the potential of an antibody design binding to given antigen by measuring protein model's likelihood on the Ab-Ag complex. We first curate, standardize, and share 9 datasets containing 9 antigens (involving influenza, anti-lysozyme, HER2, VEGF, integrin, and SARS-CoV-2) and 155,853 heavy chain mutated antibodies. Using these datasets, we systematically compare 14 protein models including masked language models, autoregressive language models, inverse folding models, diffusion-based generative models, and geometric graph models. The correlation between model likelihood and experimental affinity values is used to evaluate model performance. Additionally, in a case study to increase binding affinity of antibody F045-092 to antigen influenza H1N1, we evaluate the generative power of the top-performing models by sampling a set of new antibodies binding to the antigen and ranking them based on structural integrity and biophysical properties of the Ab-Ag complex. As a result, structure-conditioned inverse folding models outperform others in both affinity correlation and generation tasks. Overall, AbBiBench provides a unified, biologically grounded evaluation framework to facilitate the development of more effective, function-aware antibody design models.
A Fast Unsupervised Scheme for Polygonal Approximation
Authors: Bimal Kumar Ray
Date: 2025-06-05 00:00:00

This paper proposes a fast and unsupervised scheme for a polygonal approximation of a closed digital curve. It is demonstrated that the approximation scheme is faster than state-of-the-art approximation and is competitive with the same in Rosin's measure and in its aesthetic aspect. The scheme comprises of three phases: initial segmentation, iterative vertex insertion, and iterative merging, followed by vertex adjustment. The initial segmentation is used to detect sharp turnings - the vertices that seemingly have high curvature. It is likely that some of important vertices with low curvature might have been missed out at the first phase and so iterative vertex insertion is used to add vertices in a region where the curvature changes slowly but steadily. The initial phase may pick up some undesirable vertices and so merging is used to eliminate the redundant vertices. Finally, vertex adjustment is used to facilitate enhancement in the aesthetic look of the approximation. The quality of the approximations is measured using Rosin's measure. The robustness of the proposed scheme with respect to geometric transformation is observed.
Unfolding Boxes with Local Constraints
Authors: Long Qian, Eric Wang, Bernardo Subercaseaux, Marijn J. H. Heule
Date: 2025-06-01 00:00:00

We consider the problem of finding and enumerating polyominos that can be folded into multiple non-isomorphic boxes. While several computational approaches have been proposed, including SAT, randomized algorithms, and decision diagrams, none has been able to perform at scale. We argue that existing SAT encodings are hindered by the presence of global constraints (e.g., graph connectivity or acyclicity), which are generally hard to encode effectively and hard for solvers to reason about. In this work, we propose a new SAT-based approach that replaces these global constraints with simple local constraints that have substantially better propagation properties. Our approach dramatically improves the scalability of both computing and enumerating common box unfoldings: (i) while previous approaches could only find common unfoldings of two boxes up to area 88, ours easily scales beyond 150, and (ii) while previous approaches were only able to enumerate common unfoldings up to area 30, ours scales up to 60. This allows us to rule out 46, 54, and 58 as the smallest areas allowing a common unfolding of three boxes, thereby refuting a conjecture of Xu et al. (2017).
Why LLM Safety Guardrails Collapse After Fine-tuning: A Similarity Analysis Between Alignment and Fine-tuning Datasets
Authors: Lei Hsiung, Tianyu Pang, Yung-Chen Tang, Linyue Song, Tsung-Yi Ho, Pin-Yu Chen, Yaoqing Yang
Date: 2025-06-05 00:00:00
Tasks: Safety Alignment

Recent advancements in large language models (LLMs) have underscored their vulnerability to safety alignment jailbreaks, particularly when subjected to downstream fine-tuning. However, existing mitigation strategies primarily focus on reactively addressing jailbreak incidents after safety guardrails have been compromised, removing harmful gradients during fine-tuning, or continuously reinforcing safety alignment throughout fine-tuning. As such, they tend to overlook a critical upstream factor: the role of the original safety-alignment data. This paper therefore investigates the degradation of safety guardrails through the lens of representation similarity between upstream alignment datasets and downstream fine-tuning tasks. Our experiments demonstrate that high similarity between these datasets significantly weakens safety guardrails, making models more susceptible to jailbreaks. Conversely, low similarity between these two types of datasets yields substantially more robust models and thus reduces harmfulness score by up to 10.33%. By highlighting the importance of upstream dataset design in the building of durable safety guardrails and reducing real-world vulnerability to jailbreak attacks, these findings offer actionable insights for fine-tuning service providers.
Membership Inference Attacks on Sequence Models
Authors: Lorenzo Rossi, Michael Aerni, Jie Zhang, Florian Tramèr
Date: 2025-06-05 00:00:00
Tasks: Inference Attack, Membership Inference Attack, Memorization

Sequence models, such as Large Language Models (LLMs) and autoregressive image generators, have a tendency to memorize and inadvertently leak sensitive information. While this tendency has critical legal implications, existing tools are insufficient to audit the resulting risks. We hypothesize that those tools' shortcomings are due to mismatched assumptions. Thus, we argue that effectively measuring privacy leakage in sequence models requires leveraging the correlations inherent in sequential generation. To illustrate this, we adapt a state-of-the-art membership inference attack to explicitly model within-sequence correlations, thereby demonstrating how a strong existing attack can be naturally extended to suit the structure of sequence models. Through a case study, we show that our adaptations consistently improve the effectiveness of memorization audits without introducing additional computational costs. Our work hence serves as an important stepping stone toward reliable memorization audits for large sequence models.
Privacy Amplification Through Synthetic Data: Insights from Linear Regression
Authors: Clément Pierquin, Aurélien Bellet, Marc Tommasi, Matthieu Boussard
Date: 2025-06-05 00:00:00
Tasks: regression

Synthetic data inherits the differential privacy guarantees of the model used to generate it. Additionally, synthetic data may benefit from privacy amplification when the generative model is kept hidden. While empirical studies suggest this phenomenon, a rigorous theoretical understanding is still lacking. In this paper, we investigate this question through the well-understood framework of linear regression. First, we establish negative results showing that if an adversary controls the seed of the generative model, a single synthetic data point can leak as much information as releasing the model itself. Conversely, we show that when synthetic data is generated from random inputs, releasing a limited number of synthetic data points amplifies privacy beyond the model's inherent guarantees. We believe our findings in linear regression can serve as a foundation for deriving more general bounds in the future.