pwc-archive/papers-with-abstracts huggingface dataset:
Explainable Deep Learning Framework for SERS Bio-quantification
Authors: Jihan K. Zaki, Jakub Tomasik, Jade A. McCune, Sabine Bahn, Pietro Liò, Oren A. Scherman
Date: 2024-11-12 00:00:00
Tasks: Deep Learning, Denoising

Surface-enhanced Raman spectroscopy (SERS) is a potential fast and inexpensive method of analyte quantification, which can be combined with deep learning to discover biomarker-disease relationships. This study aims to address present challenges of SERS through a novel SERS bio-quantification framework, including spectral processing, analyte quantification, and model explainability. To this end,serotonin quantification in urine media was assessed as a model task with 682 SERS spectra measured in a micromolar range using cucurbit[8]uril chemical spacers. A denoising autoencoder was utilized for spectral enhancement, and convolutional neural networks (CNN) and vision transformers were utilized for biomarker quantification. Lastly, a novel context representative interpretable model explanations (CRIME) method was developed to suit the current needs of SERS mixture analysis explainability. Serotonin quantification was most efficient in denoised spectra analysed using a convolutional neural network with a three-parameter logistic output layer (mean absolute error = 0.15 {\mu}M, mean percentage error = 4.67%). Subsequently, the CRIME method revealed the CNN model to present six prediction contexts, of which three were associated with serotonin. The proposed framework could unlock a novel, untargeted hypothesis generating method of biomarker discovery considering the rapid and inexpensive nature of SERS measurements, and the potential to identify biomarkers from CRIME contexts.
Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+
Authors: Ethan Weinberger, Ryan Conrad, Tal Ashuach
Date: 2024-11-11 00:00:00

Genetic screens mediated via CRISPR-Cas9 combined with high-content readouts have emerged as powerful tools for biological discovery. However, computational analyses of these screens come with additional challenges beyond those found with standard scRNA-seq analyses. For example, perturbation-induced variations of interest may be subtle and masked by other dominant source of variation shared with controls, and variable guide efficiency results in some cells not undergoing genetic perturbation despite expressing a guide RNA. While a number of methods have been developed to address the former problem by explicitly disentangling perturbation-induced variations from those shared with controls, less attention has been paid to the latter problem of noisy perturbation labels. To address this issue, here we propose ContrastiveVI+, a generative modeling framework that both disentangles perturbation-induced from non-perturbation-related variations while also inferring whether cells truly underwent genomic edits. Applied to three large-scale Perturb-seq datasets, we find that ContrastiveVI+ better recovers known perturbation-induced variations compared to previous methods while successfully identifying cells that escaped the functional consequences of guide RNA expression. An open-source implementation of our model is available at \url{https://github.com/insitro/contrastive_vi_plus}.
Intelligent Green Efficiency for Intrusion Detection
Authors: Pedro Pereira, Paulo Mendes, João Vitorino, Eva Maia, Isabel Praça
Date: 2024-11-11 00:00:00
Tasks: Computational Efficiency, feature selection, Intrusion Detection, Network Intrusion Detection

Artificial Intelligence (AI) has emerged in popularity recently, recording great progress in various industries. However, the environmental impact of AI is a growing concern, in terms of the energy consumption and carbon footprint of Machine Learning (ML) and Deep Learning (DL) models, making essential investigate Green AI, an attempt to reduce the climate impact of AI systems. This paper presents an assessment of different programming languages and Feature Selection (FS) methods to improve computation performance of AI focusing on Network Intrusion Detection (NID) and cyber-attack classification tasks. Experiments were conducted using five ML models - Random Forest, XGBoost, LightGBM, Multi-Layer Perceptron, and Long Short-Term Memory - implemented in four programming languages - Python, Java, R, and Rust - along with three FS methods - Information Gain, Recursive Feature Elimination, and Chi-Square. The obtained results demonstrated that FS plays an important role enhancing the computational efficiency of AI models without compromising detection accuracy, highlighting languages like Python and R, that benefit from a rich AI libraries environment. These conclusions can be useful to design efficient and sustainable AI systems that still provide a good generalization and a reliable detection.
CamemBERT 2.0: A Smarter French Language Model Aged to Perfection
Authors: Wissam Antoun, Francis Kulumba, Rian Touchent, Éric de la Clergerie, Benoît Sagot, Djamé Seddah
Date: 2024-11-13 00:00:00
Tasks: Language Modeling, Language Modelling, Masked Language Modeling

French language models, such as CamemBERT, have been widely adopted across industries for natural language processing (NLP) tasks, with models like CamemBERT seeing over 4 million downloads per month. However, these models face challenges due to temporal concept drift, where outdated training data leads to a decline in performance, especially when encountering new topics and terminology. This issue emphasizes the need for updated models that reflect current linguistic trends. In this paper, we introduce two new versions of the CamemBERT base model-CamemBERTav2 and CamemBERTv2-designed to address these challenges. CamemBERTav2 is based on the DeBERTaV3 architecture and makes use of the Replaced Token Detection (RTD) objective for better contextual understanding, while CamemBERTv2 is built on RoBERTa, which uses the Masked Language Modeling (MLM) objective. Both models are trained on a significantly larger and more recent dataset with longer context length and an updated tokenizer that enhances tokenization performance for French. We evaluate the performance of these models on both general-domain NLP tasks and domain-specific applications, such as medical field tasks, demonstrating their versatility and effectiveness across a range of use cases. Our results show that these updated models vastly outperform their predecessors, making them valuable tools for modern NLP systems. All our new models, as well as intermediate checkpoints, are made openly available on Huggingface.
Multi-Perspective Stance Detection
Authors: Benedetta Muscato, Praveen Bushipaka, Gizem Gezici, Lucia Passaro, Fosca Giannotti
Date: 2024-11-13 00:00:00
Tasks: Classification, Diversity, Stance Detection

Subjective NLP tasks usually rely on human annotations provided by multiple annotators, whose judgments may vary due to their diverse backgrounds and life experiences. Traditional methods often aggregate multiple annotations into a single ground truth, disregarding the diversity in perspectives that arises from annotator disagreement. In this preliminary study, we examine the effect of including multiple annotations on model accuracy in classification. Our methodology investigates the performance of perspective-aware classification models in stance detection task and further inspects if annotator disagreement affects the model confidence. The results show that multi-perspective approach yields better classification performance outperforming the baseline which uses the single label. This entails that designing more inclusive perspective-aware AI models is not only an essential first step in implementing responsible and ethical AI, but it can also achieve superior results than using the traditional approaches.
A Comparative Study of Discrete Speech Tokens for Semantic-Related Tasks with Large Language Models
Authors: Dingdong Wang, Mingyu Cui, Dongchao Yang, Xueyuan Chen, Helen Meng
Date: 2024-11-13 00:00:00

With the rise of Speech Large Language Models (Speech LLMs), there has been growing interest in discrete speech tokens for their ability to integrate with text-based tokens seamlessly. Compared to most studies that focus on continuous speech features, although discrete-token based LLMs have shown promising results on certain tasks, the performance gap between these two paradigms is rarely explored. In this paper, we present a fair and thorough comparison between discrete and continuous features across a variety of semantic-related tasks using a light-weight LLM (Qwen1.5-0.5B). Our findings reveal that continuous features generally outperform discrete tokens, particularly in tasks requiring fine-grained semantic understanding. Moreover, this study goes beyond surface-level comparison by identifying key factors behind the under-performance of discrete tokens, such as limited token granularity and inefficient information retention. To enhance the performance of discrete tokens, we explore potential aspects based on our analysis. We hope our results can offer new insights into the opportunities for advancing discrete speech tokens in Speech LLMs.
Dynamic Rewarding with Prompt Optimization Enables Tuning-free Self-Alignment of Language Models
Authors: Somanshu Singla, Zhen Wang, Tianyang Liu, Abdullah Ashfaq, Zhiting Hu, Eric P. Xing
Date: 2024-11-13 00:00:00

Aligning Large Language Models (LLMs) traditionally relies on costly training and human preference annotations. Self-alignment seeks to reduce these expenses by enabling models to align themselves. To further lower costs and achieve alignment without any expensive tuning or annotations, we introduce a new tuning-free approach for self-alignment, Dynamic Rewarding with Prompt Optimization (DRPO). Our approach leverages a search-based optimization framework that allows LLMs to iteratively self-improve and craft the optimal alignment instructions, all without additional training or human intervention. The core of DRPO is a dynamic rewarding mechanism, which identifies and rectifies model-specific alignment weaknesses, allowing LLMs to adapt efficiently to diverse alignment challenges. Empirical evaluations on eight recent LLMs, both open- and closed-sourced, demonstrate that DRPO significantly enhances alignment performance, with base models outperforming their SFT/RLHF-tuned counterparts. Moreover, the prompts automatically optimized by DRPO surpass those curated by human experts, further validating the effectiveness of our approach. Our findings highlight the great potential of current LLMs to achieve adaptive self-alignment through inference-time optimization, complementing tuning-based alignment methods.
Analyst Reports and Stock Performance: Evidence from the Chinese Market
Authors: Rui Liu, Jiayou Liang, Haolong Chen, Yujia Hu
Date: 2024-11-13 00:00:00
Tasks: Sentiment Analysis

This article applies natural language processing (NLP) to extract and quantify textual information to predict stock performance. Using an extensive dataset of Chinese analyst reports and employing a customized BERT deep learning model for Chinese text, this study categorizes the sentiment of the reports as positive, neutral, or negative. The findings underscore the predictive capacity of this sentiment indicator for stock volatility, excess returns, and trading volume. Specifically, analyst reports with strong positive sentiment will increase excess return and intraday volatility, and vice versa, reports with strong negative sentiment also increase volatility and trading volume, but decrease future excess return. The magnitude of this effect is greater for positive sentiment reports than for negative sentiment reports. This article contributes to the empirical literature on sentiment analysis and the response of the stock market to news in the Chinese stock market.
Are Triggers Needed for Document-Level Event Extraction?
Authors: Shaden Shaar, Wayne Chen, Maitreyi Chatterjee, Barry Wang, Wenting Zhao, Claire Cardie
Date: 2024-11-13 00:00:00
Tasks: Document-level Event Extraction, Event Extraction, Sentence

Most existing work on event extraction has focused on sentence-level texts and presumes the identification of a trigger-span -- a word or phrase in the input that evokes the occurrence of an event of interest. Event arguments are then extracted with respect to the trigger. Indeed, triggers are treated as integral to, and trigger detection as an essential component of, event extraction. In this paper, we provide the first investigation of the role of triggers for the more difficult and much less studied task of document-level event extraction. We analyze their usefulness in multiple end-to-end and pipelined neural event extraction models for three document-level event extraction datasets, measuring performance using triggers of varying quality (human-annotated, LLM-generated, keyword-based, and random). Our research shows that trigger effectiveness varies based on the extraction task's characteristics and data quality, with basic, automatically-generated triggers serving as a viable alternative to human-annotated ones. Furthermore, providing detailed event descriptions to the extraction model helps maintain robust performance even when trigger quality degrades. Perhaps surprisingly, we also find that the mere existence of trigger input, even random ones, is important for prompt-based LLM approaches to the task.
Theoretical Analysis of Byte-Pair Encoding
Authors: László Kozma, Johannes Voderholzer
Date: 2024-11-13 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model, Machine Translation, Text Compression

Byte-Pair Encoding (BPE) is a widely used method for subword tokenization, with origins in grammar-based text compression. It is employed in a variety of language processing tasks such as machine translation or large language model (LLM) pretraining, to create a token dictionary of a prescribed size. Most evaluations of BPE to date are empirical, and the reasons for its good practical performance are not well understood. In this paper we focus on the optimization problem underlying BPE: finding a pair encoding that achieves optimal compression utility. We show that this problem is APX-complete, indicating that it is unlikely to admit a polynomial-time approximation scheme. This answers, in a stronger form, a question recently raised by Zouhar et al. On the positive side, we show that BPE approximates the compression utility of the optimal pair encoding to a worst-case factor between $0.333$ and $0.625$. Our results aim to explain the ongoing success of BPE and are, to our knowledge, the first rigorous guarantees on its compression utility that hold for all inputs.
CorrSynth -- A Correlated Sampling Method for Diverse Dataset Generation from LLMs
Authors: Suhas S Kowshik, Abhishek Divekar, Vijit Malik
Date: 2024-11-13 00:00:00
Tasks: Dataset Generation, Diversity

Large language models (LLMs) have demonstrated remarkable performance in diverse tasks using zero-shot and few-shot prompting. Even though their capabilities of data synthesis have been studied well in recent years, the generated data suffers from a lack of diversity, less adherence to the prompt, and potential biases that creep into the data from the generator model. In this work, we tackle the challenge of generating datasets with high diversity, upon which a student model is trained for downstream tasks. Taking the route of decoding-time guidance-based approaches, we propose CorrSynth, which generates data that is more diverse and faithful to the input prompt using a correlated sampling strategy. Further, our method overcomes the complexity drawbacks of some other guidance-based techniques like classifier-based guidance. With extensive experiments, we show the effectiveness of our approach and substantiate our claims. In particular, we perform intrinsic evaluation to show the improvements in diversity. Our experiments show that CorrSynth improves both student metrics and intrinsic metrics upon competitive baselines across four datasets, showing the innate advantage of our method.
Neural Topic Modeling with Large Language Models in the Loop
Authors: Xiaohao Yang, He Zhao, Weijie Xu, Yuanyuan Qi, Jueqing Lu, Dinh Phung, Lan Du
Date: 2024-11-13 00:00:00
Tasks: Topic coverage, Topic Models

Topic modeling is a fundamental task in natural language processing, allowing the discovery of latent thematic structures in text corpora. While Large Language Models (LLMs) have demonstrated promising capabilities in topic discovery, their direct application to topic modeling suffers from issues such as incomplete topic coverage, misalignment of topics, and inefficiency. To address these limitations, we propose LLM-ITL, a novel LLM-in-the-loop framework that integrates LLMs with Neural Topic Models (NTMs). In LLM-ITL, global topics and document representations are learned through the NTM. Meanwhile, an LLM refines these topics using an Optimal Transport (OT)-based alignment objective, where the refinement is dynamically adjusted based on the LLM's confidence in suggesting topical words for each set of input words. With the flexibility of being integrated into many existing NTMs, the proposed approach enhances the interpretability of topics while preserving the efficiency of NTMs in learning topics and document representations. Extensive experiments demonstrate that LLM-ITL helps NTMs significantly improve their topic interpretability while maintaining the quality of document representation. Our code and datasets will be available at Github.
Tree-of-Table: Unleashing the Power of LLMs for Enhanced Large-Scale Table Understanding
Authors: Deyi Ji, Lanyun Zhu, Siqi Gao, Peng Xu, Hongtao Lu, Jieping Ye, Feng Zhao
Date: 2024-11-13 00:00:00
Tasks: Natural Language Understanding

The ubiquity and value of tables as semi-structured data across various domains necessitate advanced methods for understanding their complexity and vast amounts of information. Despite the impressive capabilities of large language models (LLMs) in advancing the natural language understanding frontier, their application to large-scale tabular data presents significant challenges, specifically regarding table size and complex intricate relationships. Existing works have shown promise with small-scale tables but often flounder when tasked with the complex reasoning required by larger, interconnected tables found in real-world scenarios. To address this gap, we introduce "Tree-of-Table", a novel approach designed to enhance LLMs' reasoning capabilities over large and complex tables. Our method employs Table Condensation and Decomposition to distill and reorganize relevant data into a manageable format, followed by the construction of a hierarchical Table-Tree that facilitates tree-structured reasoning. Through a meticulous Table-Tree Execution process, we systematically unravel the tree-structured reasoning chain to derive the solutions. Experiments across diverse datasets, including WikiTQ, TableFact, FeTaQA, and BIRD, demonstrate that Tree-of-Table sets a new benchmark with superior performance, showcasing remarkable efficiency and generalization capabilities in large-scale table reasoning.
Towards Evaluating Large Language Models for Graph Query Generation
Authors: Siraj Munir, Alessandro Aldini
Date: 2024-11-13 00:00:00
Tasks: Few-Shot Learning, Knowledge Graphs, RAG, Retrieval-augmented Generation

Large Language Models (LLMs) are revolutionizing the landscape of Generative Artificial Intelligence (GenAI), with innovative LLM-backed solutions emerging rapidly. However, when applied to database technologies, specifically query generation for graph databases and Knowledge Graphs (KGs), LLMs still face significant challenges. While research on LLM-driven query generation for Structured Query Language (SQL) exists, similar systems for graph databases remain underdeveloped. This paper presents a comparative study addressing the challenge of generating Cypher queries a powerful language for interacting with graph databases using open-access LLMs. We rigorously evaluate several LLM agents (OpenAI ChatGPT 4o, Claude Sonnet 3.5, Google Gemini Pro 1.5, and a locally deployed Llama 3.1 8B) using a designed few-shot learning prompt and Retrieval Augmented Generation (RAG) backed by Chain-of-Thoughts (CoT) reasoning. Our empirical analysis of query generation accuracy reveals that Claude Sonnet 3.5 outperforms its counterparts in this specific domain. Further, we highlight promising future research directions to address the identified limitations and advance LLM-driven query generation for graph databases.
Refining Translations with LLMs: A Constraint-Aware Iterative Prompting Approach
Authors: Shangfeng Chen, Xiayang Shi, Pu Li, YinLin Li, Jingjing Liu
Date: 2024-11-13 00:00:00
Tasks: Machine Translation, RAG, Retrieval-augmented Generation, Translation

Large language models (LLMs) have demonstrated remarkable proficiency in machine translation (MT), even without specific training on the languages in question. However, translating rare words in low-resource or domain-specific contexts remains challenging for LLMs. To address this issue, we propose a multi-step prompt chain that enhances translation faithfulness by prioritizing key terms crucial for semantic accuracy. Our method first identifies these keywords and retrieves their translations from a bilingual dictionary, integrating them into the LLM's context using Retrieval-Augmented Generation (RAG). We further mitigate potential output hallucinations caused by long prompts through an iterative self-checking mechanism, where the LLM refines its translations based on lexical and semantic constraints. Experiments using Llama and Qwen as base models on the FLORES-200 and WMT datasets demonstrate significant improvements over baselines, highlighting the effectiveness of our approach in enhancing translation faithfulness and robustness, particularly in low-resource scenarios.
A Large-Scale Study of Relevance Assessments with Large Language Models: An Initial Look
Authors: Shivani Upadhyay, Ronak Pradeep, Nandan Thakur, Daniel Campos, Nick Craswell, Ian Soboroff, Hoa Trang Dang, Jimmy Lin
Date: 2024-11-13 00:00:00
Tasks: Information Retrieval, RAG

The application of large language models to provide relevance assessments presents exciting opportunities to advance information retrieval, natural language processing, and beyond, but to date many unknowns remain. This paper reports on the results of a large-scale evaluation (the TREC 2024 RAG Track) where four different relevance assessment approaches were deployed in situ: the "standard" fully manual process that NIST has implemented for decades and three different alternatives that take advantage of LLMs to different extents using the open-source UMBRELA tool. This setup allows us to correlate system rankings induced by the different approaches to characterize tradeoffs between cost and quality. We find that in terms of nDCG@20, nDCG@100, and Recall@100, system rankings induced by automatically generated relevance assessments from UMBRELA correlate highly with those induced by fully manual assessments across a diverse set of 77 runs from 19 teams. Our results suggest that automatically generated UMBRELA judgments can replace fully manual judgments to accurately capture run-level effectiveness. Surprisingly, we find that LLM assistance does not appear to increase correlation with fully manual assessments, suggesting that costs associated with human-in-the-loop processes do not bring obvious tangible benefits. Overall, human assessors appear to be stricter than UMBRELA in applying relevance criteria. Our work validates the use of LLMs in academic TREC-style evaluations and provides the foundation for future studies.