pwc-archive/papers-with-abstracts huggingface dataset:
Explainable Graph Neural Networks Under Fire
Authors: Zhong Li, Simon Geisler, Yuhang Wang, Stephan Günnemann, Matthijs van Leeuwen
Date: 2024-06-10 00:00:00
Tasks: Adversarial Attack

Predictions made by graph neural networks (GNNs) usually lack interpretability due to their complex computational behavior and the abstract nature of graphs. In an attempt to tackle this, many GNN explanation methods have emerged. Their goal is to explain a model's predictions and thereby obtain trust when GNN models are deployed in decision critical applications. Most GNN explanation methods work in a post-hoc manner and provide explanations in the form of a small subset of important edges and/or nodes. In this paper we demonstrate that these explanations can unfortunately not be trusted, as common GNN explanation methods turn out to be highly susceptible to adversarial perturbations. That is, even small perturbations of the original graph structure that preserve the model's predictions may yield drastically different explanations. This calls into question the trustworthiness and practical utility of post-hoc explanation methods for GNNs. To be able to attack GNN explanation models, we devise a novel attack method dubbed \textit{GXAttack}, the first \textit{optimization-based} adversarial white-box attack method for post-hoc GNN explanations under such settings. Due to the devastating effectiveness of our attack, we call for an adversarial evaluation of future GNN explainers to demonstrate their robustness. For reproducibility, our code is available via GitHub.
An Empirical Design Justice Approach to Identifying Ethical Considerations in the Intersection of Large Language Models and Social Robotics
Authors: Alva Markelius
Date: 2024-06-10 00:00:00
Tasks: Misinformation

The integration of Large Language Models (LLMs) in social robotics presents a unique set of ethical challenges and social impacts. This research is set out to identify ethical considerations that arise in the design and development of these two technologies in combination. Using LLMs for social robotics may provide benefits, such as enabling natural language open-domain dialogues. However, the intersection of these two technologies also gives rise to ethical concerns related to misinformation, non-verbal cues, emotional disruption, and biases. The robot's physical social embodiment adds complexity, as ethical hazards associated with LLM-based Social AI, such as hallucinations and misinformation, can be exacerbated due to the effects of physical embodiment on social perception and communication. To address these challenges, this study employs an empirical design justice-based methodology, focusing on identifying socio-technical ethical considerations through a qualitative co-design and interaction study. The purpose of the study is to identify ethical considerations relevant to the process of co-design of, and interaction with a humanoid social robot as the interface of a LLM, and to evaluate how a design justice methodology can be used in the context of designing LLMs-based social robotics. The findings reveal a mapping of ethical considerations arising in four conceptual dimensions: interaction, co-design, terms of service and relationship and evaluates how a design justice approach can be used empirically in the intersection of LLMs and social robotics.
Should We Fine-Tune or RAG? Evaluating Different Techniques to Adapt LLMs for Dialogue
Authors: Simone Alghisi, Massimo Rizzoli, Gabriel Roccabruna, Seyed Mahed Mousavi, Giuseppe Riccardi
Date: 2024-06-10 00:00:00
Tasks: In-Context Learning, Question Answering, RAG, Response Generation, Retrieval-augmented Generation

We study the limitations of Large Language Models (LLMs) for the task of response generation in human-machine dialogue. Several techniques have been proposed in the literature for different dialogue types (e.g., Open-Domain). However, the evaluations of these techniques have been limited in terms of base LLMs, dialogue types and evaluation metrics. In this work, we extensively analyze different LLM adaptation techniques when applied to different dialogue types. We have selected two base LLMs, Llama-2 and Mistral, and four dialogue types Open-Domain, Knowledge-Grounded, Task-Oriented, and Question Answering. We evaluate the performance of in-context learning and fine-tuning techniques across datasets selected for each dialogue type. We assess the impact of incorporating external knowledge to ground the generation in both scenarios of Retrieval-Augmented Generation (RAG) and gold knowledge. We adopt consistent evaluation and explainability criteria for automatic metrics and human evaluation protocols. Our analysis shows that there is no universal best-technique for adapting large language models as the efficacy of each technique depends on both the base LLM and the specific type of dialogue. Last but not least, the assessment of the best adaptation technique should include human evaluation to avoid false expectations and outcomes derived from automatic metrics.
Contrastive learning of T cell receptor representations
Authors: Yuta Nagano, Andrew Pyo, Martina Milighetti, James Henderson, John Shawe-Taylor, Benny Chain, Andreas Tiffeau-Mayer
Date: 2024-06-10 00:00:00
Tasks: Contrastive Learning, Language Modeling, Language Modelling, Specificity, Transfer Learning

Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labelled TCR data remains sparse. In other domains, the pre-training of language models on unlabelled data has been successfully used to address data bottlenecks. However, it is unclear how to best pre-train protein language models for TCR specificity prediction. Here we introduce a TCR language model called SCEPTR (Simple Contrastive Embedding of the Primary sequence of T cell Receptors), capable of data-efficient transfer learning. Through our model, we introduce a novel pre-training strategy combining autocontrastive learning and masked-language modelling, which enables SCEPTR to achieve its state-of-the-art performance. In contrast, existing protein language models and a variant of SCEPTR pre-trained without autocontrastive learning are outperformed by sequence alignment-based methods. We anticipate that contrastive learning will be a useful paradigm to decode the rules of TCR specificity.
Low-Rank Quantization-Aware Training for LLMs
Authors: Yelysei Bondarenko, Riccardo Del Chiaro, Markus Nagel
Date: 2024-06-10 00:00:00
Tasks: GPU, parameter-efficient fine-tuning, Quantization

Large language models (LLMs) are omnipresent, however their practical deployment is challenging due to their ever increasing computational and memory demands. Quantization is one of the most effective ways to make them more compute and memory efficient. Quantization-aware training (QAT) methods, generally produce the best quantized performance, however it comes at the cost of potentially long training time and excessive memory usage, making it impractical when applying for LLMs. Inspired by parameter-efficient fine-tuning (PEFT) and low-rank adaptation (LoRA) literature, we propose LR-QAT -- a lightweight and memory-efficient QAT algorithm for LLMs. LR-QAT employs several components to save memory without sacrificing predictive performance: (a) low-rank auxiliary weights that are aware of the quantization grid; (b) a downcasting operator using fixed-point or double-packed integers and (c) checkpointing. Unlike most related work, our method (i) is inference-efficient, leading to no additional overhead compared to traditional PTQ; (ii) can be seen as a general extended pretraining framework, meaning that the resulting model can still be utilized for any downstream task afterwards; (iii) can be applied across a wide range of quantization settings, such as different choices quantization granularity, activation quantization, and seamlessly combined with many PTQ techniques. We apply LR-QAT to LLaMA-1/2/3 and Mistral model families and validate its effectiveness on several downstream tasks. Our method outperforms common post-training quantization (PTQ) approaches and reaches the same model performance as full-model QAT at the fraction of its memory usage. Specifically, we can train a 7B LLM on a single consumer grade GPU with 24GB of memory. Our source code is available at https://github.com/qualcomm-ai-research/LR-QAT
MOSA: Music Motion with Semantic Annotation Dataset for Cross-Modal Music Processing
Authors: Yu-Fen Huang, Nikki Moran, Simon Coleman, Jon Kelly, Shun-Hwa Wei, Po-Yin Chen, Yun-Hsin Huang, Tsung-Ping Chen, Yu-Chia Kuo, Yu-Chi Wei, Chih-Hsuan Li, Da-Yu Huang, Hsuan-Kai Kao, Ting-Wei Lin, Li Su
Date: 2024-06-10 00:00:00
Tasks: Information Retrieval, Music Information Retrieval

In cross-modal music processing, translation between visual, auditory, and semantic content opens up new possibilities as well as challenges. The construction of such a transformative scheme depends upon a benchmark corpus with a comprehensive data infrastructure. In particular, the assembly of a large-scale cross-modal dataset presents major challenges. In this paper, we present the MOSA (Music mOtion with Semantic Annotation) dataset, which contains high quality 3-D motion capture data, aligned audio recordings, and note-by-note semantic annotations of pitch, beat, phrase, dynamic, articulation, and harmony for 742 professional music performances by 23 professional musicians, comprising more than 30 hours and 570 K notes of data. To our knowledge, this is the largest cross-modal music dataset with note-level annotations to date. To demonstrate the usage of the MOSA dataset, we present several innovative cross-modal music information retrieval (MIR) and musical content generation tasks, including the detection of beats, downbeats, phrase, and expressive contents from audio, video and motion data, and the generation of musicians' body motion from given music audio. The dataset and codes are available alongside this publication (https://github.com/yufenhuang/MOSA-Music-mOtion-and-Semantic-Annotation-dataset).
Improving Deep Learning-based Automatic Cranial Defect Reconstruction by Heavy Data Augmentation: From Image Registration to Latent Diffusion Models
Authors: Marek Wodzinski, Kamil Kwarciak, Mateusz Daniol, Daria Hemmerling
Date: 2024-06-10 00:00:00
Tasks: Data Augmentation, Image Registration

Modeling and manufacturing of personalized cranial implants are important research areas that may decrease the waiting time for patients suffering from cranial damage. The modeling of personalized implants may be partially automated by the use of deep learning-based methods. However, this task suffers from difficulties with generalizability into data from previously unseen distributions that make it difficult to use the research outcomes in real clinical settings. Due to difficulties with acquiring ground-truth annotations, different techniques to improve the heterogeneity of datasets used for training the deep networks have to be considered and introduced. In this work, we present a large-scale study of several augmentation techniques, varying from classical geometric transformations, image registration, variational autoencoders, and generative adversarial networks, to the most recent advances in latent diffusion models. We show that the use of heavy data augmentation significantly increases both the quantitative and qualitative outcomes, resulting in an average Dice Score above 0.94 for the SkullBreak and above 0.96 for the SkullFix datasets. Moreover, we show that the synthetically augmented network successfully reconstructs real clinical defects. The work is a considerable contribution to the field of artificial intelligence in the automatic modeling of personalized cranial implants.
Automating Food Drop: The Power of Two Choices for Dynamic and Fair Food Allocation
Authors: Marios Mertzanidis, Alexandros Psomas, Paritosh Verma
Date: 2024-06-10 00:00:00
Tasks: Fairness

Food waste and food insecurity are two closely related pressing global issues. Food rescue organizations worldwide run programs aimed at addressing the two problems. In this paper, we partner with a non-profit organization in the state of Indiana that leads \emph{Food Drop}, a program that is designed to redirect rejected truckloads of food away from landfills and into food banks. The truckload to food bank matching decisions are currently made by an employee of our partner organization. In addition to this being a very time-consuming task, as perhaps expected from human-based matching decisions, the allocations are often skewed: a small percentage of the possible recipients receives the majority of donations. Our goal in this partnership is to completely automate Food Drop. In doing so, we need a matching algorithm for making real-time decisions that strikes a balance between ensuring fairness for the food banks that receive the food and optimizing efficiency for the truck drivers. In this paper, we describe the theoretical guarantees and experiments that dictated our choice of algorithm in the platform we built and deployed for our partner organization. Our work also makes contributions to the literature on load balancing and balls-into-bins games, that might be of independent interest. Specifically, we study the allocation of $m$ weighted balls into $n$ weighted bins, where each ball has two non-uniformly sampled random bin choices, and prove upper bounds, that hold with high probability, on the maximum load of any bin.
MASSW: A New Dataset and Benchmark Tasks for AI-Assisted Scientific Workflows
Authors: Xingjian Zhang, Yutong Xie, Jin Huang, Jinge Ma, Zhaoying Pan, Qijia Liu, Ziyang Xiong, Tolga Ergen, Dongsub Shim, Honglak Lee, Qiaozhu Mei
Date: 2024-06-10 00:00:00
Tasks: Navigate

Scientific innovation relies on detailed workflows, which include critical steps such as analyzing literature, generating ideas, validating these ideas, interpreting results, and inspiring follow-up research. However, scientific publications that document these workflows are extensive and unstructured. This makes it difficult for both human researchers and AI systems to effectively navigate and explore the space of scientific innovation. To address this issue, we introduce MASSW, a comprehensive text dataset on Multi-Aspect Summarization of Scientific Workflows. MASSW includes more than 152,000 peer-reviewed publications from 17 leading computer science conferences spanning the past 50 years. Using Large Language Models (LLMs), we automatically extract five core aspects from these publications -- context, key idea, method, outcome, and projected impact -- which correspond to five key steps in the research workflow. These structured summaries facilitate a variety of downstream tasks and analyses. The quality of the LLM-extracted summaries is validated by comparing them with human annotations. We demonstrate the utility of MASSW through multiple novel machine-learning tasks that can be benchmarked using this new dataset, which make various types of predictions and recommendations along the scientific workflow. MASSW holds significant potential for researchers to create and benchmark new AI methods for optimizing scientific workflows and fostering scientific innovation in the field. Our dataset is openly available at \url{https://github.com/xingjian-zhang/massw}.
Re.Dis.Cover Place with Generative AI: Exploring the Experience and Design of City Wandering with Image-to-Image AI
Authors: Peng-Kai Hung, Janet Yi-Ching Huang, Stephan Wensveen, Rung-Huei Liang
Date: 2024-06-10 00:00:00

The HCI field has demonstrated a growing interest in leveraging emerging technologies to enrich urban experiences. However, insufficient studies investigate the experience and design space of AI image technology (AIGT) applications for playful urban interaction, despite its widespread adoption. To explore this gap, we conducted an exploratory study involving four participants who wandered and photographed within Eindhoven Centre and interacted with an image-to-image AI. Preliminary findings present their observations, the effect of their familiarity with places, and how AIGT becomes an explorer's tool or co-speculator. We then highlight AIGT's capability of supporting playfulness, reimaginations, and rediscoveries of places through defamiliarizing and familiarizing cityscapes. Additionally, we propose the metaphor AIGT as a 'tourist' to discuss its opportunities for engaging explorations and risks of stereotyping places. Collectively, our research provides initial empirical insights and design considerations, inspiring future HCI endeavors for creating urban play with generative AI.
Predicting Heart Activity from Speech using Data-driven and Knowledge-based features
Authors: Gasser Elbanna, Zohreh Mostaani, Mathew Magimai. -Doss
Date: 2024-06-10 00:00:00

Accurately predicting heart activity and other biological signals is crucial for diagnosis and monitoring. Given that speech is an outcome of multiple physiological systems, a significant body of work studied the acoustic correlates of heart activity. Recently, self-supervised models have excelled in speech-related tasks compared to traditional acoustic methods. However, the robustness of data-driven representations in predicting heart activity remained unexplored. In this study, we demonstrate that self-supervised speech models outperform acoustic features in predicting heart activity parameters. We also emphasize the impact of individual variability on model generalizability. These findings underscore the value of data-driven representations in such tasks and the need for more speech-based physiological data to mitigate speaker-related challenges.
Optimisation of federated learning settings under statistical heterogeneity variations
Authors: Basem Suleiman, Muhammad Johan Alibasa, Rizka Widyarini Purwanto, Lewis Jeffries, Ali Anaissi, Jacky Song
Date: 2024-06-10 00:00:00
Tasks: Diversity, Federated Learning

Federated Learning (FL) enables local devices to collaboratively learn a shared predictive model by only periodically sharing model parameters with a central aggregator. However, FL can be disadvantaged by statistical heterogeneity produced by the diversity in each local devices data distribution, which creates different levels of Independent and Identically Distributed (IID) data. Furthermore, this can be more complex when optimising different combinations of FL parameters and choosing optimal aggregation. In this paper, we present an empirical analysis of different FL training parameters and aggregators over various levels of statistical heterogeneity on three datasets. We propose a systematic data partition strategy to simulate different levels of statistical heterogeneity and a metric to measure the level of IID. Additionally, we empirically identify the best FL model and key parameters for datasets of different characteristics. On the basis of these, we present recommended guidelines for FL parameters and aggregators to optimise model performance under different levels of IID and with different datasets
MedExQA: Medical Question Answering Benchmark with Multiple Explanations
Authors: Yunsoo Kim, Jinge Wu, Yusuf Abdulle, Honghan Wu
Date: 2024-06-10 00:00:00
Tasks: Medical Question Answering, Question Answering

This paper introduces MedExQA, a novel benchmark in medical question-answering, to evaluate large language models' (LLMs) understanding of medical knowledge through explanations. By constructing datasets across five distinct medical specialties that are underrepresented in current datasets and further incorporating multiple explanations for each question-answer pair, we address a major gap in current medical QA benchmarks which is the absence of comprehensive assessments of LLMs' ability to generate nuanced medical explanations. Our work highlights the importance of explainability in medical LLMs, proposes an effective methodology for evaluating models beyond classification accuracy, and sheds light on one specific domain, speech language pathology, where current LLMs including GPT4 lack good understanding. Our results show generation evaluation with multiple explanations aligns better with human assessment, highlighting an opportunity for a more robust automated comprehension assessment for LLMs. To diversify open-source medical LLMs (currently mostly based on Llama2), this work also proposes a new medical model, MedPhi-2, based on Phi-2 (2.7B). The model outperformed medical LLMs based on Llama2-70B in generating explanations, showing its effectiveness in the resource-constrained medical domain. We will share our benchmark datasets and the trained model.
Tx-LLM: A Large Language Model for Therapeutics
Authors: Juan Manuel Zambrano Chaves, Eric Wang, Tao Tu, Eeshit Dhaval Vaishnav, Byron Lee, S. Sara Mahdavi, Christopher Semturs, David Fleet, Vivek Natarajan, Shekoofeh Azizi
Date: 2024-06-10 00:00:00
Tasks: Drug Discovery, Language Modeling, Language Modelling, Large Language Model

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.