pwc-archive/papers-with-abstracts huggingface dataset:
BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects
Authors: Hongyang Li, Sanjoy Dey, Bum Chul Kwon, Michael Danziger, Michal Rosen-Tzvi, Jianying Hu, James Kozloski, Ching-Huei Tsou, Bharath Dandala, Pablo Meyer
Date: 2025-06-26 00:00:00
Tasks: Imputation, Promoter Detection

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic
BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis
Authors: Florian Kofler, Marcel Rosier, Mehdi Astaraki, Hendrik Möller, Ilhem Isra Mekki, Josef A. Buchner, Anton Schmick, Arianna Pfiffer, Eva Oswald, Lucas Zimmer, Ezequiel de la Rosa, Sarthak Pati, Julian Canisius, Arianna Piffer, Ujjwal Baid, Mahyar Valizadeh, Akis Linardos, Jan C. Peeken, Surprosanna Shit, Felix Steinbauer, Daniel Rueckert, Rolf Heckemann, Spyridon Bakas, Jan Kirschke, Constantin von See, Ivan Ezhov, Marie Piraud, Benedikt Wiestler, Bjoern Menze
Date: 2025-07-11 00:00:00
Tasks: Skull Stripping

BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing cognitive effort and streamlining the creation of complex workflows for clinical and scientific practice. At its core is an adaptable preprocessing module that performs co-registration, atlas registration, and optional skull-stripping and defacing on arbitrary multi-modal input images. BrainLesion Suite leverages algorithms from the BraTS challenge to synthesize missing modalities, inpaint lesions, and generate pathology-specific tumor segmentations. BrainLesion Suite also enables quantifying segmentation model performance, with tools such as panoptica to compute lesion-wise metrics. Although BrainLesion Suite was originally developed for image analysis pipelines of brain lesions such as glioma, metastasis, and multiple sclerosis, it can be adapted for other biomedical image analysis applications. The individual BrainLesion Suite packages and tutorials are accessible on GitHub.
ZipVoice-Dialog: Non-Autoregressive Spoken Dialogue Generation with Flow Matching
Authors: Han Zhu, Wei Kang, Liyong Guo, Zengwei Yao, Fangjun Kuang, Weiji Zhuang, Zhaoqing Li, Zhifeng Han, Dong Zhang, Xin Zhang, Xingchen Song, Long Lin, Daniel Povey
Date: 2025-07-12 00:00:00
Tasks: Dialogue Generation, text-to-speech, Text to Speech

Generating spoken dialogue is more challenging than monologue text-to-speech (TTS) due to the need for realistic turn-taking and distinct speaker timbres. Existing spoken dialogue generation models, being auto-regressive, suffer from slow and unstable inference. To overcome these limitations, we introduce ZipVoice-Dialog, a non-autoregressive zero-shot spoken dialogue generation model built upon flow matching. Key designs include: 1) speaker-turn embeddings for precise speaker turn-taking; 2) a curriculum learning strategy for stable speech-text alignment; 3) specialized strategies to enable stereo dialogue generation. Additionally, recognizing the lack of open-source large-scale spoken dialogue datasets, we curated OpenDialog, a 6.8k-hour spoken dialogue dataset from in-the-wild speech data. Furthermore, we established a benchmark to comprehensively evaluate various models. Experimental results demonstrate that ZipVoice-Dialog achieves superior performance in intelligibility, speaker turn-taking accuracy, speaker similarity, and inference speed. Our codes, model checkpoints, demo samples, and the OpenDialog dataset are all publicly available at https://github.com/k2-fsa/ZipVoice.
TLB-VFI: Temporal-Aware Latent Brownian Bridge Diffusion for Video Frame Interpolation
Authors: Zonglin Lyu, Chen Chen
Date: 2025-07-07 00:00:00
Tasks: Optical Flow Estimation, Video Frame Interpolation

Video Frame Interpolation (VFI) aims to predict the intermediate frame $I_n$ (we use n to denote time in videos to avoid notation overload with the timestep $t$ in diffusion models) based on two consecutive neighboring frames $I_0$ and $I_1$. Recent approaches apply diffusion models (both image-based and video-based) in this task and achieve strong performance. However, image-based diffusion models are unable to extract temporal information and are relatively inefficient compared to non-diffusion methods. Video-based diffusion models can extract temporal information, but they are too large in terms of training scale, model size, and inference time. To mitigate the above issues, we propose Temporal-Aware Latent Brownian Bridge Diffusion for Video Frame Interpolation (TLB-VFI), an efficient video-based diffusion model. By extracting rich temporal information from video inputs through our proposed 3D-wavelet gating and temporal-aware autoencoder, our method achieves 20% improvement in FID on the most challenging datasets over recent SOTA of image-based diffusion models. Meanwhile, due to the existence of rich temporal information, our method achieves strong performance while having 3times fewer parameters. Such a parameter reduction results in 2.3x speed up. By incorporating optical flow guidance, our method requires 9000x less training data and achieves over 20x fewer parameters than video-based diffusion models. Codes and results are available at our project page: https://zonglinl.github.io/tlbvfi_page.
Semantic Frame Interpolation
Authors: Yijia Hong, Jiangning Zhang, Ran Yi, Yuji Wang, Weijian Cao, Xiaobin Hu, Zhucun Xue, Yabiao Wang, Chengjie Wang, Lizhuang Ma
Date: 2025-07-07 00:00:00

Generating intermediate video content of varying lengths based on given first and last frames, along with text prompt information, offers significant research and application potential. However, traditional frame interpolation tasks primarily focus on scenarios with a small number of frames, no text control, and minimal differences between the first and last frames. Recent community developers have utilized large video models represented by Wan to endow frame-to-frame capabilities. However, these models can only generate a fixed number of frames and often fail to produce satisfactory results for certain frame lengths, while this setting lacks a clear official definition and a well-established benchmark. In this paper, we first propose a new practical Semantic Frame Interpolation (SFI) task from the perspective of academic definition, which covers the above two settings and supports inference at multiple frame rates. To achieve this goal, we propose a novel SemFi model building upon Wan2.1, which incorporates a Mixture-of-LoRA module to ensure the generation of high-consistency content that aligns with control conditions across various frame length limitations. Furthermore, we propose SFI-300K, the first general-purpose dataset and benchmark specifically designed for SFI. To support this, we collect and process data from the perspective of SFI, carefully designing evaluation metrics and methods to assess the model's performance across multiple dimensions, encompassing image and video, and various aspects, including consistency and diversity. Through extensive experiments on SFI-300K, we demonstrate that our method is particularly well-suited to meet the requirements of the SFI task.
MIRIX: Multi-Agent Memory System for LLM-Based Agents
Authors: Yu Wang, Xi Chen
Date: 2025-07-10 00:00:00
Tasks: RAG

Although memory capabilities of AI agents are gaining increasing attention, existing solutions remain fundamentally limited. Most rely on flat, narrowly scoped memory components, constraining their ability to personalize, abstract, and reliably recall user-specific information over time. To this end, we introduce MIRIX, a modular, multi-agent memory system that redefines the future of AI memory by solving the field's most critical challenge: enabling language models to truly remember. Unlike prior approaches, MIRIX transcends text to embrace rich visual and multimodal experiences, making memory genuinely useful in real-world scenarios. MIRIX consists of six distinct, carefully structured memory types: Core, Episodic, Semantic, Procedural, Resource Memory, and Knowledge Vault, coupled with a multi-agent framework that dynamically controls and coordinates updates and retrieval. This design enables agents to persist, reason over, and accurately retrieve diverse, long-term user data at scale. We validate MIRIX in two demanding settings. First, on ScreenshotVQA, a challenging multimodal benchmark comprising nearly 20,000 high-resolution computer screenshots per sequence, requiring deep contextual understanding and where no existing memory systems can be applied, MIRIX achieves 35% higher accuracy than the RAG baseline while reducing storage requirements by 99.9%. Second, on LOCOMO, a long-form conversation benchmark with single-modal textual input, MIRIX attains state-of-the-art performance of 85.4%, far surpassing existing baselines. These results show that MIRIX sets a new performance standard for memory-augmented LLM agents. To allow users to experience our memory system, we provide a packaged application powered by MIRIX. It monitors the screen in real time, builds a personalized memory base, and offers intuitive visualization and secure local storage to ensure privacy.
Evaluating Memory in LLM Agents via Incremental Multi-Turn Interactions
Authors: Yuanzhe Hu, Yu Wang, Julian McAuley
Date: 2025-07-07 00:00:00
Tasks: Large Language Model, RAG, Retrieval, Retrieval-augmented Generation

Recent benchmarks for Large Language Model (LLM) agents primarily focus on evaluating reasoning, planning, and execution capabilities, while another critical component-memory, encompassing how agents memorize, update, and retrieve long-term information-is under-evaluated due to the lack of benchmarks. We term agents with memory mechanisms as memory agents. In this paper, we identify four core competencies essential for memory agents: accurate retrieval, test-time learning, long-range understanding, and conflict resolution. Existing datasets either rely on limited context lengths or are tailored for static, long-context settings like book-based QA, which do not reflect the interactive, multi-turn nature of memory agents that incrementally accumulate information. Furthermore, no existing benchmarks cover all four competencies. Therefore, we introduce MemoryAgentBench, a new benchmark specifically designed for memory agents. Our benchmark combines reformulated existing datasets with newly constructed ones, covering the above four memory competencies, providing a systematic and challenging testbed for assessing memory quality. We evaluate a diverse set of memory agents, ranging from simple context-based and retrieval-augmented generation (RAG) systems to advanced agents with external memory modules and tool integration. Empirical results reveal that current methods fall short of mastering all four competencies, underscoring the need for further research into comprehensive memory mechanisms for LLM agents.
State and Memory is All You Need for Robust and Reliable AI Agents
Authors: Matthew Muhoberac, Atharva Parikh, Nirvi Vakharia, Saniya Virani, Aco Radujevic, Savannah Wood, Meghav Verma, Dimitri Metaxotos, Jeyaraman Soundararajan, Thierry Masquelin, Alexander G. Godfrey, Sean Gardner, Dobrila Rudnicki, Sam Michael, Gaurav Chopra
Date: 2025-06-30 00:00:00
Tasks: All, Benchmarking, Decision Making, Natural Language Understanding, Prompt Engineering

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.
Multi-Agent Retrieval-Augmented Framework for Evidence-Based Counterspeech Against Health Misinformation
Authors: Anirban Saha Anik, Xiaoying Song, Elliott Wang, Bryan Wang, Bengisu Yarimbas, Lingzi Hong
Date: 2025-07-09 00:00:00
Tasks: Informativeness, Misinformation, RAG, Retrieval, Retrieval-augmented Generation

Large language models (LLMs) incorporated with Retrieval-Augmented Generation (RAG) have demonstrated powerful capabilities in generating counterspeech against misinformation. However, current studies rely on limited evidence and offer less control over final outputs. To address these challenges, we propose a Multi-agent Retrieval-Augmented Framework to generate counterspeech against health misinformation, incorporating multiple LLMs to optimize knowledge retrieval, evidence enhancement, and response refinement. Our approach integrates both static and dynamic evidence, ensuring that the generated counterspeech is relevant, well-grounded, and up-to-date. Our method outperforms baseline approaches in politeness, relevance, informativeness, and factual accuracy, demonstrating its effectiveness in generating high-quality counterspeech. To further validate our approach, we conduct ablation studies to verify the necessity of each component in our framework. Furthermore, human evaluations reveal that refinement significantly enhances counterspeech quality and obtains human preference.
AI-VaxGuide: An Agentic RAG-Based LLM for Vaccination Decisions
Authors: Abdellah Zeggai, Ilyes Traikia, Abdelhak Lakehal, Abdennour Boulesnane
Date: 2025-07-04 00:00:00
Tasks: Question Answering, RAG, Retrieval-augmented Generation

Vaccination plays a vital role in global public health, yet healthcare professionals often struggle to access immunization guidelines quickly and efficiently. National protocols and WHO recommendations are typically extensive and complex, making it difficult to extract precise information, especially during urgent situations. This project tackles that issue by developing a multilingual, intelligent question-answering system that transforms static vaccination guidelines into an interactive and user-friendly knowledge base. Built on a Retrieval-Augmented Generation (RAG) framework and enhanced with agent-based reasoning (Agentic RAG), the system provides accurate, context-sensitive answers to complex medical queries. Evaluation shows that Agentic RAG outperforms traditional methods, particularly in addressing multi-step or ambiguous questions. To support clinical use, the system is integrated into a mobile application designed for real-time, point-of-care access to essential vaccine information. AI-VaxGuide model is publicly available on https://huggingface.co/VaxGuide
VisualTrap: A Stealthy Backdoor Attack on GUI Agents via Visual Grounding Manipulation
Authors: Ziang Ye, Yang Zhang, Wentao Shi, Xiaoyu You, Fuli Feng, Tat-Seng Chua
Date: 2025-07-09 00:00:00
Tasks: Backdoor Attack, Visual Grounding

Graphical User Interface (GUI) agents powered by Large Vision-Language Models (LVLMs) have emerged as a revolutionary approach to automating human-machine interactions, capable of autonomously operating personal devices (e.g., mobile phones) or applications within the device to perform complex real-world tasks in a human-like manner. However, their close integration with personal devices raises significant security concerns, with many threats, including backdoor attacks, remaining largely unexplored. This work reveals that the visual grounding of GUI agent-mapping textual plans to GUI elements-can introduce vulnerabilities, enabling new types of backdoor attacks. With backdoor attack targeting visual grounding, the agent's behavior can be compromised even when given correct task-solving plans. To validate this vulnerability, we propose VisualTrap, a method that can hijack the grounding by misleading the agent to locate textual plans to trigger locations instead of the intended targets. VisualTrap uses the common method of injecting poisoned data for attacks, and does so during the pre-training of visual grounding to ensure practical feasibility of attacking. Empirical results show that VisualTrap can effectively hijack visual grounding with as little as 5% poisoned data and highly stealthy visual triggers (invisible to the human eye); and the attack can be generalized to downstream tasks, even after clean fine-tuning. Moreover, the injected trigger can remain effective across different GUI environments, e.g., being trained on mobile/web and generalizing to desktop environments. These findings underscore the urgent need for further research on backdoor attack risks in GUI agents.
OpenTable-R1: A Reinforcement Learning Augmented Tool Agent for Open-Domain Table Question Answering
Authors: Zipeng Qiu
Date: 2025-07-02 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model, Question Answering, Table Retrieval

Open-domain table question answering traditionally relies on a two-stage pipeline: static table retrieval followed by a closed-domain answer. In contrast, we propose an end-to-end agentic framework that embeds multi-turn tool calls-using a BM25+-based search API and a SQLite SQL executor-directly into a large language model. To further adapt a compact 4B-parameter model, we introduce a two-stage fine-tuning process: supervised cold-start on easy questions, then Async GRPO reinforcement learning on harder cases with LoRA adapters and a rollout buffer. This unified approach enables the model to jointly retrieve, reason, and execute queries, yielding a dramatic accuracy improvement from single-digit zero-shot performance to over 0.86 exact match on a held-out test set. Our results underscore the effectiveness of integrating structured tool calls with targeted RL fine-tuning for scalable, accurate table QA. The code is available at https://github.com/TabibitoQZP/OpenTableR1.
LineRetriever: Planning-Aware Observation Reduction for Web Agents
Authors: Imene Kerboua, Sahar Omidi Shayegan, Megh Thakkar, Xing Han Lù, Massimo Caccia, Véronique Eglin, Alexandre Aussem, Jérémy Espinas, Alexandre Lacoste
Date: 2025-06-30 00:00:00
Tasks: Retrieval, Semantic Similarity, Semantic Textual Similarity

While large language models have demonstrated impressive capabilities in web navigation tasks, the extensive context of web pages, often represented as DOM or Accessibility Tree (AxTree) structures, frequently exceeds model context limits. Current approaches like bottom-up truncation or embedding-based retrieval lose critical information about page state and action history. This is particularly problematic for adaptive planning in web agents, where understanding the current state is essential for determining future actions. We hypothesize that embedding models lack sufficient capacity to capture plan-relevant information, especially when retrieving content that supports future action prediction. This raises a fundamental question: how can retrieval methods be optimized for adaptive planning in web navigation tasks? In response, we introduce \textit{LineRetriever}, a novel approach that leverages a language model to identify and retrieve observation lines most relevant to future navigation steps. Unlike traditional retrieval methods that focus solely on semantic similarity, \textit{LineRetriever} explicitly considers the planning horizon, prioritizing elements that contribute to action prediction. Our experiments demonstrate that \textit{LineRetriever} can reduce the size of the observation at each step for the web agent while maintaining consistent performance within the context limitations.
Automating MD simulations for Proteins using Large language Models: NAMD-Agent
Authors: Achuth Chandrasekhar, Amir Barati Farimani
Date: 2025-07-10 00:00:00
Tasks: Code Generation, Navigate

Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone process. In this work, we introduce an automated pipeline that leverages Large Language Models (LLMs), specifically Gemini 2.0 Flash, in conjunction with python scripting and Selenium based web automation to streamline the generation of MD input files. The pipeline exploits CHARMM GUI's comprehensive web-based interface for preparing simulation-ready inputs for NAMD. By integrating Gemini's code generation and iterative refinement capabilities, simulation scripts are automatically written, executed, and revised to navigate CHARMM GUI, extract appropriate parameters, and produce the required NAMD input files. Post processing is performed using additional software to further refine the simulation outputs, thereby enabling a complete and largely hands free workflow. Our results demonstrate that this approach reduces setup time, minimizes manual errors, and offers a scalable solution for handling multiple protein systems in parallel. This automated framework paves the way for broader application of LLMs in computational structural biology, offering a robust and adaptable platform for future developments in simulation automation.