arXiv subjects

Heng Ji

Publications and source records attributed to Heng Ji.

At least 181 records · Page 10Linked to original sources

arXiv2024

MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction

Bridging biomolecular modeling with natural language information, particularly through large language models (LLMs), has recently emerged as a promising interdisciplinary research area. LLMs, having been trained on large corpora of scientific documents, demonstrate significant potential in understanding and reasoning about biomolecules by providing enriched contextual and domain knowledge. However, the extent to which LLM-driven insights can improve performance on complex predictive tasks (e.g., toxicity) remains unclear. Further, the extent to which relevant knowledge can be extracted from LLMs also remains unknown. In this study, we present Molecule Caption Arena: the first comprehensive benchmark of LLM-augmented molecular property prediction. We evaluate over twenty LLMs, including both general-purpose and domain-specific molecule captioners, across diverse prediction tasks. To this goal, we introduce a novel, battle-based rating system. Our findings confirm the ability of LLM-extracted knowledge to enhance state-of-the-art molecular representations, with notable model-, prompt-, and dataset-specific variations. Code, resources, and data are available at github.com/Genentech/molcap-arena.

cs.CL↗

arXiv2024

Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

cs.AI↗

arXiv2024

Schema-Guided Culture-Aware Complex Event Simulation with Multi-Agent Role-Play

Complex news events, such as natural disasters and socio-political conflicts, require swift responses from the government and society. Relying on historical events to project the future is insufficient as such events are sparse and do not cover all possible conditions and nuanced situations. Simulation of these complex events can help better prepare and reduce the negative impact. We develop a controllable complex news event simulator guided by both the event schema representing domain knowledge about the scenario and user-provided assumptions representing case-specific conditions. As event dynamics depend on the fine-grained social and cultural context, we further introduce a geo-diverse commonsense and cultural norm-aware knowledge enhancement component. To enhance the coherence of the simulation, apart from the global timeline of events, we take an agent-based approach to simulate the individual character states, plans, and actions. By incorporating the schema and cultural norms, our generated simulations achieve much higher coherence and appropriateness and are received favorably by participants from a humanitarian assistance organization.

cs.AI↗

arXiv2024

Infogent: An Agent-Based Framework for Web Information Aggregation

Despite seemingly performant web agents on the task-completion benchmarks, most existing methods evaluate the agents based on a presupposition: the web navigation task consists of linear sequence of actions with an end state that marks task completion. In contrast, our work focuses on web navigation for information aggregation, wherein the agent must explore different websites to gather information for a complex query. We consider web information aggregation from two different perspectives: (i) Direct API-driven Access relies on a text-only view of the Web, leveraging external tools such as Google Search API to navigate the web and a scraper to extract website contents. (ii) Interactive Visual Access uses screenshots of the webpages and requires interaction with the browser to navigate and access information. Motivated by these diverse information access settings, we introduce Infogent, a novel modular framework for web information aggregation involving three distinct components: Navigator, Extractor and Aggregator. Experiments on different information access settings demonstrate Infogent beats an existing SOTA multi-agent search framework by 7% under Direct API-Driven Access on FRAMES, and improves over an existing information-seeking web agent by 4.3% under Interactive Visual Access on AssistantBench.

cs.AI↗

arXiv2024

MACAROON: Training Vision-Language Models To Be Your Engaged Partners

Large vision-language models (LVLMs), while proficient in following instructions and responding to diverse questions, invariably generate detailed responses even when questions are ambiguous or unanswerable, leading to hallucinations and bias issues. Thus, it is essential for LVLMs to proactively engage with humans to ask for clarifications or additional information for better responses. In this study, we aim to shift LVLMs from passive answer providers to proactive engaged partners. We begin by establishing a three-tiered hierarchy for questions of invalid, ambiguous, and personalizable nature to measure the proactive engagement capabilities of LVLMs. Utilizing this hierarchy, we create PIE, (ProactIve Engagement Evaluation) through GPT-4o and human annotators, consisting of 853 questions across six distinct, fine-grained question types that are verified by human annotators and accompanied with well-defined metrics. Our evaluations on \benchmark indicate poor performance of existing LVLMs, with the best-performing open-weights model only achieving an Aggregate Align Rate (AAR) of 0.28. In response, we introduce MACAROON, self-iMaginAtion for ContrAstive pReference OptimizatiON, which instructs LVLMs to autonomously generate contrastive response pairs for unlabeled questions given the task description and human-crafted criteria. Then, the self-imagined data is formatted for conditional reinforcement learning. Experimental results show MACAROON effectively improves LVLMs' capabilities to be proactively engaged (0.84 AAR) while maintaining comparable performance on general tasks.

cs.CL↗

arXiv2024

Mitigating the Alignment Tax of RLHF

LLMs acquire a wide range of abilities during pre-training, but aligning LLMs under Reinforcement Learning with Human Feedback (RLHF) can lead to forgetting pretrained abilities, which is also known as the alignment tax. To investigate alignment tax, we conducted experiments with existing RLHF algorithms using OpenLLaMA-3B, which revealed a pronounced alignment tax in NLP tasks. Whereas, despite various techniques to mitigate forgetting, they are often at odds with the RLHF performance, leading to a trade-off between alignment performance and forgetting mitigation, leading to an alignment-forgetting trade-off. In this paper we show that model averaging, which simply interpolates between pre and post RLHF model weights, surprisingly achieves the most strongest alignment-forgetting Pareto front among a wide range of competing methods. To understand its effectiveness, we offer theoretical insights into model averaging, revealing that it enhances performance Pareto front by increasing feature diversity on the layers where tasks share overlapped feature spaces. Empirical evidence corroborates our analysis by showing the benefits of averaging low-level transformer layers. Building on the analysis and the observation that averaging different layers of the transformer leads to significantly different alignment-forgetting trade-offs, we propose Heterogeneous Model Averaging (HMA) to Heterogeneously find various combination ratios of model layers. HMA seeks to maximize the alignment performance while incurring minimal alignment tax. Moreover, we validate HMA's performance across a range of RLHF algorithms over OpenLLaMA-3B and further extend our findings to Mistral-7B which is evaluated by open-sourced preference model and GPT4. Code available here: https://github.com/avalonstrel/Mitigating-the-Alignment-Tax-of-RLHF.git.

cs.LG↗

arXiv2024

TrustLLM: Trustworthiness in Large Language Models

Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.

cs.CL↗

arXiv2024

Search and Detect: Training-Free Long Tail Object Detection via Web-Image Retrieval

In this paper, we introduce SearchDet, a training-free long-tail object detection framework that significantly enhances open-vocabulary object detection performance. SearchDet retrieves a set of positive and negative images of an object to ground, embeds these images, and computes an input image-weighted query which is used to detect the desired concept in the image. Our proposed method is simple and training-free, yet achieves over 48.7% mAP improvement on ODinW and 59.1% mAP improvement on LVIS compared to state-of-the-art models such as GroundingDINO. We further show that our approach of basing object detection on a set of Web-retrieved exemplars is stable with respect to variations in the exemplars, suggesting a path towards eliminating costly data annotation and training procedures.

cs.CV↗

arXiv2024

Enabling Language Models to Implicitly Learn Self-Improvement

Large Language Models (LLMs) have demonstrated remarkable capabilities in open-ended text generation tasks. However, the inherent open-ended nature of these tasks implies that there is always room for improvement in the quality of model responses. To address this challenge, various approaches have been proposed to enhance the performance of LLMs. There has been a growing focus on enabling LLMs to self-improve their response quality, thereby reducing the reliance on extensive human annotation efforts for collecting diverse and high-quality training data. Recently, prompting-based methods have been widely explored among self-improvement methods owing to their effectiveness, efficiency, and convenience. However, those methods usually require explicitly and thoroughly written rubrics as inputs to LLMs. It is expensive and challenging to manually derive and provide all necessary rubrics with a real-world complex goal for improvement (e.g., being more helpful and less harmful). To this end, we propose an ImPlicit Self-ImprovemenT (PIT) framework that implicitly learns the improvement goal from human preference data. PIT only requires preference data that are used to train reward models without extra human efforts. Specifically, we reformulate the training objective of reinforcement learning from human feedback (RLHF) -- instead of maximizing response quality for a given input, we maximize the quality gap of the response conditioned on a reference response. In this way, PIT is implicitly trained with the improvement goal of better aligning with human preferences. Experiments on two real-world datasets and one synthetic dataset show that our method significantly outperforms prompting-based methods.

cs.CL↗

arXiv2024

Fragment and Geometry Aware Tokenization of Molecules for Structure-Based Drug Design Using Language Models

Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models (LMs) have excelled in natural language processing, their application in SBDD is underexplored. To bridge this gap, we introduce a method, known as Frag2Seq, to apply LMs to SBDD by generating molecules in a fragment-based manner in which fragments correspond to functional modules. We transform 3D molecules into fragment-informed sequences using SE(3)-equivariant molecule and fragment local frames, extracting SE(3)-invariant sequences that preserve geometric information of 3D fragments. Furthermore, we incorporate protein pocket embeddings obtained from a pre-trained inverse folding model into the LMs via cross-attention to capture protein-ligand interaction, enabling effective target-aware molecule generation. Benefiting from employing LMs with fragment-based generation and effective protein context encoding, our model achieves the best performance on binding vina score and chemical properties such as QED and Lipinski, which shows our model's efficacy in generating drug-like ligands with higher binding affinity against target proteins. Moreover, our method also exhibits higher sampling efficiency compared to atom-based autoregressive and diffusion baselines with at most ~300x speedup.

q-bio.BM↗

arXiv2024

ARMADA: Attribute-Based Multimodal Data Augmentation

In Multimodal Language Models (MLMs), the cost of manually annotating high-quality image-text pair data for fine-tuning and alignment is extremely high. While existing multimodal data augmentation frameworks propose ways to augment image-text pairs, they either suffer from semantic inconsistency between texts and images, or generate unrealistic images, causing knowledge gap with real world examples. To address these issues, we propose Attribute-based Multimodal Data Augmentation (ARMADA), a novel multimodal data augmentation method via knowledge-guided manipulation of visual attributes of the mentioned entities. Specifically, we extract entities and their visual attributes from the original text data, then search for alternative values for the visual attributes under the guidance of knowledge bases (KBs) and large language models (LLMs). We then utilize an image-editing model to edit the images with the extracted attributes. ARMADA is a novel multimodal data generation framework that: (i) extracts knowledge-grounded attributes from symbolic KBs for semantically consistent yet distinctive image-text pair generation, (ii) generates visually similar images of disparate categories using neighboring entities in the KB hierarchy, and (iii) uses the commonsense knowledge of LLMs to modulate auxiliary visual attributes such as backgrounds for more robust representation of original entities. Our empirical results over four downstream tasks demonstrate the efficacy of our framework to produce high-quality data and enhance the model performance. This also highlights the need to leverage external knowledge proxies for enhanced interpretability and real-world grounding.

cs.AI↗

arXiv2024

Geometry Informed Tokenization of Molecules for Language Model Generation

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing the Geo2Seq, which converts molecular geometries into $SE(3)$-invariant 1D discrete sequences. Geo2Seq consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with Geo2Seq, various LMs excel in molecular geometry generation, especially in controlled generation tasks.

cs.AI↗

arXiv2024

Tool Learning with Foundation Models

Humans possess an extraordinary ability to create and utilize tools, allowing them to overcome physical limitations and explore new frontiers. With the advent of foundation models, AI systems have the potential to be equally adept in tool use as humans. This paradigm, i.e., tool learning with foundation models, combines the strengths of specialized tools and foundation models to achieve enhanced accuracy, efficiency, and automation in problem-solving. Despite its immense potential, there is still a lack of a comprehensive understanding of key challenges, opportunities, and future endeavors in this field. To this end, we present a systematic investigation of tool learning in this paper. We first introduce the background of tool learning, including its cognitive origins, the paradigm shift of foundation models, and the complementary roles of tools and models. Then we recapitulate existing tool learning research into tool-augmented and tool-oriented learning. We formulate a general tool learning framework: starting from understanding the user instruction, models should learn to decompose a complex task into several subtasks, dynamically adjust their plan through reasoning, and effectively conquer each sub-task by selecting appropriate tools. We also discuss how to train models for improved tool-use capabilities and facilitate the generalization in tool learning. Considering the lack of a systematic tool learning evaluation in prior works, we experiment with 18 representative tools and show the potential of current foundation models in skillfully utilizing tools. Finally, we discuss several open problems that require further investigation for tool learning. In general, we hope this paper could inspire future research in integrating tools with foundation models.

cs.CL↗

arXiv2024

Dialog Flow Induction for Constrainable LLM-Based Chatbots

LLM-driven dialog systems are used in a diverse set of applications, ranging from healthcare to customer service. However, given their generalization capability, it is difficult to ensure that these chatbots stay within the boundaries of the specialized domains, potentially resulting in inaccurate information and irrelevant responses. This paper introduces an unsupervised approach for automatically inducing domain-specific dialog flows that can be used to constrain LLM-based chatbots. We introduce two variants of dialog flow based on the availability of in-domain conversation instances. Through human and automatic evaluation over various dialog domains, we demonstrate that our high-quality data-guided dialog flows achieve better domain coverage, thereby overcoming the need for extensive manual crafting of such flows.

cs.CL↗

arXiv2024

Establishing Knowledge Preference in Language Models

Language models are known to encode a great amount of factual knowledge through pretraining. However, such knowledge might be insufficient to cater to user requests, requiring the model to integrate external knowledge sources and adhere to user-provided specifications. When answering questions about ongoing events, the model should use recent news articles to update its response; when asked to provide recommendations, the model should prioritize user specifications over retrieved product reviews; when some facts are edited in the model, the updated facts should override all prior knowledge learned by the model even if they are conflicting. In all of the cases above, the model faces a decision between its own parametric knowledge, (retrieved) contextual knowledge, and user instruction knowledge. In this paper, we (1) unify such settings into the problem of knowledge preference and define a three-level preference hierarchy over these knowledge sources; (2) compile a collection of existing datasets IfQA, MQuAKE, and MRQA covering a combination of settings (with/without user specifications, with/without context documents) to systematically evaluate how well models obey the intended knowledge preference; and (3) propose a dataset synthesis method that composes diverse question-answer pairs with user assumptions and related context to directly fine-tune LMs for instilling the hierarchy of knowledge. We demonstrate that a 7B model, fine-tuned on only a few thousand examples automatically generated by our proposed method, effectively achieves superior performance (more than 18% improvement across all evaluation benchmarks) in adhering to the desired knowledge preference hierarchy.

cs.CL↗

arXiv2024

Knowledge Overshadowing Causes Amalgamated Hallucination in Large Language Models

Hallucination is often regarded as a major impediment for using large language models (LLMs), especially for knowledge-intensive tasks. Even when the training corpus consists solely of true statements, language models still generate hallucinations in the form of amalgamations of multiple facts. We coin this phenomenon as ``knowledge overshadowing'': when we query knowledge from a language model with multiple conditions, some conditions overshadow others, leading to hallucinated outputs. This phenomenon partially stems from training data imbalance, which we verify on both pretrained models and fine-tuned models, over a wide range of LM model families and sizes.From a theoretical point of view, knowledge overshadowing can be interpreted as over-generalization of the dominant conditions (patterns). We show that the hallucination rate grows with both the imbalance ratio (between the popular and unpopular condition) and the length of dominant condition description, consistent with our derived generalization bound. Finally, we propose to utilize overshadowing conditions as a signal to catch hallucination before it is produced, along with a training-free self-contrastive decoding method to alleviate hallucination during inference. Our proposed approach showcases up to 82% F1 for hallucination anticipation and 11.2% to 39.4% hallucination control, with different models and datasets.

cs.CL↗

arXiv2024

L+M-24: Building a Dataset for Language + Molecules @ ACL 2024

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the $\textit{L+M-24}$ dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, $\textit{L+M-24}$ is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

cs.CL↗

arXiv2024

LM-Infinite: Zero-Shot Extreme Length Generalization for Large Language Models

Today's large language models (LLMs) typically train on short text segments (e.g., <4K tokens) due to the quadratic complexity of their Transformer architectures. As a result, their performance suffers drastically on inputs longer than those encountered during training, substantially limiting their applications in real-world tasks involving long contexts such as encoding scientific articles, code repositories, or long dialogues. Through theoretical analysis and empirical investigation, this work identifies three major factors contributing to this length generalization failure. Our theoretical analysis further reveals that commonly used techniques like truncating the attention window or relative positional encodings are inadequate to address them. Answering these challenges, we propose LM-Infinite, a simple and effective method for enhancing LLMs' capabilities of handling long contexts. LM-Infinite is highly flexible and can be used with most modern LLMs off-the-shelf. Without any parameter updates, it allows LLMs pre-trained with 2K or 4K-long segments to generalize to up to 200M length inputs while retaining perplexity. It also improves performance on downstream tasks such as Passkey Retrieval and Qasper in the zero-shot setting. LM-Infinite brings substantial efficiency improvements: it achieves 2.7x decoding speed up and 7.5x memory saving over the original model. Our codes are released at \url{https://github.com/Glaciohound/LM-Infinite}.

cs.CL↗