pwc-archive/papers-with-abstracts huggingface dataset:
Precision at Scale: Domain-Specific Datasets On-Demand
Authors: Jesús M Rodríguez-de-Vera, Imanol G Estepa, Ignacio Sarasúa, Bhalaji Nagarajan, Petia Radeva
Date: 2024-07-03 00:00:00
Tasks: Self-Supervised Learning

In the realm of self-supervised learning (SSL), conventional wisdom has gravitated towards the utility of massive, general domain datasets for pretraining robust backbones. In this paper, we challenge this idea by exploring if it is possible to bridge the scale between general-domain datasets and (traditionally smaller) domain-specific datasets to reduce the current performance gap. More specifically, we propose Precision at Scale (PaS), a novel method for the autonomous creation of domain-specific datasets on-demand. The modularity of the PaS pipeline enables leveraging state-of-the-art foundational and generative models to create a collection of images of any given size belonging to any given domain with minimal human intervention. Extensive analysis in two complex domains, proves the superiority of PaS datasets over existing traditional domain-specific datasets in terms of diversity, scale, and effectiveness in training visual transformers and convolutional neural networks. Most notably, we prove that automatically generated domain-specific datasets lead to better pretraining than large-scale supervised datasets such as ImageNet-1k and ImageNet-21k. Concretely, models trained on domain-specific datasets constructed by PaS pipeline, beat ImageNet-1k pretrained backbones by at least 12% in all the considered domains and classification tasks and lead to better food domain performance than supervised ImageNet-21k pretrain while being 12 times smaller. Code repository: https://github.com/jesusmolrdv/Precision-at-Scale/
Collaborative Quest Completion with LLM-driven Non-Player Characters in Minecraft
Authors: Sudha Rao, Weijia Xu, Michael Xu, Jorge Leandro, Ken Lobb, Gabriel DesGarennes, Chris Brockett, Bill Dolan
Date: 2024-07-03 00:00:00
Tasks: Minecraft

The use of generative AI in video game development is on the rise, and as the conversational and other capabilities of large language models continue to improve, we expect LLM-driven non-player characters (NPCs) to become widely deployed. In this paper, we seek to understand how human players collaborate with LLM-driven NPCs to accomplish in-game goals. We design a minigame within Minecraft where a player works with two GPT4-driven NPCs to complete a quest. We perform a user study in which 28 Minecraft players play this minigame and share their feedback. On analyzing the game logs and recordings, we find that several patterns of collaborative behavior emerge from the NPCs and the human players. We also report on the current limitations of language-only models that do not have rich game-state or visual understanding. We believe that this preliminary study and analysis will inform future game developers on how to better exploit these rapidly improving generative AI models for collaborative roles in games.
Towards Asimov's Psychohistory: Harnessing Topological Data Analysis, Artificial Intelligence and Social Media data to Forecast Societal Trends
Authors: Isabela Rocha
Date: 2024-07-03 00:00:00
Tasks: Sociology, Topological Data Analysis

In the age of big data and advanced computational methods, the prediction of large-scale social behaviors, reminiscent of Isaac Asimov's fictional science of Psychohistory, is becoming increasingly feasible. This paper consists of a theoretical exploration of the integration of computational power and mathematical frameworks, particularly through Topological Data Analysis (TDA) (Carlsson, Vejdemo-Johansson, 2022) and Artificial Intelligence (AI), to forecast societal trends through social media data analysis. By examining social media as a reflective surface of collective human behavior through the systematic behaviorist approach (Glenn, et al., 2016), I argue that these tools provide unprecedented clarity into the dynamics of large communities. This study dialogues with Asimov's work, drawing parallels between his visionary concepts and contemporary methodologies, illustrating how modern computational techniques can uncover patterns and predict shifts in social behavior, contributing to the emerging field of digital sociology -- or even, Psychohistory itself.
HEMM: Holistic Evaluation of Multimodal Foundation Models
Authors: Paul Pu Liang, Akshay Goindani, Talha Chafekar, Leena Mathur, Haofei Yu, Ruslan Salakhutdinov, Louis-Philippe Morency
Date: 2024-07-03 00:00:00

Multimodal foundation models that can holistically process text alongside images, video, audio, and other sensory modalities are increasingly used in a variety of real-world applications. However, it is challenging to characterize and study progress in multimodal foundation models, given the range of possible modeling decisions, tasks, and domains. In this paper, we introduce Holistic Evaluation of Multimodal Models (HEMM) to systematically evaluate the capabilities of multimodal foundation models across a set of 3 dimensions: basic skills, information flow, and real-world use cases. Basic multimodal skills are internal abilities required to solve problems, such as learning interactions across modalities, fine-grained alignment, multi-step reasoning, and the ability to handle external knowledge. Information flow studies how multimodal content changes during a task through querying, translation, editing, and fusion. Use cases span domain-specific challenges introduced in real-world multimedia, affective computing, natural sciences, healthcare, and human-computer interaction applications. Through comprehensive experiments across the 30 tasks in HEMM, we (1) identify key dataset dimensions (e.g., basic skills, information flows, and use cases) that pose challenges to today's models, and (2) distill performance trends regarding how different modeling dimensions (e.g., scale, pre-training data, multimodal alignment, pre-training, and instruction tuning objectives) influence performance. Our conclusions regarding challenging multimodal interactions, use cases, and tasks requiring reasoning and external knowledge, the benefits of data and model scale, and the impacts of instruction tuning yield actionable insights for future work in multimodal foundation models.
M5: A Whole Genome Bacterial Encoder at Single Nucleotide Resolution
Authors: Agust Egilsson
Date: 2024-07-03 00:00:00
Tasks: GPU

A linear attention mechanism is described to extend the context length of an encoder only transformer, called M5 in this report, to a multi-million single nucleotide resolution foundation model pretrained on bacterial whole genomes. The linear attention mechanism used approximates a full quadratic attention mechanism tightly and has a simple and lightweight implementation for the use case when the key-query embedding dimensionality is low. The M5-small model is entirely trained and tested on one A100 GPU with 40gb of memory up to 196K nucleotides during training and 2M nucleotides during testing. We test the performance of the M5-small model and record notable improvements in performance as whole genome bacterial sequence lengths are increased as well as demonstrating the stability of the full multi-head attention approximation used as sequence length is increased.
Soft Begging: Modular and Efficient Shielding of LLMs against Prompt Injection and Jailbreaking based on Prompt Tuning
Authors: Simon Ostermann, Kevin Baum, Christoph Endres, Julia Masloh, Patrick Schramowski
Date: 2024-07-03 00:00:00

Prompt injection (both direct and indirect) and jailbreaking are now recognized as significant issues for large language models (LLMs), particularly due to their potential for harm in application-integrated contexts. This extended abstract explores a novel approach to protecting LLMs from such attacks, termed "soft begging." This method involves training soft prompts to counteract the effects of corrupted prompts on the LLM's output. We provide an overview of prompt injections and jailbreaking, introduce the theoretical basis of the "soft begging" technique, and discuss an evaluation of its effectiveness.
ConCodeEval: Evaluating Large Language Models for Code Constraints in Domain-Specific Languages
Authors: Mehant Kammakomati, Sameer Pimparkhede, Srikanth Tamilselvam, Prince Kumar, Pushpak Bhattacharyya
Date: 2024-07-03 00:00:00
Tasks: Text Generation

Recent work shows Large Language Models (LLMs) struggle to understand natural language constraints for various text generation tasks in zero- and few-shot settings. While, in the code domain, there is wide usage of constraints in code format to maintain the integrity of code written in Domain-Specific Languages (DSLs) like JSON and YAML which are widely used for system-level programming tasks in enterprises. Given that LLMs are increasingly used for system-level code tasks, evaluating if they can comprehend these code constraints is crucial. However, no work has been done to evaluate their controllability over code constraints. Hence, we introduce ConCodeEval, a first-of-its-kind benchmark having two novel tasks for code constraints across five representations. Our findings suggest that language models struggle with code constraints. Code languages that perform excellently for normal code tasks do not perform well when the same languages represent fine-grained constraints.
SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing
Authors: Devam Mondal, Atharva Inamdar
Date: 2024-07-02 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model

RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like Illumina's next-generation sequencing (NGS) are used to produce the raw data for this experimental procedure. This raw FASTQ data must then be prepared via a complex series of data manipulations by bioinformaticians. This process currently takes place on an unwieldy textual user interface like a terminal/command line that requires the user to install and import multiple program packages, preventing the untrained biologist from initiating data analysis. Open-source platforms like Galaxy have produced a more user-friendly pipeline, yet the visual interface remains cluttered and highly technical, remaining uninviting for the natural scientist. To address this, SeqMate is a user-friendly tool that allows for one-click analytics by utilizing the power of a large language model (LLM) to automate both data preparation and analysis (differential expression, trajectory analysis, etc). Furthermore, by utilizing the power of generative AI, SeqMate is also capable of analyzing such findings and producing written reports of upregulated/downregulated/user-prompted genes with sources cited from known repositories like PubMed, PDB, and Uniprot.
Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties
Authors: Srivathsan Badrinarayanan, Chakradhar Guntuboina, Parisa Mollaei, Amir Barati Farimani
Date: 2024-07-02 00:00:00
Tasks: Graph Learning, Property Prediction

Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.
VCoME: Verbal Video Composition with Multimodal Editing Effects
Authors: Weibo Gong, Xiaojie Jin, Xin Li, Dongliang He, Xinglong Wu
Date: 2024-07-05 00:00:00

Verbal videos, featuring voice-overs or text overlays, provide valuable content but present significant challenges in composition, especially when incorporating editing effects to enhance clarity and visual appeal. In this paper, we introduce the novel task of verbal video composition with editing effects. This task aims to generate coherent and visually appealing verbal videos by integrating multimodal editing effects across textual, visual, and audio categories. To achieve this, we curate a large-scale dataset of video effects compositions from publicly available sources. We then formulate this task as a generative problem, involving the identification of appropriate positions in the verbal content and the recommendation of editing effects for these positions. To address this task, we propose VCoME, a general framework that employs a large multimodal model to generate editing effects for video composition. Specifically, VCoME takes in the multimodal video context and autoregressively outputs where to apply effects within the verbal content and which effects are most appropriate for each position. VCoME also supports prompt-based control of composition density and style, providing substantial flexibility for diverse applications. Through extensive quantitative and qualitative evaluations, we clearly demonstrate the effectiveness of VCoME. A comprehensive user study shows that our method produces videos of professional quality while being 85$\times$ more efficient than professional editors.
Enhancing Vehicle Re-identification and Matching for Weaving Analysis
Authors: Mei Qiu, Wei Lin, Stanley Chien, Lauren Christopher, Yaobin Chen, Shu Hu
Date: 2024-07-05 00:00:00
Tasks: Management, Vehicle Re-Identification

Vehicle weaving on highways contributes to traffic congestion, raises safety issues, and underscores the need for sophisticated traffic management systems. Current tools are inadequate in offering precise and comprehensive data on lane-specific weaving patterns. This paper introduces an innovative method for collecting non-overlapping video data in weaving zones, enabling the generation of quantitative insights into lane-specific weaving behaviors. Our experimental results confirm the efficacy of this approach, delivering critical data that can assist transportation authorities in enhancing traffic control and roadway infrastructure.
Embracing Massive Medical Data
Authors: Yu-Cheng Chou, Zongwei Zhou, Alan Yuille
Date: 2024-07-05 00:00:00
Tasks: Tumor Segmentation

As massive medical data become available with an increasing number of scans, expanding classes, and varying sources, prevalent training paradigms -- where AI is trained with multiple passes over fixed, finite datasets -- face significant challenges. First, training AI all at once on such massive data is impractical as new scans/sources/classes continuously arrive. Second, training AI continuously on new scans/sources/classes can lead to catastrophic forgetting, where AI forgets old data as it learns new data, and vice versa. To address these two challenges, we propose an online learning method that enables training AI from massive medical data. Instead of repeatedly training AI on randomly selected data samples, our method identifies the most significant samples for the current AI model based on their data uniqueness and prediction uncertainty, then trains the AI on these selective data samples. Compared with prevalent training paradigms, our method not only improves data efficiency by enabling training on continual data streams, but also mitigates catastrophic forgetting by selectively training AI on significant data samples that might otherwise be forgotten, outperforming by 15% in Dice score for multi-organ and tumor segmentation. The code is available at https://github.com/MrGiovanni/OnlineLearning
Efficient Betti Matching Enables Topology-Aware 3D Segmentation via Persistent Homology
Authors: Nico Stucki, Vincent Bürgin, Johannes C. Paetzold, Ulrich Bauer
Date: 2024-07-05 00:00:00
Tasks: Segmentation, Topological Data Analysis

In this work, we propose an efficient algorithm for the calculation of the Betti matching, which can be used as a loss function to train topology aware segmentation networks. Betti matching loss builds on techniques from topological data analysis, specifically persistent homology. A major challenge is the computational cost of computing persistence barcodes. In response to this challenge, we propose a new, highly optimized implementation of Betti matching, implemented in C++ together with a python interface, which achieves significant speedups compared to the state-of-the-art implementation Cubical Ripser. We use Betti matching 3D to train segmentation networks with the Betti matching loss and demonstrate improved topological correctness of predicted segmentations across several datasets. The source code is available at https://github.com/nstucki/Betti-Matching-3D.
Unsupervised 4D Cardiac Motion Tracking with Spatiotemporal Optical Flow Networks
Authors: Long Teng, Wei Feng, Menglong Zhu, Xinchao Li
Date: 2024-07-05 00:00:00
Tasks: Optical Flow Estimation

Cardiac motion tracking from echocardiography can be used to estimate and quantify myocardial motion within a cardiac cycle. It is a cost-efficient and effective approach for assessing myocardial function. However, ultrasound imaging has the inherent characteristics of spatially low resolution and temporally random noise, which leads to difficulties in obtaining reliable annotation. Thus it is difficult to perform supervised learning for motion tracking. In addition, there is no end-to-end unsupervised method currently in the literature. This paper presents a motion tracking method where unsupervised optical flow networks are designed with spatial reconstruction loss and temporal-consistency loss. Our proposed loss functions make use of the pair-wise and temporal correlation to estimate cardiac motion from noisy background. Experiments using a synthetic 4D echocardiography dataset has shown the effectiveness of our approach, and its superiority over existing methods on both accuracy and running speed. To the best of our knowledge, this is the first work performed that uses unsupervised end-to-end deep learning optical flow network for 4D cardiac motion tracking.
SAM Fewshot Finetuning for Anatomical Segmentation in Medical Images
Authors: Weiyi Xie, Nathalie Willems, Shubham Patil, Yang Li, Mayank Kumar
Date: 2024-07-05 00:00:00
Tasks: Decoder, Segmentation

We propose a straightforward yet highly effective few-shot fine-tuning strategy for adapting the Segment Anything (SAM) to anatomical segmentation tasks in medical images. Our novel approach revolves around reformulating the mask decoder within SAM, leveraging few-shot embeddings derived from a limited set of labeled images (few-shot collection) as prompts for querying anatomical objects captured in image embeddings. This innovative reformulation greatly reduces the need for time-consuming online user interactions for labeling volumetric images, such as exhaustively marking points and bounding boxes to provide prompts slice by slice. With our method, users can manually segment a few 2D slices offline, and the embeddings of these annotated image regions serve as effective prompts for online segmentation tasks. Our method prioritizes the efficiency of the fine-tuning process by exclusively training the mask decoder through caching mechanisms while keeping the image encoder frozen. Importantly, this approach is not limited to volumetric medical images, but can generically be applied to any 2D/3D segmentation task. To thoroughly evaluate our method, we conducted extensive validation on four datasets, covering six anatomical segmentation tasks across two modalities. Furthermore, we conducted a comparative analysis of different prompting options within SAM and the fully-supervised nnU-Net. The results demonstrate the superior performance of our method compared to SAM employing only point prompts (approximately 50% improvement in IoU) and performs on-par with fully supervised methods whilst reducing the requirement of labeled data by at least an order of magnitude.
Semi-Supervised Segmentation via Embedding Matching
Authors: Weiyi Xie, Nathalie Willems, Nikolas Lessmann, Tom Gibbons, Daniele De Massari
Date: 2024-07-05 00:00:00
Tasks: Image Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation

Deep convolutional neural networks are widely used in medical image segmentation but require many labeled images for training. Annotating three-dimensional medical images is a time-consuming and costly process. To overcome this limitation, we propose a novel semi-supervised segmentation method that leverages mostly unlabeled images and a small set of labeled images in training. Our approach involves assessing prediction uncertainty to identify reliable predictions on unlabeled voxels from the teacher model. These voxels serve as pseudo-labels for training the student model. In voxels where the teacher model produces unreliable predictions, pseudo-labeling is carried out based on voxel-wise embedding correspondence using reference voxels from labeled images. We applied this method to automate hip bone segmentation in CT images, achieving notable results with just 4 CT scans. The proposed approach yielded a Hausdorff distance with 95th percentile (HD95) of 3.30 and IoU of 0.929, surpassing existing methods achieving HD95 (4.07) and IoU (0.927) at their best.
OneRestore: A Universal Restoration Framework for Composite Degradation
Authors: Yu Guo, Yuan Gao, Yuxu Lu, Huilin Zhu, Ryan Wen Liu, Shengfeng He
Date: 2024-07-05 00:00:00
Tasks: Image Dehazing, Image Restoration, Low-Light Image Enhancement, Rain Removal, Snow Removal

In real-world scenarios, image impairments often manifest as composite degradations, presenting a complex interplay of elements such as low light, haze, rain, and snow. Despite this reality, existing restoration methods typically target isolated degradation types, thereby falling short in environments where multiple degrading factors coexist. To bridge this gap, our study proposes a versatile imaging model that consolidates four physical corruption paradigms to accurately represent complex, composite degradation scenarios. In this context, we propose OneRestore, a novel transformer-based framework designed for adaptive, controllable scene restoration. The proposed framework leverages a unique cross-attention mechanism, merging degraded scene descriptors with image features, allowing for nuanced restoration. Our model allows versatile input scene descriptors, ranging from manual text embeddings to automatic extractions based on visual attributes. Our methodology is further enhanced through a composite degradation restoration loss, using extra degraded images as negative samples to fortify model constraints. Comparative results on synthetic and real-world datasets demonstrate OneRestore as a superior solution, significantly advancing the state-of-the-art in addressing complex, composite degradations.