pwc-archive/papers-with-abstracts huggingface dataset:
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses
Authors: Kamyar Zeinalipour, Neda Jamshidi, Monica Bianchini, Marco Maggini, Marco Gori
Date: 2024-08-12 00:00:00
Tasks: valid

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.
Autoregressive Enzyme Function Prediction with Multi-scale Multi-modality Fusion
Authors: Dingyi Rong, Wenzhuo Zheng, Bozitao Zhong, Zhouhan Lin, Liang Hong, Ning Liu
Date: 2024-08-11 00:00:00
Tasks: Prediction, Protein Function Prediction

Accurate prediction of enzyme function is crucial for elucidating biological mechanisms and driving innovation across various sectors. Existing deep learning methods tend to rely solely on either sequence data or structural data and predict the EC number as a whole, neglecting the intrinsic hierarchical structure of EC numbers. To address these limitations, we introduce MAPred, a novel multi-modality and multi-scale model designed to autoregressively predict the EC number of proteins. MAPred integrates both the primary amino acid sequence and the 3D tokens of proteins, employing a dual-pathway approach to capture comprehensive protein characteristics and essential local functional sites. Additionally, MAPred utilizes an autoregressive prediction network to sequentially predict the digits of the EC number, leveraging the hierarchical organization of EC classifications. Evaluations on benchmark datasets, including New-392, Price, and New-815, demonstrate that our method outperforms existing models, marking a significant advance in the reliability and granularity of protein function prediction within bioinformatics.
ViC: Virtual Compiler Is All You Need For Assembly Code Search
Authors: Zeyu Gao, Hao Wang, Yuanda Wang, Chao Zhang
Date: 2024-08-10 00:00:00
Tasks: All, Code Search, Language Modeling, Language Modelling, Large Language Model

Assembly code search is vital for reducing the burden on reverse engineers, allowing them to quickly identify specific functions using natural language within vast binary programs. Despite its significance, this critical task is impeded by the complexities involved in building high-quality datasets. This paper explores training a Large Language Model (LLM) to emulate a general compiler. By leveraging Ubuntu packages to compile a dataset of 20 billion tokens, we further continue pre-train CodeLlama as a Virtual Compiler (ViC), capable of compiling any source code of any language to assembly code. This approach allows for virtual compilation across a wide range of programming languages without the need for a real compiler, preserving semantic equivalency and expanding the possibilities for assembly code dataset construction. Furthermore, we use ViC to construct a sufficiently large dataset for assembly code search. Employing this extensive dataset, we achieve a substantial improvement in assembly code search performance, with our model surpassing the leading baseline by 26%.
Masked Graph Autoencoders with Contrastive Augmentation for Spatially Resolved Transcriptomics Data
Authors: Donghai Fang, Fangfang Zhu, Dongting Xie, Wenwen Min
Date: 2024-08-09 00:00:00
Tasks: Denoising, Triplet

With the rapid advancement of Spatial Resolved Transcriptomics (SRT) technology, it is now possible to comprehensively measure gene transcription while preserving the spatial context of tissues. Spatial domain identification and gene denoising are key objectives in SRT data analysis. We propose a Contrastively Augmented Masked Graph Autoencoder (STMGAC) to learn low-dimensional latent representations for domain identification. In the latent space, persistent signals for representations are obtained through self-distillation to guide self-supervised matching. At the same time, positive and negative anchor pairs are constructed using triplet learning to augment the discriminative ability. We evaluated the performance of STMGAC on five datasets, achieving results superior to those of existing baseline methods. All code and public datasets used in this paper are available at https://github.com/wenwenmin/STMGAC and https://zenodo.org/records/13253801.
Fingerspelling within Sign Language Translation
Authors: Garrett Tanzer
Date: 2024-08-13 00:00:00
Tasks: Sign Language Translation, Translation

Fingerspelling poses challenges for sign language processing due to its high-frequency motion and use for open-vocabulary terms. While prior work has studied fingerspelling recognition, there has been little attention to evaluating how well sign language translation models understand fingerspelling in the context of entire sentences -- and improving this capability. We manually annotate instances of fingerspelling within FLEURS-ASL and use them to evaluate the effect of two simple measures to improve fingerspelling recognition within American Sign Language to English translation: 1) use a model family (ByT5) with character- rather than subword-level tokenization, and 2) mix fingerspelling recognition data into the translation training mixture. We find that 1) substantially improves understanding of fingerspelling (and therefore translation quality overall), but the effect of 2) is mixed.
PSM: Learning Probabilistic Embeddings for Multi-scale Zero-Shot Soundscape Mapping
Authors: Subash Khanal, Eric Xing, Srikumar Sastry, Aayush Dhakal, Zhexiao Xiong, Adeel Ahmad, Nathan Jacobs
Date: 2024-08-13 00:00:00

A soundscape is defined by the acoustic environment a person perceives at a location. In this work, we propose a framework for mapping soundscapes across the Earth. Since soundscapes involve sound distributions that span varying spatial scales, we represent locations with multi-scale satellite imagery and learn a joint representation among this imagery, audio, and text. To capture the inherent uncertainty in the soundscape of a location, we design the representation space to be probabilistic. We also fuse ubiquitous metadata (including geolocation, time, and data source) to enable learning of spatially and temporally dynamic representations of soundscapes. We demonstrate the utility of our framework by creating large-scale soundscape maps integrating both audio and text with temporal control. To facilitate future research on this task, we also introduce a large-scale dataset, GeoSound, containing over $300k$ geotagged audio samples paired with both low- and high-resolution satellite imagery. We demonstrate that our method outperforms the existing state-of-the-art on both GeoSound and the existing SoundingEarth dataset. Our dataset and code is available at https://github.com/mvrl/PSM.
Efficient Human-Object-Interaction (EHOI) Detection via Interaction Label Coding and Conditional Decision
Authors: Tsung-Shan Yang, Yun-Cheng Wang, Chengwei Wei, Suya You, C. -C. Jay Kuo
Date: 2024-08-13 00:00:00
Tasks: Decision Making, Human-Object Interaction Detection

Human-Object Interaction (HOI) detection is a fundamental task in image understanding. While deep-learning-based HOI methods provide high performance in terms of mean Average Precision (mAP), they are computationally expensive and opaque in training and inference processes. An Efficient HOI (EHOI) detector is proposed in this work to strike a good balance between detection performance, inference complexity, and mathematical transparency. EHOI is a two-stage method. In the first stage, it leverages a frozen object detector to localize the objects and extract various features as intermediate outputs. In the second stage, the first-stage outputs predict the interaction type using the XGBoost classifier. Our contributions include the application of error correction codes (ECCs) to encode rare interaction cases, which reduces the model size and the complexity of the XGBoost classifier in the second stage. Additionally, we provide a mathematical formulation of the relabeling and decision-making process. Apart from the architecture, we present qualitative results to explain the functionalities of the feedforward modules. Experimental results demonstrate the advantages of ECC-coded interaction labels and the excellent balance of detection performance and complexity of the proposed EHOI method.
Low-Bitwidth Floating Point Quantization for Efficient High-Quality Diffusion Models
Authors: Cheng Chen, Christina Giannoula, Andreas Moshovos
Date: 2024-08-13 00:00:00
Tasks: Denoising, Quantization

Diffusion models are emerging models that generate images by iteratively denoising random Gaussian noise using deep neural networks. These models typically exhibit high computational and memory demands, necessitating effective post-training quantization for high-performance inference. Recent works propose low-bitwidth (e.g., 8-bit or 4-bit) quantization for diffusion models, however 4-bit integer quantization typically results in low-quality images. We observe that on several widely used hardware platforms, there is little or no difference in compute capability between floating-point and integer arithmetic operations of the same bitwidth (e.g., 8-bit or 4-bit). Therefore, we propose an effective floating-point quantization method for diffusion models that provides better image quality compared to integer quantization methods. We employ a floating-point quantization method that was effective for other processing tasks, specifically computer vision and natural language tasks, and tailor it for diffusion models by integrating weight rounding learning during the mapping of the full-precision values to the quantized values in the quantization process. We comprehensively study integer and floating-point quantization methods in state-of-the-art diffusion models. Our floating-point quantization method not only generates higher-quality images than that of integer quantization methods, but also shows no noticeable degradation compared to full-precision models (32-bit floating-point), when both weights and activations are quantized to 8-bit floating-point values, while has minimal degradation with 4-bit weights and 8-bit activations.
Prompt-Based Segmentation at Multiple Resolutions and Lighting Conditions using Segment Anything Model 2
Authors: Osher Rafaeli, Tal Svoray, Roni Blushtein-Livnon, Ariel Nahlieli
Date: 2024-08-13 00:00:00
Tasks: Image Segmentation, Semantic Segmentation

This paper provides insights on the effectiveness of the zero shot, prompt-based Segment Anything Model (SAM) and its updated versions, SAM 2 and SAM 2.1, along with the non-promptable conventional neural network (CNN), for segmenting solar panels in RGB aerial remote sensing imagery. The study evaluates these models across diverse lighting conditions, spatial resolutions, and prompt strategies. SAM 2 showed slight improvements over SAM, while SAM 2.1 demonstrated notable improvements, particularly in sub-optimal lighting and low resolution conditions. SAM models, when prompted by user-defined boxes, outperformed CNN in all scenarios; in particular, user-box prompts were found crucial for achieving reasonable performance in low resolution data. Additionally, under high resolution, YOLOv9 automatic prompting outperformed user-points prompting by providing reliable prompts to SAM. Under low resolution, SAM 2.1 prompted by user points showed similar performance to SAM 2.1 prompted by YOLOv9, highlighting its zero shot improvements with a single click. In high resolution with optimal lighting imagery, Eff-UNet outperformed SAMs prompted by YOLOv9, while under sub-optimal lighting conditions, Eff-UNet, and SAM 2.1 prompted by YOLOv9, had similar performance. However, SAM is more resource-intensive, and despite improved inference time of SAM 2.1, Eff-UNet is more suitable for automatic segmentation in high resolution data. This research details strengths and limitations of each model and outlines the robustness of user-prompted image segmentation models.
Event-Stream Super Resolution using Sigma-Delta Neural Network
Authors: Waseem Shariff, Joe Lemley, Peter Corcoran
Date: 2024-08-13 00:00:00
Tasks: Computational Efficiency, Super-Resolution

This study introduces a novel approach to enhance the spatial-temporal resolution of time-event pixels based on luminance changes captured by event cameras. These cameras present unique challenges due to their low resolution and the sparse, asynchronous nature of the data they collect. Current event super-resolution algorithms are not fully optimized for the distinct data structure produced by event cameras, resulting in inefficiencies in capturing the full dynamism and detail of visual scenes with improved computational complexity. To bridge this gap, our research proposes a method that integrates binary spikes with Sigma Delta Neural Networks (SDNNs), leveraging spatiotemporal constraint learning mechanism designed to simultaneously learn the spatial and temporal distributions of the event stream. The proposed network is evaluated using widely recognized benchmark datasets, including N-MNIST, CIFAR10-DVS, ASL-DVS, and Event-NFS. A comprehensive evaluation framework is employed, assessing both the accuracy, through root mean square error (RMSE), and the computational efficiency of our model. The findings demonstrate significant improvements over existing state-of-the-art methods, specifically, the proposed method outperforms state-of-the-art performance in computational efficiency, achieving a 17.04-fold improvement in event sparsity and a 32.28-fold increase in synaptic operation efficiency over traditional artificial neural networks, alongside a two-fold better performance over spiking neural networks.
Breaking Class Barriers: Efficient Dataset Distillation via Inter-Class Feature Compensator
Authors: Xin Zhang, Jiawei Du, Ping Liu, Joey Tianyi Zhou
Date: 2024-08-13 00:00:00
Tasks: Dataset Distillation

Dataset distillation has emerged as a technique aiming to condense informative features from large, natural datasets into a compact and synthetic form. While recent advancements have refined this technique, its performance is bottlenecked by the prevailing class-specific synthesis paradigm. Under this paradigm, synthetic data is optimized exclusively for a pre-assigned one-hot label, creating an implicit class barrier in feature condensation. This leads to inefficient utilization of the distillation budget and oversight of inter-class feature distributions, which ultimately limits the effectiveness and efficiency, as demonstrated in our analysis. To overcome these constraints, this paper presents the Inter-class Feature Compensator (INFER), an innovative distillation approach that transcends the class-specific data-label framework widely utilized in current dataset distillation methods. Specifically, INFER leverages a Universal Feature Compensator (UFC) to enhance feature integration across classes, enabling the generation of multiple additional synthetic instances from a single UFC input. This significantly improves the efficiency of the distillation budget. Moreover, INFER enriches inter-class interactions during the distillation, thereby enhancing the effectiveness and generalizability of the distilled data. By allowing for the linear interpolation of labels similar to those in the original dataset, INFER meticulously optimizes the synthetic data and dramatically reduces the size of soft labels in the synthetic dataset to almost zero, establishing a new benchmark for efficiency and effectiveness in dataset distillation.
SceneGPT: A Language Model for 3D Scene Understanding
Authors: Shivam Chandhok
Date: 2024-08-13 00:00:00
Tasks: In-Context Learning, Language Modeling, Language Modelling, model, Object, Scene Understanding, Spatial Reasoning

Building models that can understand and reason about 3D scenes is difficult owing to the lack of data sources for 3D supervised training and large-scale training regimes. In this work we ask - How can the knowledge in a pre-trained language model be leveraged for 3D scene understanding without any 3D pre-training. The aim of this work is to establish whether pre-trained LLMs possess priors/knowledge required for reasoning in 3D space and how can we prompt them such that they can be used for general purpose spatial reasoning and object understanding in 3D. To this end, we present SceneGPT, an LLM based scene understanding system which can perform 3D spatial reasoning without training or explicit 3D supervision. The key components of our framework are - 1) a 3D scene graph, that serves as scene representation, encoding the objects in the scene and their spatial relationships 2) a pre-trained LLM that can be adapted with in context learning for 3D spatial reasoning. We evaluate our framework qualitatively on object and scene understanding tasks including object semantics, physical properties and affordances (object-level) and spatial understanding (scene-level).
Divide and Conquer: Improving Multi-Camera 3D Perception with 2D Semantic-Depth Priors and Input-Dependent Queries
Authors: Qi Song, Qingyong Hu, Chi Zhang, Yongquan Chen, Rui Huang
Date: 2024-08-13 00:00:00
Tasks: 3D Object Detection, BEV Segmentation, Object, Object Categorization, object-detection, Object Detection, Position

3D perception tasks, such as 3D object detection and Bird's-Eye-View (BEV) segmentation using multi-camera images, have drawn significant attention recently. Despite the fact that accurately estimating both semantic and 3D scene layouts are crucial for this task, existing techniques often neglect the synergistic effects of semantic and depth cues, leading to the occurrence of classification and position estimation errors. Additionally, the input-independent nature of initial queries also limits the learning capacity of Transformer-based models. To tackle these challenges, we propose an input-aware Transformer framework that leverages Semantics and Depth as priors (named SDTR). Our approach involves the use of an S-D Encoder that explicitly models semantic and depth priors, thereby disentangling the learning process of object categorization and position estimation. Moreover, we introduce a Prior-guided Query Builder that incorporates the semantic prior into the initial queries of the Transformer, resulting in more effective input-aware queries. Extensive experiments on the nuScenes and Lyft benchmarks demonstrate the state-of-the-art performance of our method in both 3D object detection and BEV segmentation tasks.
EEPPR: Event-based Estimation of Periodic Phenomena Rate using Correlation in 3D
Authors: Jakub Kolář, Radim Špetlík, Jiří Matas
Date: 2024-08-13 00:00:00

We present a novel method for measuring the rate of periodic phenomena (e.g., rotation, flicker, and vibration), by an event camera, a device asynchronously reporting brightness changes at independently operating pixels with high temporal resolution. The approach assumes that for a periodic phenomenon, a highly similar set of events is generated within a spatio-temporal window at a time difference corresponding to its period. The sets of similar events are detected by a correlation in the spatio-temporal event stream space. The proposed method, EEPPR, is evaluated on a dataset of 12 sequences of periodic phenomena, i.e. flashing light and vibration, and periodic motion, e.g., rotation, ranging from 3.2 Hz to 2 kHz (equivalent to 192 - 120 000 RPM). EEPPR significantly outperforms published methods on this dataset, achieving a mean relative error of 0.1%, setting new state-of-the-art. The dataset and codes are publicly available on GitHub.
PBIR-NIE: Glossy Object Capture under Non-Distant Lighting
Authors: Guangyan Cai, Fujun Luan, Miloš Hašan, Kai Zhang, Sai Bi, Zexiang Xu, Iliyan Georgiev, Shuang Zhao
Date: 2024-08-13 00:00:00
Tasks: 3D Reconstruction, Inverse Rendering, Object Reconstruction

Glossy objects present a significant challenge for 3D reconstruction from multi-view input images under natural lighting. In this paper, we introduce PBIR-NIE, an inverse rendering framework designed to holistically capture the geometry, material attributes, and surrounding illumination of such objects. We propose a novel parallax-aware non-distant environment map as a lightweight and efficient lighting representation, accurately modeling the near-field background of the scene, which is commonly encountered in real-world capture setups. This feature allows our framework to accommodate complex parallax effects beyond the capabilities of standard infinite-distance environment maps. Our method optimizes an underlying signed distance field (SDF) through physics-based differentiable rendering, seamlessly connecting surface gradients between a triangle mesh and the SDF via neural implicit evolution (NIE). To address the intricacies of highly glossy BRDFs in differentiable rendering, we integrate the antithetic sampling algorithm to mitigate variance in the Monte Carlo gradient estimator. Consequently, our framework exhibits robust capabilities in handling glossy object reconstruction, showcasing superior quality in geometry, relighting, and material estimation.
A Comprehensive Survey on Synthetic Infrared Image synthesis
Authors: Avinash Upadhyay, Manoj Sharma, Prerana Mukherjee, Amit Singhal, Brejesh lall
Date: 2024-08-13 00:00:00
Tasks: Image Generation, Survey

Synthetic infrared (IR) scene and target generation is an important computer vision problem as it allows the generation of realistic IR images and targets for training and testing of various applications, such as remote sensing, surveillance, and target recognition. It also helps reduce the cost and risk associated with collecting real-world IR data. This survey paper aims to provide a comprehensive overview of the conventional mathematical modelling-based methods and deep learning-based methods used for generating synthetic IR scenes and targets. The paper discusses the importance of synthetic IR scene and target generation and briefly covers the mathematics of blackbody and grey body radiations, as well as IR image-capturing methods. The potential use cases of synthetic IR scenes and target generation are also described, highlighting the significance of these techniques in various fields. Additionally, the paper explores possible new ways of developing new techniques to enhance the efficiency and effectiveness of synthetic IR scenes and target generation while highlighting the need for further research to advance this field.