pwc-archive/papers-with-abstracts huggingface dataset:
Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks
Authors: Aryo Pradipta Gema, Dominik Grabarczyk, Wolf De Wulf, Piyush Borole, Javier Antonio Alfaro, Pasquale Minervini, Antonio Vergari, Ajitha Rajan
Date: 2023-05-31 00:00:00
Tasks: Graph Embedding, Knowledge Graph Embedding, Knowledge Graph Embeddings, Knowledge Graphs, Link Prediction

Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.
VILAS: Exploring the Effects of Vision and Language Context in Automatic Speech Recognition
Authors: Ziyi Ni, Minglun Han, Feilong Chen, Linghui Meng, Jing Shi, Pin Lv, Bo Xu
Date: 2023-05-31 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), speech-recognition, Speech Recognition

Enhancing automatic speech recognition (ASR) performance by leveraging additional multimodal information has shown promising results in previous studies. However, most of these works have primarily focused on utilizing visual cues derived from human lip motions. In fact, context-dependent visual and linguistic cues can also benefit in many scenarios. In this paper, we first propose ViLaS (Vision and Language into Automatic Speech Recognition), a novel multimodal ASR model based on the continuous integrate-and-fire (CIF) mechanism, which can integrate visual and textual context simultaneously or separately, to facilitate speech recognition. Next, we introduce an effective training strategy that improves performance in modal-incomplete test scenarios. Then, to explore the effects of integrating vision and language, we create VSDial, a multimodal ASR dataset with multimodal context cues in both Chinese and English versions. Finally, empirical results are reported on the public Flickr8K and self-constructed VSDial datasets. We explore various cross-modal fusion schemes, analyze fine-grained crossmodal alignment on VSDial, and provide insights into the effects of integrating multimodal information on speech recognition.
MicroSegNet: A Deep Learning Approach for Prostate Segmentation on Micro-Ultrasound Images
Authors: Hongxu Jiang, Muhammad Imran, Preethika Muralidharan, Anjali Patel, Jake Pensa, Muxuan Liang, Tarik Benidir, Joseph R. Grajo, Jason P. Joseph, Russell Terry, John Michael DiBianco, Li-Ming Su, Yuyin Zhou, Wayne G. Brisbane, Wei Shao
Date: 2023-05-31 00:00:00
Tasks: Segmentation

Micro-ultrasound (micro-US) is a novel 29-MHz ultrasound technique that provides 3-4 times higher resolution than traditional ultrasound, potentially enabling low-cost, accurate diagnosis of prostate cancer. Accurate prostate segmentation is crucial for prostate volume measurement, cancer diagnosis, prostate biopsy, and treatment planning. However, prostate segmentation on micro-US is challenging due to artifacts and indistinct borders between the prostate, bladder, and urethra in the midline. This paper presents MicroSegNet, a multi-scale annotation-guided transformer UNet model designed specifically to tackle these challenges. During the training process, MicroSegNet focuses more on regions that are hard to segment (hard regions), characterized by discrepancies between expert and non-expert annotations. We achieve this by proposing an annotation-guided binary cross entropy (AG-BCE) loss that assigns a larger weight to prediction errors in hard regions and a lower weight to prediction errors in easy regions. The AG-BCE loss was seamlessly integrated into the training process through the utilization of multi-scale deep supervision, enabling MicroSegNet to capture global contextual dependencies and local information at various scales. We trained our model using micro-US images from 55 patients, followed by evaluation on 20 patients. Our MicroSegNet model achieved a Dice coefficient of 0.939 and a Hausdorff distance of 2.02 mm, outperforming several state-of-the-art segmentation methods, as well as three human annotators with different experience levels. Our code is publicly available at https://github.com/mirthAI/MicroSegNet and our dataset is publicly available at https://zenodo.org/records/10475293.
Image Registration of In Vivo Micro-Ultrasound and Ex Vivo Pseudo-Whole Mount Histopathology Images of the Prostate: A Proof-of-Concept Study
Authors: Muhammad Imran, Brianna Nguyen, Jake Pensa, Sara M. Falzarano, Anthony E. Sisk, Muxuan Liang, John Michael DiBianco, Li-Ming Su, Yuyin Zhou, Wayne G. Brisbane, Wei Shao
Date: 2023-05-31 00:00:00
Tasks: Diagnostic, Image Registration

Early diagnosis of prostate cancer significantly improves a patient's 5-year survival rate. Biopsy of small prostate cancers is improved with image-guided biopsy. MRI-ultrasound fusion-guided biopsy is sensitive to smaller tumors but is underutilized due to the high cost of MRI and fusion equipment. Micro-ultrasound (micro-US), a novel high-resolution ultrasound technology, provides a cost-effective alternative to MRI while delivering comparable diagnostic accuracy. However, the interpretation of micro-US is challenging due to subtle gray scale changes indicating cancer vs normal tissue. This challenge can be addressed by training urologists with a large dataset of micro-US images containing the ground truth cancer outlines. Such a dataset can be mapped from surgical specimens (histopathology) onto micro-US images via image registration. In this paper, we present a semi-automated pipeline for registering in vivo micro-US images with ex vivo whole-mount histopathology images. Our pipeline begins with the reconstruction of pseudo-whole-mount histopathology images and a 3-dimensional (3D) micro-US volume. Each pseudo-whole-mount histopathology image is then registered with the corresponding axial micro-US slice using a two-stage approach that estimates an affine transformation followed by a deformable transformation. We evaluated our registration pipeline using micro-US and histopathology images from 18 patients who underwent radical prostatectomy. The results showed a Dice coefficient of 0.94 and a landmark error of 2.7 mm, indicating the accuracy of our registration pipeline. This proof-of-concept study demonstrates the feasibility of accurately aligning micro-US and histopathology images. To promote transparency and collaboration in research, we will make our code and dataset publicly available.
Breast Cancer Detection and Diagnosis: A comparative study of state-of-the-arts deep learning architectures
Authors: Brennon Maistry, Absalom E. Ezugwu
Date: 2023-05-31 00:00:00
Tasks: Breast Cancer Detection, Data Augmentation, Histopathological Image Classification, image-classification, Image Classification

Breast cancer is a prevalent form of cancer among women, with over 1.5 million women being diagnosed each year. Unfortunately, the survival rates for breast cancer patients in certain third-world countries, like South Africa, are alarmingly low, with only 40% of diagnosed patients surviving beyond five years. The inadequate availability of resources, including qualified pathologists, delayed diagnoses, and ineffective therapy planning, contribute to this low survival rate. To address this pressing issue, medical specialists and researchers have turned to domain-specific AI approaches, specifically deep learning models, to develop end-to-end solutions that can be integrated into computer-aided diagnosis (CAD) systems. By improving the workflow of pathologists, these AI models have the potential to enhance the detection and diagnosis of breast cancer. This research focuses on evaluating the performance of various cutting-edge convolutional neural network (CNN) architectures in comparison to a relatively new model called the Vision Trans-former (ViT). The objective is to determine the superiority of these models in terms of their accuracy and effectiveness. The experimental results reveal that the ViT models outperform the other selected state-of-the-art CNN architectures, achieving an impressive accuracy rate of 95.15%. This study signifies a significant advancement in the field, as it explores the utilization of data augmentation and other relevant preprocessing techniques in conjunction with deep learning models for the detection and diagnosis of breast cancer using datasets of Breast Cancer Histopathological Image Classification.
Speaking the Language of Your Listener: Audience-Aware Adaptation via Plug-and-Play Theory of Mind
Authors: Ece Takmaz, Nicolo' Brandizzi, Mario Giulianelli, Sandro Pezzelle, Raquel Fernández
Date: 2023-05-31 00:00:00
Tasks: Language Modeling, Language Modelling, Open-Ended Question Answering, Text Generation

Dialogue participants may have varying levels of knowledge about the topic under discussion. In such cases, it is essential for speakers to adapt their utterances by taking their audience into account. Yet, it is an open question how such adaptation can be modelled in computational agents. In this paper, we model a visually grounded referential game between a knowledgeable speaker and a listener with more limited visual and linguistic experience. Inspired by psycholinguistic theories, we endow our speaker with the ability to adapt its referring expressions via a simulation module that monitors the effectiveness of planned utterances from the listener's perspective. We propose an adaptation mechanism building on plug-and-play approaches to controlled language generation, where utterance generation is steered on the fly by the simulator without finetuning the speaker's underlying language model. Our results and analyses show that our approach is effective: the speaker's utterances become closer to the listener's domain of expertise, which leads to higher communicative success.
MetaDiffuser: Diffusion Model as Conditional Planner for Offline Meta-RL
Authors: Fei Ni, Jianye Hao, Yao Mu, Yifu Yuan, Yan Zheng, Bin Wang, Zhixuan Liang
Date: 2023-05-31 00:00:00
Tasks: MuJoCo, Reinforcement Learning (RL)

Recently, diffusion model shines as a promising backbone for the sequence modeling paradigm in offline reinforcement learning(RL). However, these works mostly lack the generalization ability across tasks with reward or dynamics change. To tackle this challenge, in this paper we propose a task-oriented conditioned diffusion planner for offline meta-RL(MetaDiffuser), which considers the generalization problem as conditional trajectory generation task with contextual representation. The key is to learn a context conditioned diffusion model which can generate task-oriented trajectories for planning across diverse tasks. To enhance the dynamics consistency of the generated trajectories while encouraging trajectories to achieve high returns, we further design a dual-guided module in the sampling process of the diffusion model. The proposed framework enjoys the robustness to the quality of collected warm-start data from the testing task and the flexibility to incorporate with different task representation method. The experiment results on MuJoCo benchmarks show that MetaDiffuser outperforms other strong offline meta-RL baselines, demonstrating the outstanding conditional generation ability of diffusion architecture.
Representation-Driven Reinforcement Learning
Authors: Ofir Nabati, Guy Tennenholtz, Shie Mannor
Date: 2023-05-31 00:00:00
Tasks: Multi-Armed Bandits, reinforcement-learning, Reinforcement Learning

We present a representation-driven framework for reinforcement learning. By representing policies as estimates of their expected values, we leverage techniques from contextual bandits to guide exploration and exploitation. Particularly, embedding a policy network into a linear feature space allows us to reframe the exploration-exploitation problem as a representation-exploitation problem, where good policy representations enable optimal exploration. We demonstrate the effectiveness of this framework through its application to evolutionary and policy gradient-based approaches, leading to significantly improved performance compared to traditional methods. Our framework provides a new perspective on reinforcement learning, highlighting the importance of policy representation in determining optimal exploration-exploitation strategies.
Source Code Data Augmentation for Deep Learning: A Survey
Authors: Terry Yue Zhuo, Zhou Yang, Zhensu Sun, YuFei Wang, Li Li, Xiaoning Du, Zhenchang Xing, David Lo
Date: 2023-05-31 00:00:00
Tasks: Data Augmentation, Deep Learning, Survey

The increasingly popular adoption of deep learning models in many critical source code tasks motivates the development of data augmentation (DA) techniques to enhance training data and improve various capabilities (e.g., robustness and generalizability) of these models. Although a series of DA methods have been proposed and tailored for source code models, there lacks a comprehensive survey and examination to understand their effectiveness and implications. This paper fills this gap by conducting a comprehensive and integrative survey of data augmentation for source code, wherein we systematically compile and encapsulate existing literature to provide a comprehensive overview of the field. We start with an introduction of data augmentation in source code and then provide a discussion on major representative approaches. Next, we highlight the general strategies and techniques to optimize the DA quality. Subsequently, we underscore techniques useful in real-world source code scenarios and downstream tasks. Finally, we outline the prevailing challenges and potential opportunities for future research. In essence, we aim to demystify the corpus of existing literature on source code DA for deep learning, and foster further exploration in this sphere. Complementing this, we present a continually updated GitHub repository that hosts a list of update-to-date papers on DA for source code modeling, accessible at \url{https://github.com/terryyz/DataAug4Code}.
Neural LerPlane Representations for Fast 4D Reconstruction of Deformable Tissues
Authors: Chen Yang, Kailing Wang, Yuehao Wang, Xiaokang Yang, Wei Shen
Date: 2023-05-31 00:00:00
Tasks: 4D reconstruction

Reconstructing deformable tissues from endoscopic stereo videos in robotic surgery is crucial for various clinical applications. However, existing methods relying only on implicit representations are computationally expensive and require dozens of hours, which limits further practical applications. To address this challenge, we introduce LerPlane, a novel method for fast and accurate reconstruction of surgical scenes under a single-viewpoint setting. LerPlane treats surgical procedures as 4D volumes and factorizes them into explicit 2D planes of static and dynamic fields, leading to a compact memory footprint and significantly accelerated optimization. The efficient factorization is accomplished by fusing features obtained through linear interpolation of each plane and enables using lightweight neural networks to model surgical scenes. Besides, LerPlane shares static fields, significantly reducing the workload of dynamic tissue modeling. We also propose a novel sample scheme to boost optimization and improve performance in regions with tool occlusion and large motions. Experiments on DaVinci robotic surgery videos demonstrate that LerPlane accelerates optimization by over 100$\times$ while maintaining high quality across various non-rigid deformations, showing significant promise for future intraoperative surgery applications.
Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization
Authors: KaiXuan Chen, Shunyu Liu, Tongtian Zhu, Tongya Zheng, Haofei Zhang, Zunlei Feng, Jingwen Ye, Mingli Song
Date: 2023-05-31 00:00:00

Graph Neural Networks (GNNs) have emerged as a powerful category of learning architecture for handling graph-structured data. However, existing GNNs typically ignore crucial structural characteristics in node-induced subgraphs, which thus limits their expressiveness for various downstream tasks. In this paper, we strive to strengthen the representative capabilities of GNNs by devising a dedicated plug-and-play normalization scheme, termed as SUbgraph-sPEcific FactoR Embedded Normalization (SuperNorm), that explicitly considers the intra-connection information within each node-induced subgraph. To this end, we embed the subgraph-specific factor at the beginning and the end of the standard BatchNorm, as well as incorporate graph instance-specific statistics for improved distinguishable capabilities. In the meantime, we provide theoretical analysis to support that, with the elaborated SuperNorm, an arbitrary GNN is at least as powerful as the 1-WL test in distinguishing non-isomorphism graphs. Furthermore, the proposed SuperNorm scheme is also demonstrated to alleviate the over-smoothing phenomenon. Experimental results related to predictions of graph, node, and link properties on the eight popular datasets demonstrate the effectiveness of the proposed method. The code is available at https://github.com/chenchkx/SuperNorm.
fpgaHART: A toolflow for throughput-oriented acceleration of 3D CNNs for HAR onto FPGAs
Authors: Petros Toupas, Christos-Savvas Bouganis, Dimitrios Tzovaras
Date: 2023-05-31 00:00:00
Tasks: Action Recognition, Autonomous Vehicles, Retrieval, Temporal Action Localization, Video Retrieval

Surveillance systems, autonomous vehicles, human monitoring systems, and video retrieval are just few of the many applications in which 3D Convolutional Neural Networks are exploited. However, their extensive use is restricted by their high computational and memory requirements, especially when integrated into systems with limited resources. This study proposes a toolflow that optimises the mapping of 3D CNN models for Human Action Recognition onto FPGA devices, taking into account FPGA resources and off-chip memory characteristics. The proposed system employs Synchronous Dataflow (SDF) graphs to model the designs and introduces transformations to expand and explore the design space, resulting in high-throughput designs. A variety of 3D CNN models were evaluated using the proposed toolflow on multiple FPGA devices, demonstrating its potential to deliver competitive performance compared to earlier hand-tuned and model-specific designs.
Dynamic Neighborhood Construction for Structured Large Discrete Action Spaces
Authors: Fabian Akkerman, Julius Luy, Wouter van Heeswijk, Maximilian Schiffer
Date: 2023-05-31 00:00:00
Tasks: Benchmarking, Recommendation Systems

Large discrete action spaces (LDAS) remain a central challenge in reinforcement learning. Existing solution approaches can handle unstructured LDAS with up to a few million actions. However, many real-world applications in logistics, production, and transportation systems have combinatorial action spaces, whose size grows well beyond millions of actions, even on small instances. Fortunately, such action spaces exhibit structure, e.g., equally spaced discrete resource units. With this work, we focus on handling structured LDAS (SLDAS) with sizes that cannot be handled by current benchmarks: we propose Dynamic Neighborhood Construction (DNC), a novel exploitation paradigm for SLDAS. We present a scalable neighborhood exploration heuristic that utilizes this paradigm and efficiently explores the discrete neighborhood around the continuous proxy action in structured action spaces with up to $10^{73}$ actions. We demonstrate the performance of our method by benchmarking it against three state-of-the-art approaches designed for large discrete action spaces across two distinct environments. Our results show that DNC matches or outperforms state-of-the-art approaches while being computationally more efficient. Furthermore, our method scales to action spaces that so far remained computationally intractable for existing methodologies.
Human Control: Definitions and Algorithms
Authors: Ryan Carey, Tom Everitt
Date: 2023-05-31 00:00:00

How can humans stay in control of advanced artificial intelligence systems? One proposal is corrigibility, which requires the agent to follow the instructions of a human overseer, without inappropriately influencing them. In this paper, we formally define a variant of corrigibility called shutdown instructability, and show that it implies appropriate shutdown behavior, retention of human autonomy, and avoidance of user harm. We also analyse the related concepts of non-obstruction and shutdown alignment, three previously proposed algorithms for human control, and one new algorithm.
A Survey on Large Language Models for Recommendation
Authors: Likang Wu, Zhi Zheng, Zhaopeng Qiu, Hao Wang, Hongchao Gu, Tingjia Shen, Chuan Qin, Chen Zhu, HengShu Zhu, Qi Liu, Hui Xiong, Enhong Chen
Date: 2023-05-31 00:00:00
Tasks: Recommendation Systems, Self-Supervised Learning, Survey

Large Language Models (LLMs) have emerged as powerful tools in the field of Natural Language Processing (NLP) and have recently gained significant attention in the domain of Recommendation Systems (RS). These models, trained on massive amounts of data using self-supervised learning, have demonstrated remarkable success in learning universal representations and have the potential to enhance various aspects of recommendation systems by some effective transfer techniques such as fine-tuning and prompt tuning, and so on. The crucial aspect of harnessing the power of language models in enhancing recommendation quality is the utilization of their high-quality representations of textual features and their extensive coverage of external knowledge to establish correlations between items and users. To provide a comprehensive understanding of the existing LLM-based recommendation systems, this survey presents a taxonomy that categorizes these models into two major paradigms, respectively Discriminative LLM for Recommendation (DLLM4Rec) and Generative LLM for Recommendation (GLLM4Rec), with the latter being systematically sorted out for the first time. Furthermore, we systematically review and analyze existing LLM-based recommendation systems within each paradigm, providing insights into their methodologies, techniques, and performance. Additionally, we identify key challenges and several valuable findings to provide researchers and practitioners with inspiration. We have also created a GitHub repository to index relevant papers on LLMs for recommendation, https://github.com/WLiK/LLM4Rec.