ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing. The source code is available at https://github.com/BEAM-Labs/ContraNovo.

ChatCoder: Chat-based Refine Requirement Improves LLMs' Code Generation

Large language models have shown good performances in generating code to meet human requirements. However, human requirements expressed in natural languages can be vague, incomplete, and ambiguous, leading large language models to misunderstand human requirements and make mistakes. Worse, it is difficult for a human user to refine the requirement. To help human users refine their requirements and improve large language models' code generation performances, we propose ChatCoder: a method to refine the requirements via chatting with large language models. We design a chat scheme in which the large language models will guide the human users to refine their expression of requirements to be more precise, unambiguous, and complete than before. Experiments show that ChatCoder has improved existing large language models' performance by a large margin. Besides, ChatCoder has the advantage over refine-based methods and LLMs fine-tuned via human response.

Enhancing the Spatial Awareness Capability of Multi-Modal Large Language Model

The Multi-Modal Large Language Model (MLLM) refers to an extension of the Large Language Model (LLM) equipped with the capability to receive and infer multi-modal data. Spatial awareness stands as one of the crucial abilities of MLLM, encompassing diverse skills related to understanding spatial relationships among objects and between objects and the scene area. Industries such as autonomous driving, smart healthcare, robotics, virtual, and augmented reality heavily demand MLLM's spatial awareness capabilities. However, there exists a noticeable gap between the current spatial awareness capabilities of MLLM and the requirements set by human needs. To address this issue, this paper proposes using more precise spatial position information between objects to guide MLLM in providing more accurate responses to user-related inquiries. Specifically, for a particular multi-modal task, we utilize algorithms for acquiring geometric spatial information and scene graphs to obtain relevant geometric spatial information and scene details of objects involved in the query. Subsequently, based on this information, we direct MLLM to address spatial awareness-related queries posed by the user. Extensive experiments were conducted in benchmarks such as MME, MM-Vet, and other multi-modal large language models. The experimental results thoroughly confirm the efficacy of the proposed method in enhancing the spatial awareness tasks and associated tasks of MLLM.

Large Language Model-Aware In-Context Learning for Code Generation

Large language models (LLMs) have shown impressive in-context learning (ICL) ability in code generation. LLMs take a prompt consisting of requirement-code examples and a new requirement as input, and output new programs. Existing studies have found that ICL is highly dominated by the examples and thus arises research on example selection. However, existing approaches randomly select examples or only consider the textual similarity of requirements to retrieve, leading to sub-optimal performance. In this paper, we propose a novel learning-based selection approach named LAIL (LLM-Aware In-context Learning) for code generation. Given a candidate example, we exploit LLMs themselves to estimate it by considering the generation probabilities of ground-truth programs given a requirement and the example. We then label candidate examples as positive or negative through the probability feedback. Based on the labeled data, we import a contrastive learning objective to train an effective retriever that acquires the preference of LLMs in code generation. We apply LAIL to three LLMs and evaluate it on three representative datasets (e.g., MBJP, MBPP, and MBCPP). LATA outperforms the state-of-the-art baselines by 11.58%, 6.89%, and 5.07% on CodeGen, and 4.38%, 2.85%, and 2.74% on GPT-3.5 in terms of Pass@1, respectively.

ZC3: Zero-Shot Cross-Language Code Clone Detection

Developers introduce code clones to improve programming productivity. Many existing studies have achieved impressive performance in monolingual code clone detection. However, during software development, more and more developers write semantically equivalent programs with different languages to support different platforms and help developers translate projects from one language to another. Considering that collecting cross-language parallel data, especially for low-resource languages, is expensive and time-consuming, how designing an effective cross-language model that does not rely on any parallel data is a significant problem. In this paper, we propose a novel method named ZC3 for Zero-shot Cross-language Code Clone detection. ZC3 designs the contrastive snippet prediction to form an isomorphic representation space among different programming languages. Based on this, ZC3 exploits domain-aware learning and cycle consistency learning to further constrain the model to generate representations that are aligned among different languages meanwhile are diacritical for different types of clones. To evaluate our approach, we conduct extensive experiments on four representative cross-language clone detection datasets. Experimental results show that ZC3 outperforms the state-of-the-art baselines by 67.12%, 51.39%, 14.85%, and 53.01% on the MAP score, respectively. We further investigate the representational distribution of different languages and discuss the effectiveness of our method.

EditSum: A Retrieve-and-Edit Framework for Source Code Summarization

Existing studies show that code summaries help developers understand and maintain source code. Unfortunately, these summaries are often missing or outdated in software projects. Code summarization aims to generate natural language descriptions automatically for source code. Code summaries are highly structured and have repetitive patterns. Besides the patternized words, a code summary also contains important keywords, which are the key to reflecting the functionality of the code. However, the state-of-the-art approaches perform poorly on predicting the keywords, which leads to the generated summaries suffering a loss in informativeness. To alleviate this problem, this paper proposes a novel retrieve-and-edit approach named EditSum for code summarization. Specifically, EditSum first retrieves a similar code snippet from a pre-defined corpus and treats its summary as a prototype summary to learn the pattern. Then, EditSum edits the prototype automatically to combine the pattern in the prototype with the semantic information of input code. Our motivation is that the retrieved prototype provides a good start-point for post-generation because the summaries of similar code snippets often have the same pattern. The post-editing process further reuses the patternized words in the prototype and generates keywords based on the semantic information of input code. We conduct experiments on a large-scale Java corpus and experimental results demonstrate that EditSum outperforms the state-of-the-art approaches by a substantial margin. The human evaluation also proves the summaries generated by EditSum are more informative and useful. We also verify that EditSum performs well on predicting the patternized words and keywords.

Improving Code Generation by Dynamic Temperature Sampling

Recently, Large Language Models (LLMs) have shown impressive results in code generation. However, existing decoding strategies are designed for Natural Language (NL) generation, overlooking the differences between NL and programming languages (PL). Due to this oversight, a better decoding strategy for code generation remains an open question. In this paper, we conduct the first systematic study to explore a decoding strategy specialized in code generation. With an analysis of loss distributions of code tokens, we find that code tokens can be divided into two categories: challenging tokens that are difficult to predict and confident tokens that can be easily inferred. Among them, the challenging tokens mainly appear at the beginning of a code block. Inspired by the above findings, we propose a simple yet effective method: Adaptive Temperature (AdapT) sampling, which dynamically adjusts the temperature coefficient when decoding different tokens. We apply a larger temperature when sampling for challenging tokens, allowing LLMs to explore diverse choices. We employ a smaller temperature for confident tokens avoiding the influence of tail randomness noises. We apply AdapT sampling to LLMs with different sizes and conduct evaluations on two popular datasets. Results show that AdapT sampling significantly outperforms state-of-the-art decoding strategy.

MB-TaylorFormer: Multi-branch Efficient Transformer Expanded by Taylor Formula for Image Dehazing

In recent years, Transformer networks are beginning to replace pure convolutional neural networks (CNNs) in the field of computer vision due to their global receptive field and adaptability to input. However, the quadratic computational complexity of softmax-attention limits the wide application in image dehazing task, especially for high-resolution images. To address this issue, we propose a new Transformer variant, which applies the Taylor expansion to approximate the softmax-attention and achieves linear computational complexity. A multi-scale attention refinement module is proposed as a complement to correct the error of the Taylor expansion. Furthermore, we introduce a multi-branch architecture with multi-scale patch embedding to the proposed Transformer, which embeds features by overlapping deformable convolution of different scales. The design of multi-scale patch embedding is based on three key ideas: 1) various sizes of the receptive field; 2) multi-level semantic information; 3) flexible shapes of the receptive field. Our model, named Multi-branch Transformer expanded by Taylor formula (MB-TaylorFormer), can embed coarse to fine features more flexibly at the patch embedding stage and capture long-distance pixel interactions with limited computational cost. Experimental results on several dehazing benchmarks show that MB-TaylorFormer achieves state-of-the-art (SOTA) performance with a light computational burden. The source code and pre-trained models are available at https://github.com/FVL2020/ICCV-2023-MB-TaylorFormer.