pwc-archive/papers-with-abstracts huggingface dataset:
DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings
Authors: Zhihan Zhou, Weimin Wu, Harrison Ho, Jiayi Wang, Lizhen Shi, Ramana V Davuluri, Zhong Wang, Han Liu
Date: 2024-02-13 00:00:00
Tasks: Contrastive Learning

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C$^2$LR) strategy. Empirical results on 23 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. Model, codes, and data are publicly available at \url{https://github.com/MAGICS-LAB/DNABERT_S}.
Optimal Task Assignment and Path Planning using Conflict-Based Search with Precedence and Temporal Constraints
Authors: Yu Quan Chong, Jiaoyang Li, Katia Sycara
Date: 2024-02-13 00:00:00
Tasks: Multi-Agent Path Finding, Reinforcement Learning (RL)

The Multi-Agent Path Finding (MAPF) problem entails finding collision-free paths for a set of agents, guiding them from their start to goal locations. However, MAPF does not account for several practical task-related constraints. For example, agents may need to perform actions at goal locations with specific execution times, adhering to predetermined orders and timeframes. Moreover, goal assignments may not be predefined for agents, and the optimization objective may lack an explicit definition. To incorporate task assignment, path planning, and a user-defined objective into a coherent framework, this paper examines the Task Assignment and Path Finding with Precedence and Temporal Constraints (TAPF-PTC) problem. We augment Conflict-Based Search (CBS) to simultaneously generate task assignments and collision-free paths that adhere to precedence and temporal constraints, maximizing an objective quantified by the return from a user-defined reward function in reinforcement learning (RL). Experimentally, we demonstrate that our algorithm, CBS-TA-PTC, can solve highly challenging bomb-defusing tasks with precedence and temporal constraints efficiently relative to MARL and adapted Target Assignment and Path Finding (TAPF) methods.
JAMDEC: Unsupervised Authorship Obfuscation using Constrained Decoding over Small Language Models
Authors: Jillian Fisher, Ximing Lu, JaeHun Jung, Liwei Jiang, Zaid Harchaoui, Yejin Choi
Date: 2024-02-13 00:00:00

The permanence of online content combined with the enhanced authorship identification techniques calls for stronger computational methods to protect the identity and privacy of online authorship when needed, e.g., blind reviews for scientific papers, anonymous online reviews, or anonymous interactions in the mental health forums. In this paper, we propose an unsupervised inference-time approach to authorship obfuscation to address the unique challenges of authorship obfuscation: lack of supervision data for diverse authorship and domains, and the need for a sufficient level of revision beyond simple paraphrasing to obfuscate the authorship, all the while preserving the original content and fluency. We introduce JAMDEC, a user-controlled, inference-time algorithm for authorship obfuscation that can be in principle applied to any text and authorship. Our approach builds on small language models such as GPT2-XL in order to help avoid disclosing the original content to proprietary LLM's APIs, while also reducing the performance gap between small and large language models via algorithmic enhancement. The key idea behind our approach is to boost the creative power of smaller language models through constrained decoding, while also allowing for user-specified controls and flexibility. Experimental results demonstrate that our approach based on GPT2-XL outperforms previous state-of-the-art methods based on comparably small models, while performing competitively against GPT3.5 175B, a propriety model that is two orders of magnitudes larger.
LLM-driven Imitation of Subrational Behavior : Illusion or Reality?
Authors: Andrea Coletta, Kshama Dwarakanath, Penghang Liu, Svitlana Vyetrenko, Tucker Balch
Date: 2024-02-13 00:00:00
Tasks: Imitation Learning

Modeling subrational agents, such as humans or economic households, is inherently challenging due to the difficulty in calibrating reinforcement learning models or collecting data that involves human subjects. Existing work highlights the ability of Large Language Models (LLMs) to address complex reasoning tasks and mimic human communication, while simulation using LLMs as agents shows emergent social behaviors, potentially improving our comprehension of human conduct. In this paper, we propose to investigate the use of LLMs to generate synthetic human demonstrations, which are then used to learn subrational agent policies though Imitation Learning. We make an assumption that LLMs can be used as implicit computational models of humans, and propose a framework to use synthetic demonstrations derived from LLMs to model subrational behaviors that are characteristic of humans (e.g., myopic behavior or preference for risk aversion). We experimentally evaluate the ability of our framework to model sub-rationality through four simple scenarios, including the well-researched ultimatum game and marshmallow experiment. To gain confidence in our framework, we are able to replicate well-established findings from prior human studies associated with the above scenarios. We conclude by discussing the potential benefits, challenges and limitations of our framework.
PRDP: Proximal Reward Difference Prediction for Large-Scale Reward Finetuning of Diffusion Models
Authors: Fei Deng, Qifei Wang, Wei Wei, Matthias Grundmann, Tingbo Hou
Date: 2024-02-13 00:00:00
Proceeding: CVPR 2024 1
Tasks: Denoising, Reinforcement Learning (RL)

Reward finetuning has emerged as a promising approach to aligning foundation models with downstream objectives. Remarkable success has been achieved in the language domain by using reinforcement learning (RL) to maximize rewards that reflect human preference. However, in the vision domain, existing RL-based reward finetuning methods are limited by their instability in large-scale training, rendering them incapable of generalizing to complex, unseen prompts. In this paper, we propose Proximal Reward Difference Prediction (PRDP), enabling stable black-box reward finetuning for diffusion models for the first time on large-scale prompt datasets with over 100K prompts. Our key innovation is the Reward Difference Prediction (RDP) objective that has the same optimal solution as the RL objective while enjoying better training stability. Specifically, the RDP objective is a supervised regression objective that tasks the diffusion model with predicting the reward difference of generated image pairs from their denoising trajectories. We theoretically prove that the diffusion model that obtains perfect reward difference prediction is exactly the maximizer of the RL objective. We further develop an online algorithm with proximal updates to stably optimize the RDP objective. In experiments, we demonstrate that PRDP can match the reward maximization ability of well-established RL-based methods in small-scale training. Furthermore, through large-scale training on text prompts from the Human Preference Dataset v2 and the Pick-a-Pic v1 dataset, PRDP achieves superior generation quality on a diverse set of complex, unseen prompts whereas RL-based methods completely fail.
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
Authors: Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein
Date: 2024-02-13 00:00:00
Tasks: Drug Design

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.
PRompt Optimization in Multi-Step Tasks (PROMST): Integrating Human Feedback and Heuristic-based Sampling
Authors: Yongchao Chen, Jacob Arkin, Yilun Hao, Yang Zhang, Nicholas Roy, Chuchu Fan
Date: 2024-02-13 00:00:00
Tasks: Language Modelling, Large Language Model

Prompt optimization aims to find the best prompt to a large language model (LLM) for a given task. LLMs have been successfully used to help find and improve prompt candidates for single-step tasks. However, realistic tasks for agents are multi-step and introduce new challenges: (1) Prompt content is likely to be more extensive and complex, making it more difficult for LLMs to analyze errors, (2) the impact of an individual step is difficult to evaluate, and (3) different people may have varied preferences about task execution. While humans struggle to optimize prompts, they are good at providing feedback about LLM outputs; we therefore introduce a new LLM-driven discrete prompt optimization framework PRompt Optimization in Multi-Step Tasks (PROMST) that incorporates human-designed feedback rules to automatically offer direct suggestions for improvement. We also use an extra learned heuristic model that predicts prompt performance to efficiently sample from prompt candidates. This approach significantly outperforms both human-engineered prompts and several other prompt optimization methods across 11 representative multi-step tasks (an average 10.6\%-29.3\% improvement to current best methods on five LLMs respectively). We believe our work can serve as a benchmark for automatic prompt optimization for LLM-driven multi-step tasks. Datasets and Codes are available at https://github.com/yongchao98/PROMST. Project Page is available at https://yongchao98.github.io/MIT-REALM-PROMST.
Analyzing Prompt Influence on Automated Method Generation: An Empirical Study with Copilot
Authors: Ionut Daniel Fagadau, Leonardo Mariani, Daniela Micucci, Oliviero Riganelli
Date: 2024-02-13 00:00:00
Tasks: Prompt Engineering

Generative AI is changing the way developers interact with software systems, providing services that can produce and deliver new content, crafted to satisfy the actual needs of developers. For instance, developers can ask for new code directly from within their IDEs by writing natural language prompts, and integrated services based on generative AI, such as Copilot, immediately respond to prompts by providing ready-to-use code snippets. Formulating the prompt appropriately, and incorporating the useful information while avoiding any information overload, can be an important factor in obtaining the right piece of code. The task of designing good prompts is known as prompt engineering. In this paper, we systematically investigate the influence of eight prompt features on the style and the content of prompts, on the level of correctness, complexity, size, and similarity to the developers' code of the generated code. We specifically consider the task of using Copilot with 124,800 prompts obtained by systematically combining the eight considered prompt features to generate the implementation of 200 Java methods. Results show how some prompt features, such as the presence of examples and the summary of the purpose of the method, can significantly influence the quality of the result.
Evaluation of Activated Sludge Settling Characteristics from Microscopy Images with Deep Convolutional Neural Networks and Transfer Learning
Authors: Sina Borzooei, Leonardo Scabini, Gisele Miranda, Saba Daneshgar, Lukas Deblieck, Piet De Langhe, Odemir Bruno, Bernard De Baets, Ingmar Nopens, Elena Torfs
Date: 2024-02-14 00:00:00
Tasks: Data Augmentation, Transfer Learning

Microbial communities play a key role in biological wastewater treatment processes. Activated sludge settling characteristics, for example, are affected by microbial community composition, varying by changes in operating conditions and influent characteristics of wastewater treatment plants (WWTPs). Timely assessment and prediction of changes in microbial composition leading to settling problems, such as filamentous bulking (FB), can prevent operational challenges, reductions in treatment efficiency, and adverse environmental impacts. This study presents an innovative computer vision-based approach to assess activated sludge-settling characteristics based on the morphological properties of flocs and filaments in microscopy images. Implementing the transfer learning of deep convolutional neural network (CNN) models, this approach aims to overcome the limitations of existing quantitative image analysis techniques. The offline microscopy image dataset was collected over two years, with weekly sampling at a full-scale industrial WWTP in Belgium. Multiple data augmentation techniques were employed to enhance the generalizability of the CNN models. Various CNN architectures, including Inception v3, ResNet18, ResNet152, ConvNeXt-nano, and ConvNeXt-S, were tested to evaluate their performance in predicting sludge settling characteristics. The sludge volume index was used as the final prediction variable, but the method can easily be adjusted to predict any other settling metric of choice. The results showed that the suggested CNN-based approach provides less labour-intensive, objective, and consistent assessments, while transfer learning notably minimises the training phase, resulting in a generalizable system that can be employed in real-time applications.
Pruning Sparse Tensor Neural Networks Enables Deep Learning for 3D Ultrasound Localization Microscopy
Authors: Brice Rauby, Paul Xing, Jonathan Porée, Maxime Gasse, Jean Provost
Date: 2024-02-14 00:00:00
Tasks: Deep Learning

Ultrasound Localization Microscopy (ULM) is a non-invasive technique that allows for the imaging of micro-vessels in vivo, at depth and with a resolution on the order of ten microns. ULM is based on the sub-resolution localization of individual microbubbles injected in the bloodstream. Mapping the whole angioarchitecture requires the accumulation of microbubbles trajectories from thousands of frames, typically acquired over a few minutes. ULM acquisition times can be reduced by increasing the microbubble concentration, but requires more advanced algorithms to detect them individually. Several deep learning approaches have been proposed for this task, but they remain limited to 2D imaging, in part due to the associated large memory requirements. Herein, we propose to use sparse tensor neural networks to reduce memory usage in 2D and to improve the scaling of the memory requirement for the extension of deep learning architecture to 3D. We study several approaches to efficiently convert ultrasound data into a sparse format and study the impact of the associated loss of information. When applied in 2D, the sparse formulation reduces the memory requirements by a factor 2 at the cost of a small reduction of performance when compared against dense networks. In 3D, the proposed approach reduces memory requirements by two order of magnitude while largely outperforming conventional ULM in high concentration settings. We show that Sparse Tensor Neural Networks in 3D ULM allow for the same benefits as dense deep learning based method in 2D ULM i.e. the use of higher concentration in silico and reduced acquisition time.
DoRA: Weight-Decomposed Low-Rank Adaptation
Authors: Shih-Yang Liu, Chien-Yi Wang, Hongxu Yin, Pavlo Molchanov, Yu-Chiang Frank Wang, Kwang-Ting Cheng, Min-Hung Chen
Date: 2024-02-14 00:00:00
Tasks: parameter-efficient fine-tuning

Among the widely used parameter-efficient fine-tuning (PEFT) methods, LoRA and its variants have gained considerable popularity because of avoiding additional inference costs. However, there still often exists an accuracy gap between these methods and full fine-tuning (FT). In this work, we first introduce a novel weight decomposition analysis to investigate the inherent differences between FT and LoRA. Aiming to resemble the learning capacity of FT from the findings, we propose Weight-Decomposed Low-Rank Adaptation (DoRA). DoRA decomposes the pre-trained weight into two components, magnitude and direction, for fine-tuning, specifically employing LoRA for directional updates to efficiently minimize the number of trainable parameters. By employing \ours, we enhance both the learning capacity and training stability of LoRA while avoiding any additional inference overhead. \ours~consistently outperforms LoRA on fine-tuning LLaMA, LLaVA, and VL-BART on various downstream tasks, such as commonsense reasoning, visual instruction tuning, and image/video-text understanding. Code is available at https://github.com/NVlabs/DoRA.
Registration of Longitudinal Spine CTs for Monitoring Lesion Growth
Authors: Malika Sanhinova, Nazim Haouchine, Steve D. Pieper, William M. Wells III, Tracy A. Balboni, Alexander Spektor, Mai Anh Huynh, Jeffrey P. Guenette, Bryan Czajkowski, Sarah Caplan, Patrick Doyle, Heejoo Kang, David B. Hackney, Ron N. Alkalay
Date: 2024-02-14 00:00:00

Accurate and reliable registration of longitudinal spine images is essential for assessment of disease progression and surgical outcome. Implementing a fully automatic and robust registration is crucial for clinical use, however, it is challenging due to substantial change in shape and appearance due to lesions. In this paper we present a novel method to automatically align longitudinal spine CTs and accurately assess lesion progression. Our method follows a two-step pipeline where vertebrae are first automatically localized, labeled and 3D surfaces are generated using a deep learning model, then longitudinally aligned using a Gaussian mixture model surface registration. We tested our approach on 37 vertebrae, from 5 patients, with baseline CTs and 3, 6, and 12 months follow-ups leading to 111 registrations. Our experiment showed accurate registration with an average Hausdorff distance of 0.65 mm and average Dice score of 0.92.
YOLOv8-AM: YOLOv8 Based on Effective Attention Mechanisms for Pediatric Wrist Fracture Detection
Authors: Chun-Tse Chien, Rui-Yang Ju, Kuang-Yi Chou, Enkaer Xieerke, Jen-Shiun Chiang
Date: 2024-02-14 00:00:00
Tasks: Fracture detection, medical image detection, Medical Object Detection, Object Detection, Open Vocabulary Object Detection

Wrist trauma and even fractures occur frequently in daily life, particularly among children who account for a significant proportion of fracture cases. Before performing surgery, surgeons often request patients to undergo X-ray imaging first and prepare for it based on the analysis of the radiologist. With the development of neural networks, You Only Look Once (YOLO) series models have been widely used in fracture detection as computer-assisted diagnosis (CAD). In 2023, Ultralytics presented the latest version of the YOLO models, which has been employed for detecting fractures across various parts of the body. Attention mechanism is one of the hottest methods to improve the model performance. This research work proposes YOLOv8-AM, which incorporates the attention mechanism into the original YOLOv8 architecture. Specifically, we respectively employ four attention modules, Convolutional Block Attention Module (CBAM), Global Attention Mechanism (GAM), Efficient Channel Attention (ECA), and Shuffle Attention (SA), to design the improved models and train them on GRAZPEDWRI-DX dataset. Experimental results demonstrate that the mean Average Precision at IoU 50 (mAP 50) of the YOLOv8-AM model based on ResBlock + CBAM (ResCBAM) increased from 63.6% to 65.8%, which achieves the state-of-the-art (SOTA) performance. Conversely, YOLOv8-AM model incorporating GAM obtains the mAP 50 value of 64.2%, which is not a satisfactory enhancement. Therefore, we combine ResBlock and GAM, introducing ResGAM to design another new YOLOv8-AM model, whose mAP 50 value is increased to 65.0%. The implementation code for this study is available on GitHub at https://github.com/RuiyangJu/Fracture_Detection_Improved_YOLOv8.
PC-NeRF: Parent-Child Neural Radiance Fields Using Sparse LiDAR Frames in Autonomous Driving Environments
Authors: Xiuzhong Hu, Guangming Xiong, Zheng Zang, Peng Jia, Yuxuan Han, Junyi Ma
Date: 2024-02-14 00:00:00
Tasks: 3D Reconstruction, 3D Scene Reconstruction, Autonomous Driving, Autonomous Vehicles, NeRF, Novel LiDAR View Synthesis, Novel View Synthesis

Large-scale 3D scene reconstruction and novel view synthesis are vital for autonomous vehicles, especially utilizing temporally sparse LiDAR frames. However, conventional explicit representations remain a significant bottleneck towards representing the reconstructed and synthetic scenes at unlimited resolution. Although the recently developed neural radiance fields (NeRF) have shown compelling results in implicit representations, the problem of large-scale 3D scene reconstruction and novel view synthesis using sparse LiDAR frames remains unexplored. To bridge this gap, we propose a 3D scene reconstruction and novel view synthesis framework called parent-child neural radiance field (PC-NeRF). Based on its two modules, parent NeRF and child NeRF, the framework implements hierarchical spatial partitioning and multi-level scene representation, including scene, segment, and point levels. The multi-level scene representation enhances the efficient utilization of sparse LiDAR point cloud data and enables the rapid acquisition of an approximate volumetric scene representation. With extensive experiments, PC-NeRF is proven to achieve high-precision novel LiDAR view synthesis and 3D reconstruction in large-scale scenes. Moreover, PC-NeRF can effectively handle situations with sparse LiDAR frames and demonstrate high deployment efficiency with limited training epochs. Our approach implementation and the pre-trained models are available at https://github.com/biter0088/pc-nerf.