PharmaGPT: Domain-Specific Large Language Models for Bio-Pharmaceutical and Chemistry

Large language models (LLMs) have revolutionized Natural Language Processing (NLP) by by minimizing the need for complex feature engineering. However, the application of LLMs in specialized domains like biopharmaceuticals and chemistry remains largely unexplored. These fields are characterized by intricate terminologies, specialized knowledge, and a high demand for precision areas where general purpose LLMs often fall short. In this study, we introduce PharmGPT, a suite of multilingual LLMs with 13 billion and 70 billion parameters, specifically trained on a comprehensive corpus of hundreds of billions of tokens tailored to the Bio-Pharmaceutical and Chemical sectors. Our evaluation shows that PharmGPT matches or surpasses existing general models on key benchmarks, such as NAPLEX, demonstrating its exceptional capability in domain-specific tasks. This advancement establishes a new benchmark for LLMs in the Bio-Pharmaceutical and Chemical fields, addressing the existing gap in specialized language modeling. Furthermore, this suggests a promising path for enhanced research and development in these specialized areas, paving the way for more precise and effective applications of NLP in specialized domains.

PharmGPT: Domain-Specific Large Language Models for Bio-Pharmaceutical and Chemistry

Large language models (LLMs) have revolutionized Natural Language Processing (NLP) by by minimizing the need for complex feature engineering. However, the application of LLMs in specialized domains like biopharmaceuticals and chemistry remains largely unexplored. These fields are characterized by intricate terminologies, specialized knowledge, and a high demand for precision areas where general purpose LLMs often fall short. In this study, we introduce PharmGPT, a suite of multilingual LLMs with 13 billion and 70 billion parameters, specifically trained on a comprehensive corpus of hundreds of billions of tokens tailored to the Bio-Pharmaceutical and Chemical sectors. Our evaluation shows that PharmGPT matches or surpasses existing general models on key benchmarks, such as NAPLEX, demonstrating its exceptional capability in domain-specific tasks. This advancement establishes a new benchmark for LLMs in the Bio-Pharmaceutical and Chemical fields, addressing the existing gap in specialized language modeling. Furthermore, this suggests a promising path for enhanced research and development in these specialized areas, paving the way for more precise and effective applications of NLP in specialized domains.

Pre-training on High Definition X-ray Images: An Experimental Study

Existing X-ray based pre-trained vision models are usually conducted on a relatively small-scale dataset (less than 500k samples) with limited resolution (e.g., 224 $\times$ 224). However, the key to the success of self-supervised pre-training large models lies in massive training data, and maintaining high resolution in the field of X-ray images is the guarantee of effective solutions to difficult miscellaneous diseases. In this paper, we address these issues by proposing the first high-definition (1280 $\times$ 1280) X-ray based pre-trained foundation vision model on our newly collected large-scale dataset which contains more than 1 million X-ray images. Our model follows the masked auto-encoder framework which takes the tokens after mask processing (with a high rate) is used as input, and the masked image patches are reconstructed by the Transformer encoder-decoder network. More importantly, we introduce a novel context-aware masking strategy that utilizes the chest contour as a boundary for adaptive masking operations. We validate the effectiveness of our model on two downstream tasks, including X-ray report generation and disease recognition. Extensive experiments demonstrate that our pre-trained medical foundation vision model achieves comparable or even new state-of-the-art performance on downstream benchmark datasets. The source code and pre-trained models of this paper will be released on https://github.com/Event-AHU/Medical_Image_Analysis.

State Space Model for New-Generation Network Alternative to Transformers: A Survey

In the post-deep learning era, the Transformer architecture has demonstrated its powerful performance across pre-trained big models and various downstream tasks. However, the enormous computational demands of this architecture have deterred many researchers. To further reduce the complexity of attention models, numerous efforts have been made to design more efficient methods. Among them, the State Space Model (SSM), as a possible replacement for the self-attention based Transformer model, has drawn more and more attention in recent years. In this paper, we give the first comprehensive review of these works and also provide experimental comparisons and analysis to better demonstrate the features and advantages of SSM. Specifically, we first give a detailed description of principles to help the readers quickly capture the key ideas of SSM. After that, we dive into the reviews of existing SSMs and their various applications, including natural language processing, computer vision, graph, multi-modal and multi-media, point cloud/event stream, time series data, and other domains. In addition, we give statistical comparisons and analysis of these models and hope it helps the readers to understand the effectiveness of different structures on various tasks. Then, we propose possible research points in this direction to better promote the development of the theoretical model and application of SSM. More related works will be continuously updated on the following GitHub: https://github.com/Event-AHU/Mamba_State_Space_Model_Paper_List.

Budget-aware Query Tuning: An AutoML Perspective

Modern database systems rely on cost-based query optimizers to come up with good execution plans for input queries. Such query optimizers rely on cost models to estimate the costs of candidate query execution plans. A cost model represents a function from a set of cost units to query execution cost, where each cost unit specifies the unit cost of executing a certain type of query processing operation (such as table scan or join). These cost units are traditionally viewed as constants, whose values only depend on the platform configuration where the database system runs on top of but are invariant for queries processed by the database system. In this paper, we challenge this classic view by thinking of these cost units as variables instead. We show that, by varying the cost-unit values one can obtain query plans that significantly outperform the default query plans returned by the query optimizer when viewing the cost units as constants. We term this cost-unit tuning process "query tuning" (QT) and show that it is similar to the well-known hyper-parameter optimization (HPO) problem in AutoML. As a result, any state-of-the-art HPO technologies can be applied to QT. We study the QT problem in the context of anytime tuning, which is desirable in practice by constraining the total time spent on QT within a given budget -- we call this problem budget-aware query tuning. We further extend our study from tuning a single query to tuning a workload with multiple queries, and we call this generalized problem budget-aware workload tuning (WT), which aims for minimizing the execution time of the entire workload. WT is more challenging as one needs to further prioritize individual query tuning within the given time budget. We propose solutions to both QT and WT and experimental evaluation using both benchmark and real workloads demonstrates the efficacy of our proposed solutions.

TablePuppet: A Generic Framework for Relational Federated Learning

Current federated learning (FL) approaches view decentralized training data as a single table, divided among participants either horizontally (by rows) or vertically (by columns). However, these approaches are inadequate for handling distributed relational tables across databases. This scenario requires intricate SQL operations like joins and unions to obtain the training data, which is either costly or restricted by privacy concerns. This raises the question: can we directly run FL on distributed relational tables? In this paper, we formalize this problem as relational federated learning (RFL). We propose TablePuppet, a generic framework for RFL that decomposes the learning process into two steps: (1) learning over join (LoJ) followed by (2) learning over union (LoU). In a nutshell, LoJ pushes learning down onto the vertical tables being joined, and LoU further pushes learning down onto the horizontal partitions of each vertical table. TablePuppet incorporates computation/communication optimizations to deal with the duplicate tuples introduced by joins, as well as differential privacy (DP) to protect against both feature and label leakages. We demonstrate the efficiency of TablePuppet in combination with two widely-used ML training algorithms, stochastic gradient descent (SGD) and alternating direction method of multipliers (ADMM), and compare their computation/communication complexity. We evaluate the SGD/ADMM algorithms developed atop TablePuppet by training diverse ML models. Our experimental results show that TablePuppet achieves model accuracy comparable to the centralized baselines running directly atop the SQL results. Moreover, ADMM takes less communication time than SGD to converge to similar model accuracy.

Structural Information Guided Multimodal Pre-training for Vehicle-centric Perception

Understanding vehicles in images is important for various applications such as intelligent transportation and self-driving system. Existing vehicle-centric works typically pre-train models on large-scale classification datasets and then fine-tune them for specific downstream tasks. However, they neglect the specific characteristics of vehicle perception in different tasks and might thus lead to sub-optimal performance. To address this issue, we propose a novel vehicle-centric pre-training framework called VehicleMAE, which incorporates the structural information including the spatial structure from vehicle profile information and the semantic structure from informative high-level natural language descriptions for effective masked vehicle appearance reconstruction. To be specific, we explicitly extract the sketch lines of vehicles as a form of the spatial structure to guide vehicle reconstruction. The more comprehensive knowledge distilled from the CLIP big model based on the similarity between the paired/unpaired vehicle image-text sample is further taken into consideration to help achieve a better understanding of vehicles. A large-scale dataset is built to pre-train our model, termed Autobot1M, which contains about 1M vehicle images and 12693 text information. Extensive experiments on four vehicle-based downstream tasks fully validated the effectiveness of our VehicleMAE. The source code and pre-trained models will be released at https://github.com/Event-AHU/VehicleMAE.

From Scarcity to Efficiency: Improving CLIP Training via Visual-enriched Captions

Web-crawled datasets are pivotal to the success of pre-training vision-language models, exemplified by CLIP. However, web-crawled AltTexts can be noisy and potentially irrelevant to images, thereby undermining the crucial image-text alignment. Existing methods for rewriting captions using large language models (LLMs) have shown promise on small, curated datasets like CC3M and CC12M. Nevertheless, their efficacy on massive web-captured captions is constrained by the inherent noise and randomness in such data. In this study, we address this limitation by focusing on two key aspects: data quality and data variety. Unlike recent LLM rewriting techniques, we emphasize exploiting visual concepts and their integration into the captions to improve data quality. For data variety, we propose a novel mixed training scheme that optimally leverages AltTexts alongside newly generated Visual-enriched Captions (VeC). We use CLIP as one example and adapt the method for CLIP training on large-scale web-crawled datasets, named VeCLIP. We conduct a comprehensive evaluation of VeCLIP across small, medium, and large scales of raw data. Our results show significant advantages in image-text alignment and overall model performance, underscoring the effectiveness of VeCLIP in improving CLIP training. For example, VeCLIP achieves a remarkable over 20% improvement in COCO and Flickr30k retrieval tasks under the 12M setting. For data efficiency, we also achieve a notable over 3% improvement while using only 14% of the data employed in the vanilla CLIP and 11% in ALIGN.

ML-Powered Index Tuning: An Overview of Recent Progress and Open Challenges

The scale and complexity of workloads in modern cloud services have brought into sharper focus a critical challenge in automated index tuning -- the need to recommend high-quality indexes while maintaining index tuning scalability. This challenge is further compounded by the requirement for automated index implementations to introduce minimal query performance regressions in production deployments, representing a significant barrier to achieving scalability and full automation. This paper directs attention to these challenges within automated index tuning and explores ways in which machine learning (ML) techniques provide new opportunities in their mitigation. In particular, we reflect on recent efforts in developing ML techniques for workload selection, candidate index filtering, speeding up index configuration search, reducing the amount of query optimizer calls, and lowering the chances of performance regressions. We highlight the key takeaways from these efforts and underline the gaps that need to be closed for their effective functioning within the traditional index tuning framework. Additionally, we present a preliminary cross-platform design aimed at democratizing index tuning across multiple SQL-like systems -- an imperative in today's continuously expanding data system landscape. We believe our findings will help provide context and impetus to the research and development efforts in automated index tuning.

MOFI: Learning Image Representations from Noisy Entity Annotated Images

We present MOFI, a new vision foundation model designed to learn image representations from noisy entity annotated images. MOFI differs from previous work in two key aspects: ($i$) pre-training data, and ($ii$) training recipe. Regarding data, we introduce a new approach to automatically assign entity labels to images from noisy image-text pairs. Our approach involves employing a named entity recognition model to extract entities from the alt-text, and then using a CLIP model to select the correct entities as labels of the paired image. The approach is simple, does not require costly human annotation, and can be readily scaled up to billions of image-text pairs mined from the web. Through this method, we have created Image-to-Entities (I2E), a new large-scale dataset with 1 billion images and 2 million distinct entities, covering rich visual concepts in the wild. Building upon the I2E dataset, we study different training recipes, including supervised pre-training, contrastive pre-training, and multi-task learning. For constrastive pre-training, we treat entity names as free-form text, and further enrich them with entity descriptions. Experiments show that supervised pre-training with large-scale fine-grained entity labels is highly effective for image retrieval tasks, and multi-task training further improves the performance. The final MOFI model achieves 86.66% mAP on the challenging GPR1200 dataset, surpassing the previous state-of-the-art performance of 72.19% from OpenAI's CLIP model. Further experiments on zero-shot and linear probe image classification also show that MOFI outperforms a CLIP model trained on the original image-text data, demonstrating the effectiveness of the I2E dataset in learning strong image representations.