Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model

Recent advancements in computational chemistry have increasingly focused on synthesizing molecules based on textual instructions. Integrating graph generation with these instructions is complex, leading most current methods to use molecular sequences with pre-trained large language models. In response to this challenge, we propose a novel framework, named $\textbf{UTGDiff (Unified Text-Graph Diffusion Model)}$, which utilizes language models for discrete graph diffusion to generate molecular graphs from instructions. UTGDiff features a unified text-graph transformer as the denoising network, derived from pre-trained language models and minimally modified to process graph data through attention bias. Our experimental results demonstrate that UTGDiff consistently outperforms sequence-based baselines in tasks involving instruction-based molecule generation and editing, achieving superior performance with fewer parameters given an equivalent level of pretraining corpus. Our code is availble at https://github.com/ran1812/UTGDiff.

A Survey of Neural Code Intelligence: Paradigms, Advances and Beyond

Neural Code Intelligence -- leveraging deep learning to understand, generate, and optimize code -- holds immense potential for transformative impacts on the whole society. Bridging the gap between Natural Language and Programming Language, this domain has drawn significant attention from researchers in both research communities over the past few years. This survey presents a systematic and chronological review of the advancements in code intelligence, encompassing over 50 representative models and their variants, more than 20 categories of tasks, and an extensive coverage of over 680 related works. We follow the historical progression to trace the paradigm shifts across different research phases (e.g., from modeling code with recurrent neural networks to the era of Large Language Models). Concurrently, we highlight the major technical transitions in models, tasks, and evaluations spanning through different stages. For applications, we also observe a co-evolving shift. It spans from initial endeavors to tackling specific scenarios, through exploring a diverse array of tasks during its rapid expansion, to currently focusing on tackling increasingly complex and varied real-world challenges. Building on our examination of the developmental trajectories, we further investigate the emerging synergies between code intelligence and broader machine intelligence, uncovering new cross-domain opportunities and illustrating the substantial influence of code intelligence across various domains. Finally, we delve into both the opportunities and challenges associated with this field, alongside elucidating our insights on the most promising research directions. An ongoing, dynamically updated project and resources associated with this survey have been released at https://github.com/QiushiSun/NCISurvey.

Empowering Large Language Model Agents through Action Learning

Large Language Model (LLM) Agents have recently garnered increasing interest yet they are limited in their ability to learn from trial and error, a key element of intelligent behavior. In this work, we argue that the capacity to learn new actions from experience is fundamental to the advancement of learning in LLM agents. While humans naturally expand their action spaces and develop skills through experiential learning, LLM agents typically operate within fixed action spaces, limiting their potential for growth. To address these challenges, our study explores open-action learning for language agents. We introduce a framework LearnAct with an iterative learning strategy to create and improve actions in the form of Python functions. In each iteration, LLM revises and updates the currently available actions based on the errors identified in unsuccessful training tasks, thereby enhancing action effectiveness. Our experimental evaluations across Robotic Planning and Alfworld environments reveal that after learning on a few training task instances, our approach to open-action learning markedly improves agent performance for the type of task (by 32 percent in AlfWorld compared to ReAct+Reflexion, for instance) highlighting the importance of experiential action learning in the development of more intelligent LLM agents.

KS-Lottery: Finding Certified Lottery Tickets for Multilingual Language Models

The lottery ticket hypothesis posits the existence of ``winning tickets'' within a randomly initialized neural network. Do winning tickets exist for LLMs in fine-tuning scenarios? How can we find such winning tickets? In this paper, we propose KS-Lottery, a method to identify a small subset of LLM parameters highly effective in multilingual fine-tuning. Our key idea is to use Kolmogorov-Smirnov Test to analyze the distribution shift of parameters before and after fine-tuning. We further theoretically prove that KS-Lottery can find the certified winning tickets in the embedding layer, fine-tuning on the found parameters is guaranteed to perform as well as full fine-tuning. Comparing KS-Lottery with other parameter-efficient tuning algorithms on translation tasks, the experimental results show that KS-Lottery finds a much smaller set of parameters for fine-tuning while achieving the comparable performance as full fine-tuning LLM. Surprisingly, we find that fine-tuning 18 tokens' embedding of LLaMA suffices to reach the fine-tuning translation performance. Code and model will be released to the public.

AgentBoard: An Analytical Evaluation Board of Multi-turn LLM Agents

Evaluating large language models (LLMs) as general-purpose agents is essential for understanding their capabilities and facilitating their integration into practical applications. However, the evaluation process presents substantial challenges. A primary obstacle is the benchmarking of agent performance across diverse scenarios within a unified framework, especially in maintaining partially-observable environments and ensuring multi-round interactions. Moreover, current evaluation frameworks mostly focus on the final success rate, revealing few insights during the process and failing to provide a deep understanding of the model abilities. To address these challenges, we introduce AgentBoard, a pioneering comprehensive benchmark and accompanied open-source evaluation framework tailored to analytical evaluation of LLM agents. AgentBoard offers a fine-grained progress rate metric that captures incremental advancements as well as a comprehensive evaluation toolkit that features easy assessment of agents for multi-faceted analysis through interactive visualization. This not only sheds light on the capabilities and limitations of LLM agents but also propels the interpretability of their performance to the forefront. Ultimately, AgentBoard serves as a significant step towards demystifying agent behaviors and accelerating the development of stronger LLM agents.

A Challenging Benchmark for Low-Resource Learning

With promising yet saturated results in high-resource settings, low-resource datasets have gradually become popular benchmarks for evaluating the learning ability of advanced neural networks (e.g., BigBench, superGLUE). Some models even surpass humans according to benchmark test results. However, we find that there exists a set of hard examples in low-resource settings that challenge neural networks but are not well evaluated, which causes over-estimated performance. We first give a theoretical analysis on which factors bring the difficulty of low-resource learning. It then motivate us to propose a challenging benchmark hardBench to better evaluate the learning ability, which covers 11 datasets, including 3 computer vision (CV) datasets and 8 natural language process (NLP) datasets. Experiments on a wide range of models show that neural networks, even pre-trained language models, have sharp performance drops on our benchmark, demonstrating the effectiveness on evaluating the weaknesses of neural networks. On NLP tasks, we surprisingly find that despite better results on traditional low-resource benchmarks, pre-trained networks, does not show performance improvements on our benchmarks. These results demonstrate that there are still a large robustness gap between existing models and human-level performance.

Retrieved Sequence Augmentation for Protein Representation Learning

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the latest version of AlphaFold rely on Multiple Sequence Alignments (MSA) to feed in the evolutionary knowledge. Despite their success, heavy computational overheads, as well as the de novo and orphan proteins remain great challenges in protein representation learning. In this work, we show that MSAaugmented models inherently belong to retrievalaugmented methods. Motivated by this finding, we introduce Retrieved Sequence Augmentation(RSA) for protein representation learning without additional alignment or pre-processing. RSA links query protein sequences to a set of sequences with similar structures or properties in the database and combines these sequences for downstream prediction. We show that protein language models benefit from the retrieval enhancement on both structure prediction and property prediction tasks, with a 5% improvement on MSA Transformer on average while being 373 times faster. In addition, we show that our model can transfer to new protein domains better and outperforms MSA Transformer on de novo protein prediction. Our study fills a much-encountered gap in protein prediction and brings us a step closer to demystifying the domain knowledge needed to understand protein sequences. Code is available on https://github.com/HKUNLP/RSA.

PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark will be open-sourced soon.

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.

Domain Adaptation via Maximizing Surrogate Mutual Information

Unsupervised domain adaptation (UDA), which is an important topic in transfer learning, aims to predict unlabeled data from target domain with access to labeled data from the source domain. In this work, we propose a novel framework called SIDA (Surrogate Mutual Information Maximization Domain Adaptation) with strong theoretical guarantees. To be specific, SIDA implements adaptation by maximizing mutual information (MI) between features. In the framework, a surrogate joint distribution models the underlying joint distribution of the unlabeled target domain. Our theoretical analysis validates SIDA by bounding the expected risk on target domain with MI and surrogate distribution bias. Experiments show that our approach is comparable with state-of-the-art unsupervised adaptation methods on standard UDA tasks.