pwc-archive/papers-with-abstracts huggingface dataset:
AntibodyFlow: Normalizing Flow Model for Designing Antibody Complementarity-Determining Regions
Authors: Bohao Xu, Yanbo Wang, Wenyu Chen, Shimin Shan
Date: 2024-06-19 00:00:00
Tasks: Drug Discovery, valid

Therapeutic antibodies have been extensively studied in drug discovery and development in the past decades. Antibodies are specialized protective proteins that bind to antigens in a lock-to-key manner. The binding strength/affinity between an antibody and a specific antigen is heavily determined by the complementarity-determining regions (CDRs) on the antibodies. Existing machine learning methods cast in silico development of CDRs as either sequence or 3D graph (with a single chain) generation tasks and have achieved initial success. However, with CDR loops having specific geometry shapes, learning the 3D geometric structures of CDRs remains a challenge. To address this issue, we propose AntibodyFlow, a 3D flow model to design antibody CDR loops. Specifically, AntibodyFlow first constructs the distance matrix, then predicts amino acids conditioned on the distance matrix. Also, AntibodyFlow conducts constraint learning and constrained generation to ensure valid 3D structures. Experimental results indicate that AntibodyFlow outperforms the best baseline consistently with up to 16.0% relative improvement in validity rate and 24.3% relative reduction in geometric graph level error (root mean square deviation, RMSD).
APPL: A Prompt Programming Language for Harmonious Integration of Programs and Large Language Model Prompts
Authors: Honghua Dong, Qidong Su, Yubo Gao, Zhaoyu Li, Yangjun Ruan, Gennady Pekhimenko, Chris J. Maddison, Xujie Si
Date: 2024-06-19 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model

Large Language Models (LLMs) have become increasingly capable of handling diverse tasks with the aid of well-crafted prompts and integration of external tools, but as task complexity rises, the workflow involving LLMs can be complicated and thus challenging to implement and maintain. To address this challenge, we propose APPL, A Prompt Programming Language that acts as a bridge between computer programs and LLMs, allowing seamless embedding of prompts into Python functions, and vice versa. APPL provides an intuitive and Python-native syntax, an efficient parallelized runtime with asynchronous semantics, and a tracing module supporting effective failure diagnosis and replaying without extra costs. We demonstrate that APPL programs are intuitive, concise, and efficient through three representative scenarios: Chain-of-Thought with self-consistency (CoT-SC), ReAct tool use agent, and multi-agent chat. Experiments on three parallelizable workflows further show that APPL can effectively parallelize independent LLM calls, with a significant speedup ratio that almost matches the estimation.
Convolutional Kolmogorov-Arnold Networks
Authors: Alexander Dylan Bodner, Antonio Santiago Tepsich, Jack Natan Spolski, Santiago Pourteau
Date: 2024-06-19 00:00:00
Tasks: Kolmogorov-Arnold Networks

In this paper, we present Convolutional Kolmogorov-Arnold Networks, a novel architecture that integrates the learnable spline-based activation functions of Kolmogorov-Arnold Networks (KANs) into convolutional layers. By replacing traditional fixed-weight kernels with learnable non-linear functions, Convolutional KANs offer a significant improvement in parameter efficiency and expressive power over standard Convolutional Neural Networks (CNNs). We empirically evaluate Convolutional KANs on the Fashion-MNIST dataset, demonstrating competitive accuracy with up to 50% fewer parameters compared to baseline classic convolutions. This suggests that the KAN Convolution can effectively capture complex spatial relationships with fewer resources, offering a promising alternative for parameter-efficient deep learning models.
Conditional score-based diffusion models for solving inverse problems in mechanics
Authors: Agnimitra Dasgupta, Harisankar Ramaswamy, Javier Murgoitio-Esandi, Ken Foo, Runze Li, Qifa Zhou, Brendan Kennedy, Assad Oberai
Date: 2024-06-19 00:00:00
Tasks: Bayesian Inference

We propose a framework to perform Bayesian inference using conditional score-based diffusion models to solve a class of inverse problems in mechanics involving the inference of a specimen's spatially varying material properties from noisy measurements of its mechanical response to loading. Conditional score-based diffusion models are generative models that learn to approximate the score function of a conditional distribution using samples from the joint distribution. More specifically, the score functions corresponding to multiple realizations of the measurement are approximated using a single neural network, the so-called score network, which is subsequently used to sample the posterior distribution using an appropriate Markov chain Monte Carlo scheme based on Langevin dynamics. Training the score network only requires simulating the forward model. Hence, the proposed approach can accommodate black-box forward models and complex measurement noise. Moreover, once the score network has been trained, it can be re-used to solve the inverse problem for different realizations of the measurements. We demonstrate the efficacy of the proposed approach on a suite of high-dimensional inverse problems in mechanics that involve inferring heterogeneous material properties from noisy measurements. Some examples we consider involve synthetic data, while others include data collected from actual elastography experiments. Further, our applications demonstrate that the proposed approach can handle different measurement modalities, complex patterns in the inferred quantities, non-Gaussian and non-additive noise models, and nonlinear black-box forward models. The results show that the proposed framework can solve large-scale physics-based inverse problems efficiently.
DialSim: A Real-Time Simulator for Evaluating Long-Term Multi-Party Dialogue Understanding of Conversational Agents
Authors: Jiho Kim, Woosog Chay, Hyeonji Hwang, Daeun Kyung, Hyunseung Chung, Eunbyeol Cho, Yohan Jo, Edward Choi
Date: 2024-06-19 00:00:00
Tasks: Dialogue Understanding, Question Answering

Recent advancements in Large Language Models (LLMs) have significantly enhanced the capabilities of conversational agents, making them applicable to various fields (e.g., education). Despite their progress, the evaluation of the agents often overlooks the complexities of real-world conversations, such as real-time interactions, multi-party dialogues, and extended contextual dependencies. To bridge this gap, we introduce DialSim, a real-time dialogue simulator. In this simulator, an agent is assigned the role of a character from popular TV shows, requiring it to respond to spontaneous questions using past dialogue information and to distinguish between known and unknown information. Key features of DialSim include assessing the agent's ability to respond within a reasonable time limit, handling long-term multi-party dialogues, and evaluating performance under randomized questioning with LongDialQA, a novel, high-quality question-answering dataset. Our experiments using DialSim reveal the strengths and weaknesses of the latest conversational agents, offering valuable insights for future advancements in conversational AI. DialSim is available at https://dialsim.github.io/.
Large Language Models are Biased Because They Are Large Language Models
Authors: Philip Resnik
Date: 2024-06-19 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model

This paper's primary goal is to provoke thoughtful discussion about the relationship between bias and fundamental properties of large language models. We do this by seeking to convince the reader that harmful biases are an inevitable consequence arising from the design of any large language model as LLMs are currently formulated. To the extent that this is true, it suggests that the problem of harmful bias cannot be properly addressed without a serious reconsideration of AI driven by LLMs, going back to the foundational assumptions underlying their design.
Oralytics Reinforcement Learning Algorithm
Authors: Anna L. Trella, Kelly W. Zhang, Stephanie M. Carpenter, David Elashoff, Zara M. Greer, Inbal Nahum-Shani, Dennis Ruenger, Vivek Shetty, Susan A. Murphy
Date: 2024-06-19 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Dental disease is still one of the most common chronic diseases in the United States. While dental disease is preventable through healthy oral self-care behaviors (OSCB), this basic behavior is not consistently practiced. We have developed Oralytics, an online, reinforcement learning (RL) algorithm that optimizes the delivery of personalized intervention prompts to improve OSCB. In this paper, we offer a full overview of algorithm design decisions made using prior data, domain expertise, and experiments in a simulation test bed. The finalized RL algorithm was deployed in the Oralytics clinical trial, conducted from fall 2023 to summer 2024.
A Unified Framework for Combinatorial Optimization Based on Graph Neural Networks
Authors: Yaochu Jin, Xueming Yan, Shiqing Liu, Xiangyu Wang
Date: 2024-06-19 00:00:00
Tasks: Combinatorial Optimization

Graph neural networks (GNNs) have emerged as a powerful tool for solving combinatorial optimization problems (COPs), exhibiting state-of-the-art performance in both graph-structured and non-graph-structured domains. However, existing approaches lack a unified framework capable of addressing a wide range of COPs. After presenting a summary of representative COPs and a brief review of recent advancements in GNNs for solving COPs, this paper proposes a unified framework for solving COPs based on GNNs, including graph representation of COPs, equivalent conversion of non-graph structured COPs to graph-structured COPs, graph decomposition, and graph simplification. The proposed framework leverages the ability of GNNs to effectively capture the relational information and extract features from the graph representation of COPs, offering a generic solution to COPs that can address the limitations of state-of-the-art in solving non-graph-structured and highly complex graph-structured COPs.
ViLCo-Bench: VIdeo Language COntinual learning Benchmark
Authors: Tianqi Tang, Shohreh Deldari, Hao Xue, Celso de Melo, Flora D. Salim
Date: 2024-06-19 00:00:00
Tasks: Continual Learning, Self-Supervised Learning

Video language continual learning involves continuously adapting to information from video and text inputs, enhancing a model's ability to handle new tasks while retaining prior knowledge. This field is a relatively under-explored area, and establishing appropriate datasets is crucial for facilitating communication and research in this field. In this study, we present the first dedicated benchmark, ViLCo-Bench, designed to evaluate continual learning models across a range of video-text tasks. The dataset comprises ten-minute-long videos and corresponding language queries collected from publicly available datasets. Additionally, we introduce a novel memory-efficient framework that incorporates self-supervised learning and mimics long-term and short-term memory effects. This framework addresses challenges including memory complexity from long video clips, natural language complexity from open queries, and text-video misalignment. We posit that ViLCo-Bench, with greater complexity compared to existing continual learning benchmarks, would serve as a critical tool for exploring the video-language domain, extending beyond conventional class-incremental tasks, and addressing complex and limited annotation issues. The curated data, evaluations, and our novel method are available at https://github.com/cruiseresearchgroup/ViLCo.
Can Long-Context Language Models Subsume Retrieval, RAG, SQL, and More?
Authors: Jinhyuk Lee, Anthony Chen, Zhuyun Dai, Dheeru Dua, Devendra Singh Sachan, Michael Boratko, Yi Luan, Sébastien M. R. Arnold, Vincent Perot, Siddharth Dalmia, Hexiang Hu, Xudong Lin, Panupong Pasupat, Aida Amini, Jeremy R. Cole, Sebastian Riedel, Iftekhar Naim, Ming-Wei Chang, Kelvin Guu
Date: 2024-06-19 00:00:00
Tasks: RAG, Retrieval

Long-context language models (LCLMs) have the potential to revolutionize our approach to tasks traditionally reliant on external tools like retrieval systems or databases. Leveraging LCLMs' ability to natively ingest and process entire corpora of information offers numerous advantages. It enhances user-friendliness by eliminating the need for specialized knowledge of tools, provides robust end-to-end modeling that minimizes cascading errors in complex pipelines, and allows for the application of sophisticated prompting techniques across the entire system. To assess this paradigm shift, we introduce LOFT, a benchmark of real-world tasks requiring context up to millions of tokens designed to evaluate LCLMs' performance on in-context retrieval and reasoning. Our findings reveal LCLMs' surprising ability to rival state-of-the-art retrieval and RAG systems, despite never having been explicitly trained for these tasks. However, LCLMs still face challenges in areas like compositional reasoning that are required in SQL-like tasks. Notably, prompting strategies significantly influence performance, emphasizing the need for continued research as context lengths grow. Overall, LOFT provides a rigorous testing ground for LCLMs, showcasing their potential to supplant existing paradigms and tackle novel tasks as model capabilities scale.
State-of-the-Art Review: The Use of Digital Twins to Support Artificial Intelligence-Guided Predictive Maintenance
Authors: Sizhe Ma, Katherine A. Flanigan, Mario Bergés
Date: 2024-06-19 00:00:00

In recent years, predictive maintenance (PMx) has gained prominence for its potential to enhance efficiency, automation, accuracy, and cost-effectiveness while reducing human involvement. Importantly, PMx has evolved in tandem with digital advancements, such as Big Data and the Internet of Things (IOT). These technological strides have enabled Artificial Intelligence (AI) to revolutionize PMx processes, with increasing capacities for real-time automation of monitoring, analysis, and prediction tasks. However, PMx still faces challenges such as poor explainability and sample inefficiency in data-driven methods and high complexity in physics-based models, hindering broader adoption. This paper posits that Digital Twins (DTs) can be integrated into PMx to overcome these challenges, paving the way for more automated PMx applications across various stakeholders. Despite their potential, current DTs have not fully matured to bridge existing gaps. Our paper provides a comprehensive roadmap for DT evolution, addressing current limitations to foster large-scale automated PMx progression. We structure our approach in three stages: First, we reference prior work where we identified and defined the Information Requirements (IRs) and Functional Requirements (FRs) for PMx, forming the blueprint for a unified framework. Second, we conduct a literature review to assess current DT applications integrating these IRs and FRs, revealing standardized DT models and tools that support automated PMx. Lastly, we highlight gaps in current DT implementations, particularly those IRs and FRs not fully supported, and outline the necessary components for a comprehensive, automated PMx system. Our paper concludes with research directions aimed at seamlessly integrating DTs into the PMx paradigm to achieve this ambitious vision.
Multi-Stage Balanced Distillation: Addressing Long-Tail Challenges in Sequence-Level Knowledge Distillation
Authors: YuHang Zhou, Jing Zhu, Paiheng Xu, Xiaoyu Liu, Xiyao Wang, Danai Koutra, Wei Ai, Furong Huang
Date: 2024-06-19 00:00:00
Tasks: Knowledge Distillation

Large language models (LLMs) have significantly advanced various natural language processing tasks, but deploying them remains computationally expensive. Knowledge distillation (KD) is a promising solution, enabling the transfer of capabilities from larger teacher LLMs to more compact student models. Particularly, sequence-level KD, which distills rationale-based reasoning processes instead of merely final outcomes, shows great potential in enhancing students' reasoning capabilities. However, current methods struggle with sequence level KD under long-tailed data distributions, adversely affecting generalization on sparsely represented domains. We introduce the Multi-Stage Balanced Distillation (BalDistill) framework, which iteratively balances training data within a fixed computational budget. By dynamically selecting representative head domain examples and synthesizing tail domain examples, BalDistill achieves state-of-the-art performance across diverse long-tailed datasets, enhancing both the efficiency and efficacy of the distilled models.
CU-Net: a U-Net architecture for efficient brain-tumor segmentation on BraTS 2019 dataset
Authors: Qimin Zhang, Weiwei Qi, Huili Zheng, Xinyu Shen
Date: 2024-06-19 00:00:00
Tasks: Brain Tumor Segmentation, Segmentation, Tumor Segmentation

Accurately segmenting brain tumors from MRI scans is important for developing effective treatment plans and improving patient outcomes. This study introduces a new implementation of the Columbia-University-Net (CU-Net) architecture for brain tumor segmentation using the BraTS 2019 dataset. The CU-Net model has a symmetrical U-shaped structure and uses convolutional layers, max pooling, and upsampling operations to achieve high-resolution segmentation. Our CU-Net model achieved a Dice score of 82.41%, surpassing two other state-of-the-art models. This improvement in segmentation accuracy highlights the robustness and effectiveness of the model, which helps to accurately delineate tumor boundaries, which is crucial for surgical planning and radiation therapy, and ultimately has the potential to improve patient outcomes.
Accelerating Complex Disease Treatment through Network Medicine and GenAI: A Case Study on Drug Repurposing for Breast Cancer
Authors: Ahmed Abdeen Hamed, Tamer E. Fandy
Date: 2024-06-18 00:00:00
Tasks: Prompt Engineering, Specificity

The objective of this research is to introduce a network specialized in predicting drugs that can be repurposed by investigating real-world evidence sources, such as clinical trials and biomedical literature. Specifically, it aims to generate drug combination therapies for complex diseases (e.g., cancer, Alzheimer's). We present a multilayered network medicine approach, empowered by a highly configured ChatGPT prompt engineering system, which is constructed on the fly to extract drug mentions in clinical trials. Additionally, we introduce a novel algorithm that connects real-world evidence with disease-specific signaling pathways (e.g., KEGG database). This sheds light on the repurposability of drugs if they are found to bind with one or more protein constituents of a signaling pathway. To demonstrate, we instantiated the framework for breast cancer and found that, out of 46 breast cancer signaling pathways, the framework identified 38 pathways that were covered by at least two drugs. This evidence signals the potential for combining those drugs. Specifically, the most covered signaling pathway, ID hsa:2064, was covered by 108 drugs, some of which can be combined. Conversely, the signaling pathway ID hsa:1499 was covered by only two drugs, indicating a significant gap for further research. Our network medicine framework, empowered by GenAI, shows promise in identifying drug combinations with a high degree of specificity, knowing the exact signaling pathways and proteins that serve as targets. It is noteworthy that ChatGPT successfully accelerated the process of identifying drug mentions in clinical trials, though further investigations are required to determine the relationships among the drug mentions.
A Generic Method for Fine-grained Category Discovery in Natural Language Texts
Authors: Chang Tian, Matthew B. Blaschko, Wenpeng Yin, Mingzhe Xing, Yinliang Yue, Marie-Francine Moens
Date: 2024-06-18 00:00:00
Tasks: Contrastive Learning

Fine-grained category discovery using only coarse-grained supervision is a cost-effective yet challenging task. Previous training methods focus on aligning query samples with positive samples and distancing them from negatives. They often neglect intra-category and inter-category semantic similarities of fine-grained categories when navigating sample distributions in the embedding space. Furthermore, some evaluation techniques that rely on pre-collected test samples are inadequate for real-time applications. To address these shortcomings, we introduce a method that successfully detects fine-grained clusters of semantically similar texts guided by a novel objective function. The method uses semantic similarities in a logarithmic space to guide sample distributions in the Euclidean space and to form distinct clusters that represent fine-grained categories. We also propose a centroid inference mechanism to support real-time applications. The efficacy of the method is both theoretically justified and empirically confirmed on three benchmark tasks. The proposed objective function is integrated in multiple contrastive learning based neural models. Its results surpass existing state-of-the-art approaches in terms of Accuracy, Adjusted Rand Index and Normalized Mutual Information of the detected fine-grained categories. Code and data will be available at https://github.com/XX upon publication.
Exploring and Benchmarking the Planning Capabilities of Large Language Models
Authors: Bernd Bohnet, Azade Nova, Aaron T Parisi, Kevin Swersky, Katayoon Goshvadi, Hanjun Dai, Dale Schuurmans, Noah Fiedel, Hanie Sedghi
Date: 2024-06-18 00:00:00
Tasks: Benchmarking, In-Context Learning

Classical and natural language planning tasks remain a difficult domain for modern large language models (LLMs). In this work, we lay the foundations for improving planning capabilities of LLMs. First, we construct a comprehensive benchmark suite encompassing both classical planning benchmarks and natural language scenarios. This suite includes algorithms to methodically generate instances of tasks with varying levels of difficulty, allowing for rigorous and systematic evaluation of LLM performance. Next, we investigate the use of many-shot in-context learning to enhance LLM planning, exploring the relationship between increased context length and improved planning performance. In addition, we demonstrate the positive impact of fine-tuning LLMs on optimal planning paths. We also probe the efficacy of chain-of-thought reasoning methods to improve LLM planning performance. Moreover, we probe the performance of the proposed methods in out-of-distribution scenarios, assessing the ability to generalize to novel and unseen planning challenges. Finally, we investigate model's failure modes and reveal insights that hold true across different benchmarks.
RITA: A Real-time Interactive Talking Avatars Framework
Authors: Wuxinlin Cheng, Cheng Wan, Yupeng Cao, Sihan Chen
Date: 2024-06-18 00:00:00

RITA presents a high-quality real-time interactive framework built upon generative models, designed with practical applications in mind. Our framework enables the transformation of user-uploaded photos into digital avatars that can engage in real-time dialogue interactions. By leveraging the latest advancements in generative modeling, we have developed a versatile platform that not only enhances the user experience through dynamic conversational avatars but also opens new avenues for applications in virtual reality, online education, and interactive gaming. This work showcases the potential of integrating computer vision and natural language processing technologies to create immersive and interactive digital personas, pushing the boundaries of how we interact with digital content.