Leveraging CORAL-Correlation Consistency Network for Semi-Supervised Left Atrium MRI Segmentation

Semi-supervised learning (SSL) has been widely used to learn from both a few labeled images and many unlabeled images to overcome the scarcity of labeled samples in medical image segmentation. Most current SSL-based segmentation methods use pixel values directly to identify similar features in labeled and unlabeled data. They usually fail to accurately capture the intricate attachment structures in the left atrium, such as the areas of inconsistent density or exhibit outward curvatures, adding to the complexity of the task. In this paper, we delve into this issue and introduce an effective solution, CORAL(Correlation-Aligned)-Correlation Consistency Network (CORN), to capture the global structure shape and local details of Left Atrium. Diverging from previous methods focused on each local pixel value, the CORAL-Correlation Consistency Module (CCM) in the CORN leverages second-order statistical information to capture global structural features by minimizing the distribution discrepancy between labeled and unlabeled samples in feature space. Yet, direct construction of features from unlabeled data frequently results in ``Sample Selection Bias'', leading to flawed supervision. We thus further propose the Dynamic Feature Pool (DFP) for the CCM, which utilizes a confidence-based filtering strategy to remove incorrectly selected features and regularize both teacher and student models by constraining the similarity matrix to be consistent. Extensive experiments on the Left Atrium dataset have shown that the proposed CORN outperforms previous state-of-the-art semi-supervised learning methods.

Building A Coding Assistant via the Retrieval-Augmented Language Model

Pretrained language models have shown strong effectiveness in code-related tasks, such as code retrieval, code generation, code summarization, and code completion tasks. In this paper, we propose COde assistaNt viA retrieval-augmeNted language model (CONAN), which aims to build a code assistant by mimicking the knowledge-seeking behaviors of humans during coding. Specifically, it consists of a code structure aware retriever (CONAN-R) and a dual-view code representation-based retrieval-augmented generation model (CONAN-G). CONAN-R pretrains CodeT5 using Code-Documentation Alignment and Masked Entity Prediction tasks to make language models code structure-aware and learn effective representations for code snippets and documentation. Then CONAN-G designs a dual-view code representation mechanism for implementing a retrieval-augmented code generation model. CONAN-G regards the code documentation descriptions as prompts, which help language models better understand the code semantics. Our experiments show that CONAN achieves convincing performance on different code generation tasks and significantly outperforms previous retrieval augmented code generation models. Our further analyses show that CONAN learns tailored representations for both code snippets and documentation by aligning code-documentation data pairs and capturing structural semantics by masking and predicting entities in the code data. Additionally, the retrieved code snippets and documentation provide necessary information from both program language and natural language to assist the code generation process. CONAN can also be used as an assistant for Large Language Models (LLMs), providing LLMs with external knowledge in shorter code document lengths to improve their effectiveness on various code tasks. It shows the ability of CONAN to extract necessary information and help filter out the noise from retrieved code documents.

RAG-DDR: Optimizing Retrieval-Augmented Generation Using Differentiable Data Rewards

Retrieval-Augmented Generation (RAG) has proven its effectiveness in mitigating hallucinations in Large Language Models (LLMs) by retrieving knowledge from external resources. To adapt LLMs for RAG pipelines, current approaches use instruction tuning to optimize LLMs, improving their ability to utilize retrieved knowledge. This supervised fine-tuning (SFT) approach focuses on equipping LLMs to handle diverse RAG tasks using different instructions. However, it trains RAG modules to overfit training signals and overlooks the varying data preferences among agents within the RAG system. In this paper, we propose a Differentiable Data Rewards (DDR) method, which end-to-end trains RAG systems by aligning data preferences between different RAG modules. DDR works by collecting the rewards to optimize each agent with a rollout method. This method prompts agents to sample some potential responses as perturbations, evaluates the impact of these perturbations on the whole RAG system, and subsequently optimizes the agent to produce outputs that improve the performance of the RAG system. Our experiments on various knowledge-intensive tasks demonstrate that DDR significantly outperforms the SFT method, particularly for LLMs with smaller-scale parameters that depend more on the retrieved knowledge. Additionally, DDR exhibits a stronger capability to align the data preference between RAG modules. The DDR method makes generation module more effective in extracting key information from documents and mitigating conflicts between parametric memory and external knowledge. All codes are available at https://github.com/OpenMatch/RAG-DDR.

Enhancing the Code Debugging Ability of LLMs via Communicative Agent Based Data Refinement

Debugging is a vital aspect of software development, yet the debugging capabilities of Large Language Models (LLMs) remain largely unexplored. This paper first introduces DEBUGEVAL, a comprehensive benchmark designed to evaluate the debugging capabilities of LLMs. DEBUGEVAL collects data from existing high-quality datasets and designs four different tasks to evaluate the debugging effectiveness, including BUG Localization, BUG Identification, Code Review, and Code Repair. Additionally, to enhance the code debugging ability of LLMs, this paper proposes a CoMmunicative Agent BaSed DaTa REfinement FRamework (MASTER), which generates the refined code debugging data for supervised finetuning. Specifically, MASTER employs the Code Quizzer to generate refined data according to the defined tasks of DEBUGEVAL. Then the Code Learner acts as a critic and reserves the generated problems that it can not solve. Finally, the Code Teacher provides a detailed Chain-of-Thought based solution to deal with the generated problem. We collect the synthesized data and finetune the Code Learner to enhance the debugging ability and conduct the NeuDebugger model. Our experiments evaluate various LLMs and NeuDebugger in the zero-shot setting on DEBUGEVAL. Experimental results demonstrate that these 7B-scale LLMs have weaker debugging capabilities, even these code-oriented LLMs. On the contrary, these larger models (over 70B) show convincing debugging ability. Our further analyses illustrate that MASTER is an effective method to enhance the code debugging ability by synthesizing data for Supervised Fine-Tuning (SFT) LLMs.

MMLongBench-Doc: Benchmarking Long-context Document Understanding with Visualizations

Understanding documents with rich layouts and multi-modal components is a long-standing and practical task. Recent Large Vision-Language Models (LVLMs) have made remarkable strides in various tasks, particularly in single-page document understanding (DU). However, their abilities on long-context DU remain an open problem. This work presents MMLongBench-Doc, a long-context, multi-modal benchmark comprising 1,062 expert-annotated questions. Distinct from previous datasets, it is constructed upon 130 lengthy PDF-formatted documents with an average of 49.4 pages and 20,971 textual tokens. Towards comprehensive evaluation, answers to these questions rely on pieces of evidence from (1) different sources (text, image, chart, table, and layout structure) and (2) various locations (i.e. page number). Moreover, 33.2% of the questions are cross-page questions requiring evidence across multiple pages. 22.8% of the questions are designed to be unanswerable for detecting potential hallucinations. Experiments on 14 LVLMs demonstrate that long-context DU greatly challenges current models. Notably, the best-performing model, GPT-4o, achieves an F1 score of only 42.7%, while the second-best, GPT-4V, scores 31.4%. Furthermore, 12 LVLMs (all except GPT-4o and GPT-4V) even present worse performance than their LLM counterparts which are fed with lossy-parsed OCR documents. These results validate the necessity of future research toward more capable long-context LVLMs. Project Page: https://mayubo2333.github.io/MMLongBench-Doc

AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing methods still suffer from invalid local structure or unrealistic conformation issues, which are mainly due to the poor leaning of bond angles or torsional angles. To alleviate these problems, we propose AUTODIFF, a diffusion-based fragment-wise autoregressive generation model. Specifically, we design a novel molecule assembly strategy named conformal motif that preserves the conformation of local structures of molecules first, then we encode the interaction of the protein-ligand complex with an SE(3)-equivariant convolutional network and generate molecules motif-by-motif with diffusion modeling. In addition, we also improve the evaluation framework of SBDD by constraining the molecular weights of the generated molecules in the same range, together with some new metrics, which make the evaluation more fair and practical. Extensive experiments on CrossDocked2020 demonstrate that our approach outperforms the existing models in generating realistic molecules with valid structures and conformations while maintaining high binding affinity.

Data Augmentation using LLMs: Data Perspectives, Learning Paradigms and Challenges

In the rapidly evolving field of machine learning (ML), data augmentation (DA) has emerged as a pivotal technique for enhancing model performance by diversifying training examples without the need for additional data collection. This survey explores the transformative impact of Large Language Models (LLMs) on DA, particularly addressing the unique challenges and opportunities they present in the context of natural language processing (NLP) and beyond. From a data perspective and a learning perspective, we examine various strategies that utilize Large Language Models for data augmentation, including a novel exploration of learning paradigms where LLM-generated data is used for further training. Additionally, this paper delineates the primary challenges faced in this domain, ranging from controllable data augmentation to multi modal data augmentation. This survey highlights the paradigm shift introduced by LLMs in DA, aims to serve as a foundational guide for researchers and practitioners in this field.

Say More with Less: Understanding Prompt Learning Behaviors through Gist Compression

Large language models (LLMs) require lengthy prompts as the input context to produce output aligned with user intentions, a process that incurs extra costs during inference. In this paper, we propose the Gist COnditioned deCOding (Gist-COCO) model, introducing a novel method for compressing prompts which also can assist the prompt interpretation and engineering. Gist-COCO employs an encoder-decoder based language model and then incorporates an additional encoder as a plugin module to compress prompts with inputs using gist tokens. It finetunes the compression plugin module and uses the representations of gist tokens to emulate the raw prompts in the vanilla language model. By verbalizing the representations of gist tokens into gist prompts, the compression ability of Gist-COCO can be generalized to different LLMs with high compression rates. Our experiments demonstrate that Gist-COCO outperforms previous prompt compression models in both passage and instruction compression tasks. Further analysis on gist verbalization results suggests that our gist prompts serve different functions in aiding language models. They may directly provide potential answers, generate the chain-of-thought, or simply repeat the inputs. All data and codes are available at https://github.com/OpenMatch/Gist-COCO .

Unlock Multi-Modal Capability of Dense Retrieval via Visual Module Plugin

This paper proposes Multi-modAl Retrieval model via Visual modulE pLugin (MARVEL) to learn an embedding space for queries and multi-modal documents to conduct retrieval. MARVEL encodes queries and multi-modal documents with a unified encoder model, which helps to alleviate the modality gap between images and texts. Specifically, we enable the image understanding ability of a well-trained dense retriever, T5-ANCE, by incorporating the image features encoded by the visual module as its inputs. To facilitate the multi-modal retrieval tasks, we build the ClueWeb22-MM dataset based on the ClueWeb22 dataset, which regards anchor texts as queries, and exact the related texts and image documents from anchor linked web pages. Our experiments show that MARVEL significantly outperforms the state-of-the-art methods on the multi-modal retrieval dataset WebQA and ClueWeb22-MM. Our further analyses show that the visual module plugin method is tailored to enable the image understanding ability for an existing dense retrieval model. Besides, we also show that the language model has the ability to extract image semantics from image encoders and adapt the image features in the input space of language models. All codes are available at https://github.com/OpenMatch/MARVEL.

Towards Verifiable Generation: A Benchmark for Knowledge-aware Language Model Attribution

Although achieving great success, Large Language Models (LLMs) usually suffer from unreliable hallucinations. In this paper, we define a new task of Knowledge-aware Language Model Attribution (KaLMA) that improves upon three core concerns on conventional attributed LMs. First, we extend attribution source from unstructured texts to Knowledge Graph (KG), whose rich structures benefit both the attribution performance and working scenarios. Second, we propose a new ``Conscious Incompetence" setting considering the incomplete knowledge repository, where the model identifies the need for supporting knowledge beyond the provided KG. Third, we propose a comprehensive automatic evaluation metric encompassing text quality, citation quality, and text citation alignment. To implement the above innovations, we build a dataset in biography domain BioKaLMA via a well-designed evolutionary question generation strategy, to control the question complexity and necessary knowledge to the answer. For evaluation, we develop a baseline solution and demonstrate the room for improvement in LLMs' citation generation, emphasizing the importance of incorporating the "Conscious Incompetence" setting, and the critical role of retrieval accuracy.