pwc-archive/papers-with-abstracts huggingface dataset:
Learning the rules of peptide self-assembly through data mining with large language models
Authors: Zhenze Yang, Sarah K. Yorke, Tuomas P. J. Knowles, Markus J. Buehler
Date: 2024-11-08 00:00:00
Tasks: Large Language Model, Literature Mining

Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external environmental stimuli on the self-assembly behaviour of these systems. However, there is yet to be a systematic study that gathers this rich literature data and collectively examines these experimental factors to provide a global picture of the fundamental rules that govern protein self-assembly behavior. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining facilitated by a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the collected data, ML models are trained and evaluated, demonstrating excellent accuracy (>80\%) and efficiency in peptide assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. We find that this workflow can substantially improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly. In doing so, novel structures can be accessed for a range of applications including sensing, catalysis and biomaterials.
WeatherGFM: Learning A Weather Generalist Foundation Model via In-context Learning
Authors: Xiangyu Zhao, Zhiwang Zhou, Wenlong Zhang, Yihao Liu, Xiangyu Chen, Junchao Gong, Hao Chen, Ben Fei, Shiqi Chen, Wanli Ouyang, Xiao-Ming Wu, Lei Bai
Date: 2024-11-08 00:00:00
Tasks: In-Context Learning, Question Answering, Super-Resolution, Visual Prompting, Weather Forecasting

The Earth's weather system encompasses intricate weather data modalities and diverse weather understanding tasks, which hold significant value to human life. Existing data-driven models focus on single weather understanding tasks (e.g., weather forecasting). Although these models have achieved promising results, they fail to tackle various complex tasks within a single and unified model. Moreover, the paradigm that relies on limited real observations for a single scenario hinders the model's performance upper bound. In response to these limitations, we draw inspiration from the in-context learning paradigm employed in state-of-the-art visual foundation models and large language models. In this paper, we introduce the first generalist weather foundation model (WeatherGFM), designed to address a wide spectrum of weather understanding tasks in a unified manner. More specifically, we initially unify the representation and definition of the diverse weather understanding tasks. Subsequently, we devised weather prompt formats to manage different weather data modalities, namely single, multiple, and temporal modalities. Finally, we adopt a visual prompting question-answering paradigm for the training of unified weather understanding tasks. Extensive experiments indicate that our WeatherGFM can effectively handle up to ten weather understanding tasks, including weather forecasting, super-resolution, weather image translation, and post-processing. Our method also showcases generalization ability on unseen tasks.
Web Archives Metadata Generation with GPT-4o: Challenges and Insights
Authors: Ashwin Nair, Zhen Rong Goh, Tianrui Liu, Abigail Yongping Huang
Date: 2024-11-08 00:00:00
Tasks: Prompt Engineering

Current metadata creation for web archives is time consuming and costly due to reliance on human effort. This paper explores the use of gpt-4o for metadata generation within the Web Archive Singapore, focusing on scalability, efficiency, and cost effectiveness. We processed 112 Web ARChive (WARC) files using data reduction techniques, achieving a notable 99.9% reduction in metadata generation costs. By prompt engineering, we generated titles and abstracts, which were evaluated both intrinsically using Levenshtein Distance and BERTScore, and extrinsically with human cataloguers using McNemar's test. Results indicate that while our method offers significant cost savings and efficiency gains, human curated metadata maintains an edge in quality. The study identifies key challenges including content inaccuracies, hallucinations, and translation issues, suggesting that Large Language Models (LLMs) should serve as complements rather than replacements for human cataloguers. Future work will focus on refining prompts, improving content filtering, and addressing privacy concerns through experimentation with smaller models. This research advances the integration of LLMs in web archiving, offering valuable insights into their current capabilities and outlining directions for future enhancements. The code is available at https://github.com/masamune-prog/warc2summary for further development and use by institutions facing similar challenges.
Benchmarking Distributional Alignment of Large Language Models
Authors: Nicole Meister, Carlos Guestrin, Tatsunori Hashimoto
Date: 2024-11-08 00:00:00
Tasks: Benchmarking

Language models (LMs) are increasingly used as simulacra for people, yet their ability to match the distribution of views of a specific demographic group and be \textit{distributionally aligned} remains uncertain. This notion of distributional alignment is complex, as there is significant variation in the types of attributes that are simulated. Prior works have underexplored the role of three critical variables -- the question domain, steering method, and distribution expression method -- which motivates our contribution of a benchmark explicitly addressing these dimensions. We construct a dataset expanding beyond political values, create human baselines for this task, and evaluate the extent to which an LM can align with a particular group's opinion distribution to inform design choices of such simulation systems. Our analysis reveals open problems regarding if, and how, LMs can be used to simulate humans, and that LLMs can more accurately describe the opinion distribution than simulate such distributions.
Advancing Meteorological Forecasting: AI-based Approach to Synoptic Weather Map Analysis
Authors: Yo-Hwan Choi, Seon-Yu Kang, Minjong Cheon
Date: 2024-11-08 00:00:00
Tasks: Weather Forecasting

As global warming increases the complexity of weather patterns; the precision of weather forecasting becomes increasingly important. Our study proposes a novel preprocessing method and convolutional autoencoder model developed to improve the interpretation of synoptic weather maps. These are critical for meteorologists seeking a thorough understanding of weather conditions. This model could recognize historical synoptic weather maps that nearly match current atmospheric conditions, marking a significant step forward in modern technology in meteorological forecasting. This comprises unsupervised learning models like VQ-VQE, as well as supervised learning models like VGG16, VGG19, Xception, InceptionV3, and ResNet50 trained on the ImageNet dataset, as well as research into newer models like EfficientNet and ConvNeXt. Our findings proved that, while these models perform well in various settings, their ability to identify comparable synoptic weather maps has certain limits. Our research, motivated by the primary goal of significantly increasing meteorologists' efficiency in labor-intensive tasks, discovered that cosine similarity is the most effective metric, as determined by a combination of quantitative and qualitative assessments to accurately identify relevant historical weather patterns. This study broadens our understanding by shifting the emphasis from numerical precision to practical application, ensuring that our model is effective in theory practical, and accessible in the complex and dynamic field of meteorology.
Ev2R: Evaluating Evidence Retrieval in Automated Fact-Checking
Authors: Mubashara Akhtar, Michael Schlichtkrull, Andreas Vlachos
Date: 2024-11-08 00:00:00
Tasks: Fact Checking, nlg evaluation, Retrieval, Text Generation

Current automated fact-checking (AFC) approaches commonly evaluate evidence either implicitly via the predicted verdicts or by comparing retrieved evidence with a predefined closed knowledge source, such as Wikipedia. However, these methods suffer from limitations, resulting from their reliance on evaluation metrics developed for different purposes and constraints imposed by closed knowledge sources. Recent advances in natural language generation (NLG) evaluation offer new possibilities for evidence assessment. In this work, we introduce Ev2R, an evaluation framework for AFC that comprises three types of approaches for evidence evaluation: reference-based, proxy-reference, and reference-less. We evaluate their effectiveness through agreement with human ratings and adversarial tests, and demonstrate that prompt-based scorers, particularly those leveraging LLMs and reference evidence, outperform traditional evaluation approaches.
Agricultural Landscape Understanding At Country-Scale
Authors: Radhika Dua, Nikita Saxena, Aditi Agarwal, Alex Wilson, Gaurav Singh, Hoang Tran, Ishan Deshpande, Amandeep Kaur, Gaurav Aggarwal, Chandan Nath, Arnab Basu, Vishal Batchu, Sharath Holla, Bindiya Kurle, Olana Missura, Rahul Aggarwal, Shubhika Garg, Nishi Shah, Avneet Singh, Dinesh Tewari, Agata Dondzik, Bharat Adsul, Milind Sohoni, Asim Rama Praveen, Aaryan Dangi, Lisan Kadivar, E Abhishek, Niranjan Sudhansu, Kamlakar Hattekar, Sameer Datar, Musty Krishna Chaithanya, Anumas Ranjith Reddy, Aashish Kumar, Betala Laxmi Tirumala, Alok Talekar
Date: 2024-11-08 00:00:00
Tasks: Decision Making, Panoptic Segmentation

Agricultural landscapes are quite complex, especially in the Global South where fields are smaller, and agricultural practices are more varied. In this paper we report on our progress in digitizing the agricultural landscape (natural and man-made) in our study region of India. We use high resolution imagery and a UNet style segmentation model to generate the first of its kind national-scale multi-class panoptic segmentation output. Through this work we have been able to identify individual fields across 151.7M hectares, and delineating key features such as water resources and vegetation. We share how this output was validated by our team and externally by downstream users, including some sample use cases that can lead to targeted data driven decision making. We believe this dataset will contribute towards digitizing agriculture by generating the foundational baselayer.
Controlling Grokking with Nonlinearity and Data Symmetry
Authors: Ahmed Salah, David Yevick
Date: 2024-11-08 00:00:00

This paper demonstrates that grokking behavior in modular arithmetic with a modulus P in a neural network can be controlled by modifying the profile of the activation function as well as the depth and width of the model. Plotting the even PCA projections of the weights of the last NN layer against their odd projections further yields patterns which become significantly more uniform when the nonlinearity is increased by incrementing the number of layers. These patterns can be employed to factor P when P is nonprime. Finally, a metric for the generalization ability of the network is inferred from the entropy of the layer weights while the degree of nonlinearity is related to correlations between the local entropy of the weights of the neurons in the final layer.
Enhancing Cluster Resilience: LLM-agent Based Autonomous Intelligent Cluster Diagnosis System and Evaluation Framework
Authors: Honghao Shi, Longkai Cheng, Wenli Wu, Yuhang Wang, Xuan Liu, Shaokai Nie, Weixv Wang, Xuebin Min, Chunlei Men, Yonghua Lin
Date: 2024-11-08 00:00:00
Tasks: RAG, Retrieval, Retrieval-augmented Generation

Recent advancements in Large Language Models (LLMs) and related technologies such as Retrieval-Augmented Generation (RAG) and Diagram of Thought (DoT) have enabled the creation of autonomous intelligent systems capable of performing cluster diagnostics and troubleshooting. By integrating these technologies with self-play methodologies, we have developed an LLM-agent system designed to autonomously diagnose and resolve issues within AI clusters. Our innovations include a knowledge base tailored for cluster diagnostics, enhanced LLM algorithms, practical deployment strategies for agents, and a benchmark specifically designed for evaluating LLM capabilities in this domain. Through extensive experimentation across multiple dimensions, we have demonstrated the superiority of our system in addressing the challenges faced in cluster diagnostics, particularly in detecting and rectifying performance issues more efficiently and accurately than traditional methods.
LLM-PySC2: Starcraft II learning environment for Large Language Models
Authors: Zongyuan Li, Yanan Ni, Runnan Qi, Lumin Jiang, Chang Lu, Xiaojie Xu, Xiangbei Liu, Pengfei Li, Yunzheng Guo, Zhe Ma, Xian Guo, Kuihua Huang, Xuebo Zhang
Date: 2024-11-08 00:00:00
Tasks: Decision Making, Language Modelling, Large Language Model, SMAC, SMAC+, Starcraft, Starcraft II

This paper introduces a new environment LLM-PySC2 (the Large Language Model StarCraft II Learning Environment), a platform derived from DeepMind's StarCraft II Learning Environment that serves to develop Large Language Models (LLMs) based decision-making methodologies. This environment is the first to offer the complete StarCraft II action space, multi-modal observation interfaces, and a structured game knowledge database, which are seamlessly connected with various LLMs to facilitate the research of LLMs-based decision-making. To further support multi-agent research, we developed an LLM collaborative framework that supports multi-agent concurrent queries and multi-agent communication. In our experiments, the LLM-PySC2 environment is adapted to be compatible with the StarCraft Multi-Agent Challenge (SMAC) task group and provided eight new scenarios focused on macro-decision abilities. We evaluated nine mainstream LLMs in the experiments, and results show that sufficient parameters are necessary for LLMs to make decisions, but improving reasoning ability does not directly lead to better decision-making outcomes. Our findings further indicate the importance of enabling large models to learn autonomously in the deployment environment through parameter training or train-free learning techniques. Ultimately, we expect that the LLM-PySC2 environment can promote research on learning methods for LLMs, helping LLM-based methods better adapt to task scenarios.
Reasoning Robustness of LLMs to Adversarial Typographical Errors
Authors: Esther Gan, Yiran Zhao, Liying Cheng, Yancan Mao, Anirudh Goyal, Kenji Kawaguchi, Min-Yen Kan, Michael Shieh
Date: 2024-11-08 00:00:00
Tasks: GSM8K, MMLU

Large Language Models (LLMs) have demonstrated impressive capabilities in reasoning using Chain-of-Thought (CoT) prompting. However, CoT can be biased by users' instruction. In this work, we study the reasoning robustness of LLMs to typographical errors, which can naturally occur in users' queries. We design an Adversarial Typo Attack ($\texttt{ATA}$) algorithm that iteratively samples typos for words that are important to the query and selects the edit that is most likely to succeed in attacking. It shows that LLMs are sensitive to minimal adversarial typographical changes. Notably, with 1 character edit, Mistral-7B-Instruct's accuracy drops from 43.7% to 38.6% on GSM8K, while with 8 character edits the performance further drops to 19.2%. To extend our evaluation to larger and closed-source LLMs, we develop the $\texttt{R$^2$ATA}$ benchmark, which assesses models' $\underline{R}$easoning $\underline{R}$obustness to $\underline{\texttt{ATA}}$. It includes adversarial typographical questions derived from three widely used reasoning datasets-GSM8K, BBH, and MMLU-by applying $\texttt{ATA}$ to open-source LLMs. $\texttt{R$^2$ATA}$ demonstrates remarkable transferability and causes notable performance drops across multiple super large and closed-source LLMs.
Improving Multi-Domain Task-Oriented Dialogue System with Offline Reinforcement Learning
Authors: Dharmendra Prajapat, Durga Toshniwal
Date: 2024-11-08 00:00:00
Tasks: Language Modeling, Language Modelling, Reinforcement Learning (RL)

Task-oriented dialogue (TOD) system is designed to accomplish user-defined tasks through dialogues. The TOD system has progressed towards end-to-end modeling by leveraging pre-trained large language models. Fine-tuning the pre-trained language models using only supervised learning leads to the exposure bias and token loss problem and it deviates the models from completing the user's task. To address these issues, we propose a TOD system that leverages a unified pre-trained language model, GPT2, as a base model. It is optimized using supervised learning and reinforcement learning (RL). The issues in the TOD system are mitigated using a non-differentiable reward function. The reward is calculated using the weighted sum of the success rate and BLEU evaluation metrics. The success rate and BLEU metrics in reward calculation guide the language model for user task completion while ensuring a coherent and fluent response. Our model is acquired by fine-tuning a pre-trained model on the dialogue-session level which comprises user utterance, belief state, system act, and system response. Experimental results on MultiWOZ2.1 demonstrate that our model increases the inform rate by 1.60% and the success rate by 3.17% compared to the baseline.
Inversion-based Latent Bayesian Optimization
Authors: Jaewon Chu, Jinyoung Park, Seunghun Lee, Hyunwoo J. Kim
Date: 2024-11-08 00:00:00
Tasks: Bayesian Optimization, Decoder

Latent Bayesian optimization (LBO) approaches have successfully adopted Bayesian optimization over a continuous latent space by employing an encoder-decoder architecture to address the challenge of optimization in a high dimensional or discrete input space. LBO learns a surrogate model to approximate the black-box objective function in the latent space. However, we observed that most LBO methods suffer from the `misalignment problem`, which is induced by the reconstruction error of the encoder-decoder architecture. It hinders learning an accurate surrogate model and generating high-quality solutions. In addition, several trust region-based LBO methods select the anchor, the center of the trust region, based solely on the objective function value without considering the trust region`s potential to enhance the optimization process. To address these issues, we propose Inversion-based Latent Bayesian Optimization (InvBO), a plug-and-play module for LBO. InvBO consists of two components: an inversion method and a potential-aware trust region anchor selection. The inversion method searches the latent code that completely reconstructs the given target data. The potential-aware trust region anchor selection considers the potential capability of the trust region for better local optimization. Experimental results demonstrate the effectiveness of InvBO on nine real-world benchmarks, such as molecule design and arithmetic expression fitting tasks. Code is available at https://github.com/mlvlab/InvBO.
Aligning Large Language Models and Geometric Deep Models for Protein Representation
Authors: Dong Shu, Bingbing Duan, Kai Guo, Kaixiong Zhou, Jiliang Tang, Mengnan Du
Date: 2024-11-08 00:00:00

Latent representation alignment has become a foundational technique for constructing multimodal large language models (MLLM) by mapping embeddings from different modalities into a shared space, often aligned with the embedding space of large language models (LLMs) to enable effective cross-modal understanding. While preliminary protein-focused MLLMs have emerged, they have predominantly relied on heuristic approaches, lacking a fundamental understanding of optimal alignment practices across representations. In this study, we explore the alignment of multimodal representations between LLMs and Geometric Deep Models (GDMs) in the protein domain. We comprehensively evaluate three state-of-the-art LLMs (Gemma2-2B, LLaMa3.1-8B, and LLaMa3.1-70B) with four protein-specialized GDMs (GearNet, GVP, ScanNet, GAT). Our work examines alignment factors from both model and protein perspectives, identifying challenges in current alignment methodologies and proposing strategies to improve the alignment process. Our key findings reveal that GDMs incorporating both graph and 3D structural information align better with LLMs, larger LLMs demonstrate improved alignment capabilities, and protein rarity significantly impacts alignment performance. We also find that increasing GDM embedding dimensions, using two-layer projection heads, and fine-tuning LLMs on protein-specific data substantially enhance alignment quality. These strategies offer potential enhancements to the performance of protein-related multimodal models. Our code and data are available at https://github.com/Tizzzzy/LLM-GDM-alignment.
Revisiting Network Perturbation for Semi-Supervised Semantic Segmentation
Authors: Sien Li, Tao Wang, Ruizhe Hu, Wenxi Liu
Date: 2024-11-08 00:00:00
Tasks: Semantic Segmentation, Semi-Supervised Semantic Segmentation

In semi-supervised semantic segmentation (SSS), weak-to-strong consistency regularization techniques are widely utilized in recent works, typically combined with input-level and feature-level perturbations. However, the integration between weak-to-strong consistency regularization and network perturbation has been relatively rare. We note several problems with existing network perturbations in SSS that may contribute to this phenomenon. By revisiting network perturbations, we introduce a new approach for network perturbation to expand the existing weak-to-strong consistency regularization for unlabeled data. Additionally, we present a volatile learning process for labeled data, which is uncommon in existing research. Building upon previous work that includes input-level and feature-level perturbations, we present MLPMatch (Multi-Level-Perturbation Match), an easy-to-implement and efficient framework for semi-supervised semantic segmentation. MLPMatch has been validated on the Pascal VOC and Cityscapes datasets, achieving state-of-the-art performance. Code is available from https://github.com/LlistenL/MLPMatch.
On Training of Kolmogorov-Arnold Networks
Authors: Shairoz Sohail
Date: 2024-11-08 00:00:00
Tasks: Kolmogorov-Arnold Networks

Kolmogorov-Arnold Networks have recently been introduced as a flexible alternative to multi-layer Perceptron architectures. In this paper, we examine the training dynamics of different KAN architectures and compare them with corresponding MLP formulations. We train with a variety of different initialization schemes, optimizers, and learning rates, as well as utilize back propagation free approaches like the HSIC Bottleneck. We find that (when judged by test accuracy) KANs are an effective alternative to MLP architectures on high-dimensional datasets and have somewhat better parameter efficiency, but suffer from more unstable training dynamics. Finally, we provide recommendations for improving training stability of larger KAN models.