Tao Feng

Pengcheng Xu, Tao Feng, Tianfan Fu et al.

In this work, we introduce a method to fine-tune a Transformer-based generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can generate molecular structures with desired properties effectively. In contrast to the traditional RNN-based models, our proposed method exhibits superior performance in generating compounds predicted to be active against various biological targets, capturing long-term dependencies in the molecular structure sequence. The model's efficacy is demonstrated across numerous tasks, including generating analogues to a query structure and producing compounds with particular attributes, outperforming the baseline RNN-based methods. Our approach can be used for scaffold hopping, library expansion starting from a single molecule, and generating compounds with high predicted activity against biological targets.

Guanyu Lin, Tao Feng, Pengrui Han et al.

As scientific research proliferates, researchers face the daunting task of navigating and reading vast amounts of literature. Existing solutions, such as document QA, fail to provide personalized and up-to-date information efficiently. We present Paper Copilot, a self-evolving, efficient LLM system designed to assist researchers, based on thought-retrieval, user profile and high performance optimization. Specifically, Paper Copilot can offer personalized research services, maintaining a real-time updated database. Quantitative evaluation demonstrates that Paper Copilot saves 69.92\% of time after efficient deployment. This paper details the design and implementation of Paper Copilot, highlighting its contributions to personalized academic support and its potential to streamline the research process.

Haozhen Zhang, Tao Feng, Jiaxuan You

Retrieval-augmented generation (RAG) has revitalized Large Language Models (LLMs) by injecting non-parametric factual knowledge. Compared with long-context LLMs, RAG is considered an effective summarization tool in a more concise and lightweight manner, which can interact with LLMs multiple times using diverse queries to get comprehensive responses. However, the LLM-generated historical responses, which contain potentially insightful information, are largely neglected and discarded by existing approaches, leading to suboptimal results. In this paper, we propose $\textit{graph of records}$ ($\textbf{GoR}$), which leverages historical responses generated by LLMs to enhance RAG for long-context global summarization. Inspired by the $\textit{retrieve-then-generate}$ paradigm of RAG, we construct a graph by establishing an edge between the retrieved text chunks and the corresponding LLM-generated response. To further uncover the intricate correlations between them, GoR features a $\textit{graph neural network}$ and an elaborately designed $\textit{BERTScore}$-based objective for self-supervised model training, enabling seamless supervision signal backpropagation between reference summaries and node embeddings. We comprehensively compare GoR with 12 baselines across four long-context summarization datasets, and the results indicate that our proposed method reaches the best performance ($\textit{e.g.}$, 15%, 8%, and 19% improvement over retrievers w.r.t. Rouge-L, Rouge-1, and Rouge-2 on the WCEP dataset). Extensive experiments further demonstrate the effectiveness of GoR.

Yifan Xie, Jingge Wang, Tao Feng et al.

Colonoscopy is crucial for identifying adenomatous polyps and preventing colorectal cancer. However, developing robust models for polyp detection is challenging by the limited size and accessibility of existing colonoscopy datasets. While previous efforts have attempted to synthesize colonoscopy images, current methods suffer from instability and insufficient data diversity. Moreover, these approaches lack precise control over the generation process, resulting in images that fail to meet clinical quality standards. To address these challenges, we propose CCIS-DIFF, a Controlled generative model for high-quality Colonoscopy Image Synthesis based on a Diffusion architecture. Our method offers precise control over both the spatial attributes (polyp location and shape) and clinical characteristics of polyps that align with clinical descriptions. Specifically, we introduce a blur mask weighting strategy to seamlessly blend synthesized polyps with the colonic mucosa, and a text-aware attention mechanism to guide the generated images to reflect clinical characteristics. Notably, to achieve this, we construct a new multi-modal colonoscopy dataset that integrates images, mask annotations, and corresponding clinical text descriptions. Experimental results demonstrate that our method generates high-quality, diverse colonoscopy images with fine control over both spatial constraints and clinical consistency, offering valuable support for downstream segmentation and diagnostic tasks.

Chenglin Li, Qianglong Chen, Zhi Li et al.

Instruction tuning is a crucial technique for aligning language models with humans' actual goals in the real world. Extensive research has highlighted the quality of instruction data is essential for the success of this alignment. However, creating high-quality data manually is labor-intensive and time-consuming, which leads researchers to explore using LLMs to synthesize data. Recent studies have focused on using a stronger LLM to iteratively enhance existing instruction data, showing promising results. Nevertheless, previous work often lacks control over the evolution direction, resulting in high uncertainty in the data synthesis process and low-quality instructions. In this paper, we introduce a general and scalable framework, IDEA-MCTS (Instruction Data Enhancement using Monte Carlo Tree Search), a scalable framework for efficiently synthesizing instructions. With tree search and evaluation models, it can efficiently guide each instruction to evolve into a high-quality form, aiding in instruction fine-tuning. Experimental results show that IDEA-MCTS significantly enhances the seed instruction data, raising the average evaluation scores of quality, diversity, and complexity from 2.19 to 3.81. Furthermore, in open-domain benchmarks, experimental results show that IDEA-MCTS improves the accuracy of real-world instruction-following skills in LLMs by an average of 5\% in low-resource settings.

Jingjun Xu, Chongshan Lin, Haofei Yu et al.

Academic research generates diverse data sources, and as researchers increasingly use machine learning to assist research tasks, a crucial question arises: Can we build a unified data interface to support the development of machine learning models for various academic tasks? Models trained on such a unified interface can better support human researchers throughout the research process, eventually accelerating knowledge discovery. In this work, we introduce ResearchArcade, a graph-based interface that connects multiple academic data sources, unifies task definitions, and supports a wide range of base models to address key academic challenges. ResearchArcade utilizes a coherent multi-table format with graph structures to organize data from different sources, including academic corpora from ArXiv and peer reviews from OpenReview, while capturing information with multiple modalities, such as text, figures, and tables. ResearchArcade also preserves temporal evolution at both the manuscript and community levels, supporting the study of paper revisions as well as broader research trends over time. Additionally, ResearchArcade unifies diverse academic task definitions and supports various models with distinct input requirements. Our experiments across six academic tasks demonstrate that combining cross-source and multi-modal information enables a broader range of tasks, while incorporating graph structures consistently improves performance over baseline methods. This highlights the effectiveness of ResearchArcade and its potential to advance research progress.

Huixin Zhan, Feng Tao, Yongcan Cao

Human demonstrations can provide trustful samples to train reinforcement learning algorithms for robots to learn complex behaviors in real-world environments. However, obtaining sufficient demonstrations may be impractical because many behaviors are difficult for humans to demonstrate. A more practical approach is to replace human demonstrations by human queries, i.e., preference-based reinforcement learning. One key limitation of the existing algorithms is the need for a significant amount of human queries because a large number of labeled data is needed to train neural networks for the approximation of a continuous, high-dimensional reward function. To reduce and minimize the need for human queries, we propose a new GAN-assisted human preference-based reinforcement learning approach that uses a generative adversarial network (GAN) to actively learn human preferences and then replace the role of human in assigning preferences. The adversarial neural network is simple and only has a binary output, hence requiring much less human queries to train. Moreover, a maximum entropy based reinforcement learning algorithm is designed to shape the loss towards the desired regions or away from the undesired regions. To show the effectiveness of the proposed approach, we present some studies on complex robotic tasks without access to the environment reward in a typical MuJoCo robot locomotion environment. The obtained results show our method can achieve a reduction of about 99.8% human time without performance sacrifice.

Feng Tao, Rengan Suresh, Johnathan Votion et al.

In this paper, we focus on developing a novel unsupervised machine learning algorithm, named graph based multi-layer k-means++ (G-MLKM), to solve data-target association problem when targets move on a constrained space and minimal information of the targets can be obtained by sensors. Instead of employing the traditional data-target association methods that are based on statistical probabilities, the G-MLKM solves the problem via data clustering. We first will develop the Multi-layer K-means++ (MLKM) method for data-target association at local space given a simplified constrained space situation. Then a p-dual graph is proposed to represent the general constrained space when local spaces are interconnected. Based on the dual graph and graph theory, we then generalize MLKM to G-MLKM by first understanding local data-target association and then extracting cross-local data-target association mathematically analyze the data association at intersections of that space. To exclude potential data-target association errors that disobey physical rules, we also develop error correction mechanisms to further improve the accuracy. Numerous simulation examples are conducted to demonstrate the performance of G-MLKM.

Feng Tao, Yongcan Cao

In this paper, we study the problem of obtaining a control policy that can mimic and then outperform expert demonstrations in Markov decision processes where the reward function is unknown to the learning agent. One main relevant approach is the inverse reinforcement learning (IRL), which mainly focuses on inferring a reward function from expert demonstrations. The obtained control policy by IRL and the associated algorithms, however, can hardly outperform expert demonstrations. To overcome this limitation, we propose a novel method that enables the learning agent to outperform the demonstrator via a new concurrent reward and action policy learning approach. In particular, we first propose a new stereo utility definition that aims to address the bias in the interpretation of expert demonstrations. We then propose a loss function for the learning agent to learn reward and action policies concurrently such that the learning agent can outperform expert demonstrations. The performance of the proposed method is first demonstrated in OpenAI environments. Further efforts are conducted to experimentally validate the proposed method via an indoor drone flight scenario.

Samuel Silva, Rengan Suresh, Feng Tao et al.

Data-target association is an important step in multi-target localization for the intelligent operation of un- manned systems in numerous applications such as search and rescue, traffic management and surveillance. The objective of this paper is to present an innovative data association learning approach named multi-layer K-means (MLKM) based on leveraging the advantages of some existing machine learning approaches, including K-means, K-means++, and deep neural networks. To enable the accurate data association from different sensors for efficient target localization, MLKM relies on the clustering capabilities of K-means++ structured in a multi-layer framework with the error correction feature that is motivated by the backpropogation that is well-known in deep learning research. To show the effectiveness of the MLKM method, numerous simulation examples are conducted to compare its performance with K-means, K-means++, and deep neural networks.