pwc-archive/papers-with-abstracts huggingface dataset:
Uncertainty Decomposition and Error Margin Detection of Homodyned-K Distribution in Quantitative Ultrasound
Authors: Dorsa Ameri, Ali K. Z. Tehrani, Ivan M. Rosado-Mendez, Hassan Rivaz
Date: 2024-09-17 00:00:00
Tasks: parameter estimation

Homodyned K-distribution (HK-distribution) parameter estimation in quantitative ultrasound (QUS) has been recently addressed using Bayesian Neural Networks (BNNs). BNNs have been shown to significantly reduce computational time in speckle statistics-based QUS without compromising accuracy and precision. Additionally, they provide estimates of feature uncertainty, which can guide the clinician's trust in the reported feature value. The total predictive uncertainty in Bayesian modeling can be decomposed into epistemic (uncertainty over the model parameters) and aleatoric (uncertainty inherent in the data) components. By decomposing the predictive uncertainty, we can gain insights into the factors contributing to the total uncertainty. In this study, we propose a method to compute epistemic and aleatoric uncertainties for HK-distribution parameters ($\alpha$ and $k$) estimated by a BNN, in both simulation and experimental data. In addition, we investigate the relationship between the prediction error and both uncertainties, shedding light on the interplay between these uncertainties and HK parameters errors.
Automating proton PBS treatment planning for head and neck cancers using policy gradient-based deep reinforcement learning
Authors: Qingqing Wang, Chang Chang
Date: 2024-09-17 00:00:00
Tasks: Deep Reinforcement Learning, Q-Learning

Proton pencil beam scanning (PBS) treatment planning for head and neck (H&N) cancers is a time-consuming and experience-demanding task where a large number of planning objectives are involved. Deep reinforcement learning (DRL) has recently been introduced to the planning processes of intensity-modulated radiation therapy and brachytherapy for prostate, lung, and cervical cancers. However, existing approaches are built upon the Q-learning framework and weighted linear combinations of clinical metrics, suffering from poor scalability and flexibility and only capable of adjusting a limited number of planning objectives in discrete action spaces. We propose an automatic treatment planning model using the proximal policy optimization (PPO) algorithm and a dose distribution-based reward function for proton PBS treatment planning of H&N cancers. Specifically, a set of empirical rules is used to create auxiliary planning structures from target volumes and organs-at-risk (OARs), along with their associated planning objectives. These planning objectives are fed into an in-house optimization engine to generate the spot monitor unit (MU) values. A decision-making policy network trained using PPO is developed to iteratively adjust the involved planning objective parameters in a continuous action space and refine the PBS treatment plans using a novel dose distribution-based reward function. Proton H&N treatment plans generated by the model show improved OAR sparing with equal or superior target coverage when compared with human-generated plans. Moreover, additional experiments on liver cancer demonstrate that the proposed method can be successfully generalized to other treatment sites. To the best of our knowledge, this is the first DRL-based automatic treatment planning model capable of achieving human-level performance for H&N cancers.
Preference Tuning with Human Feedback on Language, Speech, and Vision Tasks: A Survey
Authors: Genta Indra Winata, Hanyang Zhao, Anirban Das, Wenpin Tang, David D. Yao, Shi-Xiong Zhang, Sambit Sahu
Date: 2024-09-17 00:00:00

Preference tuning is a crucial process for aligning deep generative models with human preferences. This survey offers a thorough overview of recent advancements in preference tuning and the integration of human feedback. The paper is organized into three main sections: 1) introduction and preliminaries: an introduction to reinforcement learning frameworks, preference tuning tasks, models, and datasets across various modalities: language, speech, and vision, as well as different policy approaches, 2) in-depth exploration of each preference tuning approach: a detailed analysis of the methods used in preference tuning, and 3) applications, discussion, and future directions: an exploration of the applications of preference tuning in downstream tasks, including evaluation methods for different modalities, and an outlook on future research directions. Our objective is to present the latest methodologies in preference tuning and model alignment, enhancing the understanding of this field for researchers and practitioners. We hope to encourage further engagement and innovation in this area.
Multi-Domain Data Aggregation for Axon and Myelin Segmentation in Histology Images
Authors: Armand Collin, Arthur Boschet, Mathieu Boudreau, Julien Cohen-Adad
Date: 2024-09-17 00:00:00
Tasks: Segmentation

Quantifying axon and myelin properties (e.g., axon diameter, myelin thickness, g-ratio) in histology images can provide useful information about microstructural changes caused by neurodegenerative diseases. Automatic tissue segmentation is an important tool for these datasets, as a single stained section can contain up to thousands of axons. Advances in deep learning have made this task quick and reliable with minimal overhead, but a deep learning model trained by one research group will hardly ever be usable by other groups due to differences in their histology training data. This is partly due to subject diversity (different body parts, species, genetics, pathologies) and also to the range of modern microscopy imaging techniques resulting in a wide variability of image features (i.e., contrast, resolution). There is a pressing need to make AI accessible to neuroscience researchers to facilitate and accelerate their workflow, but publicly available models are scarce and poorly maintained. Our approach is to aggregate data from multiple imaging modalities (bright field, electron microscopy, Raman spectroscopy) and species (mouse, rat, rabbit, human), to create an open-source, durable tool for axon and myelin segmentation. Our generalist model makes it easier for researchers to process their data and can be fine-tuned for better performance on specific domains. We study the benefits of different aggregation schemes. This multi-domain segmentation model performs better than single-modality dedicated learners (p=0.03077), generalizes better on out-of-distribution data and is easier to use and maintain. Importantly, we package the segmentation tool into a well-maintained open-source software ecosystem (see https://github.com/axondeepseg/axondeepseg).
Small Language Models can Outperform Humans in Short Creative Writing: A Study Comparing SLMs with Humans and LLMs
Authors: Guillermo Marco, Luz Rello, Julio Gonzalo
Date: 2024-09-17 00:00:00
Tasks: Language Modelling, Small Language Model

In this paper, we evaluate the creative fiction writing abilities of a fine-tuned small language model (SLM), BART-large, and compare its performance to human writers and two large language models (LLMs): GPT-3.5 and GPT-4o. Our evaluation consists of two experiments: (i) a human study in which 68 participants rated short stories from humans and the SLM on grammaticality, relevance, creativity, and attractiveness, and (ii) a qualitative linguistic analysis examining the textual characteristics of stories produced by each model. In the first experiment, BART-large outscored average human writers overall (2.11 vs. 1.85), a 14% relative improvement, though the slight human advantage in creativity was not statistically significant. In the second experiment, qualitative analysis showed that while GPT-4o demonstrated near-perfect coherence and used less cliche phrases, it tended to produce more predictable language, with only 3% of its synopses featuring surprising associations (compared to 15% for BART). These findings highlight how model size and fine-tuning influence the balance between creativity, fluency, and coherence in creative writing tasks, and demonstrate that smaller models can, in certain contexts, rival both humans and larger models.
NCT-CRC-HE: Not All Histopathological Datasets Are Equally Useful
Authors: Andrey Ignatov, Grigory Malivenko
Date: 2024-09-17 00:00:00
Tasks: All, Color Normalization

Numerous deep learning-based solutions have been proposed for histopathological image analysis over the past years. While they usually demonstrate exceptionally high accuracy, one key question is whether their precision might be affected by low-level image properties not related to histopathology but caused by microscopy image handling and pre-processing. In this paper, we analyze a popular NCT-CRC-HE-100K colorectal cancer dataset used in numerous prior works and show that both this dataset and the obtained results may be affected by data-specific biases. The most prominent revealed dataset issues are inappropriate color normalization, severe JPEG artifacts inconsistent between different classes, and completely corrupted tissue samples resulting from incorrect image dynamic range handling. We show that even the simplest model using only 3 features per image (red, green and blue color intensities) can demonstrate over 50% accuracy on this 9-class dataset, while using color histogram not explicitly capturing cell morphology features yields over 82% accuracy. Moreover, we show that a basic EfficientNet-B0 ImageNet pretrained model can achieve over 97.7% accuracy on this dataset, outperforming all previously proposed solutions developed for this task, including dedicated foundation histopathological models and large cell morphology-aware neural networks. The NCT-CRC-HE dataset is publicly available and can be freely used to replicate the presented results. The codes and pre-trained models used in this paper are available at https://github.com/gmalivenko/NCT-CRC-HE-experiments
Improving LLM Reasoning with Multi-Agent Tree-of-Thought Validator Agent
Authors: Fatemeh Haji, Mazal Bethany, Maryam Tabar, Jason Chiang, Anthony Rios, Peyman Najafirad
Date: 2024-09-17 00:00:00
Tasks: GSM8K, Question Answering, valid

Multi-agent strategies have emerged as a promising approach to enhance the reasoning abilities of Large Language Models (LLMs) by assigning specialized roles in the problem-solving process. Concurrently, Tree of Thoughts (ToT) methods have shown potential in improving reasoning for complex question-answering tasks by exploring diverse reasoning paths. A critical limitation in multi-agent reasoning is the 'Reasoner' agent's shallow exploration of reasoning paths. While ToT strategies could help mitigate this problem, they may generate flawed reasoning branches, which could harm the trustworthiness of the final answer. To leverage the strengths of both multi-agent reasoning and ToT strategies, we introduce a novel approach combining ToT-based Reasoner agents with a Thought Validator agent. Multiple Reasoner agents operate in parallel, employing ToT to explore diverse reasoning paths. The Thought Validator then scrutinizes these paths, considering a Reasoner's conclusion only if its reasoning is valid. This method enables a more robust voting strategy by discarding faulty reasoning paths, enhancing the system's ability to tackle tasks requiring systematic and trustworthy reasoning. Our method demonstrates superior performance compared to existing techniques when evaluated on the GSM8K dataset, outperforming the standard ToT strategy by an average 5.6% across four LLMs. The code and related content can be found in: https://github.com/SecureAIAutonomyLab/MA-ToT
Mamba Fusion: Learning Actions Through Questioning
Authors: Zhikang Dong, Apoorva Beedu, Jason Sheinkopf, Irfan Essa
Date: 2024-09-17 00:00:00
Tasks: Action Anticipation, Action Recognition, GPU, Mamba, Question Answering

Video Language Models (VLMs) are crucial for generalizing across diverse tasks and using language cues to enhance learning. While transformer-based architectures have been the de facto in vision-language training, they face challenges like quadratic computational complexity, high GPU memory usage, and difficulty with long-term dependencies. To address these limitations, we introduce MambaVL, a novel model that leverages recent advancements in selective state space modality fusion to efficiently capture long-range dependencies and learn joint representations for vision and language data. MambaVL utilizes a shared state transition matrix across both modalities, allowing the model to capture information about actions from multiple perspectives within the scene. Furthermore, we propose a question-answering task that helps guide the model toward relevant cues. These questions provide critical information about actions, objects, and environmental context, leading to enhanced performance. As a result, MambaVL achieves state-of-the-art performance in action recognition on the Epic-Kitchens-100 dataset and outperforms baseline methods in action anticipation.
FedNE: Surrogate-Assisted Federated Neighbor Embedding for Dimensionality Reduction
Authors: Ziwei Li, Xiaoqi Wang, Hong-You Chen, Han-Wei Shen, Wei-Lun Chao
Date: 2024-09-17 00:00:00
Tasks: Dimensionality Reduction, Federated Learning, Graph Learning

Federated learning (FL) has rapidly evolved as a promising paradigm that enables collaborative model training across distributed participants without exchanging their local data. Despite its broad applications in fields such as computer vision, graph learning, and natural language processing, the development of a data projection model that can be effectively used to visualize data in the context of FL is crucial yet remains heavily under-explored. Neighbor embedding (NE) is an essential technique for visualizing complex high-dimensional data, but collaboratively learning a joint NE model is difficult. The key challenge lies in the objective function, as effective visualization algorithms like NE require computing loss functions among pairs of data. In this paper, we introduce \textsc{FedNE}, a novel approach that integrates the \textsc{FedAvg} framework with the contrastive NE technique, without any requirements of shareable data. To address the lack of inter-client repulsion which is crucial for the alignment in the global embedding space, we develop a surrogate loss function that each client learns and shares with each other. Additionally, we propose a data-mixing strategy to augment the local data, aiming to relax the problems of invisible neighbors and false neighbors constructed by the local $k$NN graphs. We conduct comprehensive experiments on both synthetic and real-world datasets. The results demonstrate that our \textsc{FedNE} can effectively preserve the neighborhood data structures and enhance the alignment in the global embedding space compared to several baseline methods.
Egalitarian Language Representation in Language Models: It All Begins with Tokenizers
Authors: Menan Velayuthan, Kengatharaiyer Sarveswaran
Date: 2024-09-17 00:00:00
Tasks: All

Tokenizers act as a bridge between human language and the latent space of language models, influencing how language is represented in these models. Due to the immense popularity of English-Centric Large Language Models (LLMs), efforts are being made to adapt them for other languages. However, we demonstrate that, from a tokenization standpoint, not all tokenizers offer fair representation for complex script languages such as Tamil, Sinhala, and Hindi, primarily due to the choice of pre-tokenization methods. We go further to show that pre-tokenization plays a more critical role than the tokenization algorithm itself in achieving an egalitarian representation of these complex script languages. To address this, we introduce an improvement to the Byte Pair Encoding (BPE) algorithm by incorporating graphemes, which we term Grapheme Pair Encoding (GPE). Our experiments show that grapheme-based character extraction outperforms byte-level tokenizers for complex scripts. We validate this approach through experiments on Tamil, Sinhala, and Hindi.
Multi-Document Grounded Multi-Turn Synthetic Dialog Generation
Authors: Young-suk Lee, Chulaka Gunasekara, Danish Contractor, Ramón Fernandez Astudillo, Radu Florian
Date: 2024-09-17 00:00:00

We introduce a technique for multi-document grounded multi-turn synthetic dialog generation that incorporates three main ideas. First, we control the overall dialog flow using taxonomy-driven user queries that are generated with Chain-of-Thought (CoT) prompting. Second, we support the generation of multi-document grounded dialogs by mimicking real-world use of retrievers to update the grounding documents after every user-turn in the dialog. Third, we apply LLM-as-a-Judge to filter out queries with incorrect answers. Human evaluation of the synthetic dialog data suggests that the data is diverse, coherent, and includes mostly correct answers. Both human and automatic evaluations of answerable queries indicate that models fine-tuned on synthetic dialogs consistently out-perform those fine-tuned on existing human generated training data across four publicly available multi-turn document grounded benchmark test sets.
Augment, Drop & Swap: Improving Diversity in LLM Captions for Efficient Music-Text Representation Learning
Authors: Ilaria Manco, Justin Salamon, Oriol Nieto
Date: 2024-09-17 00:00:00
Tasks: Diversity, Representation Learning, Text Augmentation

Audio-text contrastive models have become a powerful approach in music representation learning. Despite their empirical success, however, little is known about the influence of key design choices on the quality of music-text representations learnt through this framework. In this work, we expose these design choices within the constraints of limited data and computation budgets, and establish a more solid understanding of their impact grounded in empirical observations along three axes: the choice of base encoders, the level of curation in training data, and the use of text augmentation. We find that data curation is the single most important factor for music-text contrastive training in resource-constrained scenarios. Motivated by this insight, we introduce two novel techniques, Augmented View Dropout and TextSwap, which increase the diversity and descriptiveness of text inputs seen in training. Through our experiments we demonstrate that these are effective at boosting performance across different pre-training regimes, model architectures, and downstream data distributions, without incurring higher computational costs or requiring additional training data.
Beyond Algorithmic Fairness: A Guide to Develop and Deploy Ethical AI-Enabled Decision-Support Tools
Authors: Rosemarie Santa Gonzalez, Ryan Piansky, Sue M Bae, Justin Biddle, Daniel Molzahn
Date: 2024-09-17 00:00:00
Tasks: Decision Making, Fairness

The integration of artificial intelligence (AI) and optimization hold substantial promise for improving the efficiency, reliability, and resilience of engineered systems. Due to the networked nature of many engineered systems, ethically deploying methodologies at this intersection poses challenges that are distinct from other AI settings, thus motivating the development of ethical guidelines tailored to AI-enabled optimization. This paper highlights the need to go beyond fairness-driven algorithms to systematically address ethical decisions spanning the stages of modeling, data curation, results analysis, and implementation of optimization-based decision support tools. Accordingly, this paper identifies ethical considerations required when deploying algorithms at the intersection of AI and optimization via case studies in power systems as well as supply chain and logistics. Rather than providing a prescriptive set of rules, this paper aims to foster reflection and awareness among researchers and encourage consideration of ethical implications at every step of the decision-making process.
Two Stage Segmentation of Cervical Tumors using PocketNet
Authors: Awj Twam, Megan Jacobsen, Rachel Glenn, Peng Wei, Jia Sun, Ann Klopp, Aradhana M. Venkatesan, David Fuentes
Date: 2024-09-17 00:00:00
Tasks: Anatomy, Computed Tomography (CT), Organ Segmentation, Segmentation, Tumor Segmentation

Cervical cancer remains the fourth most common malignancy amongst women worldwide.1 Concurrent chemoradiotherapy (CRT) serves as the mainstay definitive treatment regimen for locally advanced cervical cancers and includes external beam radiation followed by brachytherapy.2 Integral to radiotherapy treatment planning is the routine contouring of both the target tumor at the level of the cervix, associated gynecologic anatomy and the adjacent organs at risk (OARs). However, manual contouring of these structures is both time and labor intensive and associated with known interobserver variability that can impact treatment outcomes. While multiple tools have been developed to automatically segment OARs and the high-risk clinical tumor volume (HR-CTV) using computed tomography (CT) images,3,4,5,6 the development of deep learning-based tumor segmentation tools using routine T2-weighted (T2w) magnetic resonance imaging (MRI) addresses an unmet clinical need to improve the routine contouring of both anatomical structures and cervical cancers, thereby increasing quality and consistency of radiotherapy planning. This work applied a novel deep-learning model (PocketNet) to segment the cervix, vagina, uterus, and tumor(s) on T2w MRI. The performance of the PocketNet architecture was evaluated, when trained on data via 5-fold cross validation. PocketNet achieved a mean Dice-Sorensen similarity coefficient (DSC) exceeding 70% for tumor segmentation and 80% for organ segmentation. These results suggest that PocketNet is robust to variations in contrast protocols, providing reliable segmentation of the regions of interest.
Evaluation of pretrained language models on music understanding
Authors: Yannis Vasilakis, Rachel Bittner, Johan Pauwels
Date: 2024-09-17 00:00:00
Tasks: Music Captioning, Negation, Sensitivity, Text to Audio Retrieval, Triplet

Music-text multimodal systems have enabled new approaches to Music Information Research (MIR) applications such as audio-to-text and text-to-audio retrieval, text-based song generation, and music captioning. Despite the reported success, little effort has been put into evaluating the musical knowledge of Large Language Models (LLM). In this paper, we demonstrate that LLMs suffer from 1) prompt sensitivity, 2) inability to model negation (e.g. 'rock song without guitar'), and 3) sensitivity towards the presence of specific words. We quantified these properties as a triplet-based accuracy, evaluating the ability to model the relative similarity of labels in a hierarchical ontology. We leveraged the Audioset ontology to generate triplets consisting of an anchor, a positive (relevant) label, and a negative (less relevant) label for the genre and instruments sub-tree. We evaluated the triplet-based musical knowledge for six general-purpose Transformer-based models. The triplets obtained through this methodology required filtering, as some were difficult to judge and therefore relatively uninformative for evaluation purposes. Despite the relatively high accuracy reported, inconsistencies are evident in all six models, suggesting that off-the-shelf LLMs need adaptation to music before use.