MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce \ours, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol), outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Graph Chain-of-Thought: Augmenting Large Language Models by Reasoning on Graphs

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

TriSum: Learning Summarization Ability from Large Language Models with Structured Rationale

The advent of large language models (LLMs) has significantly advanced natural language processing tasks like text summarization. However, their large size and computational demands, coupled with privacy concerns in data transmission, limit their use in resource-constrained and privacy-centric settings. To overcome this, we introduce TriSum, a framework for distilling LLMs' text summarization abilities into a compact, local model. Initially, LLMs extract a set of aspect-triple rationales and summaries, which are refined using a dual-scoring method for quality. Next, a smaller local model is trained with these tasks, employing a curriculum learning strategy that evolves from simple to complex tasks. Our method enhances local model performance on various benchmarks (CNN/DailyMail, XSum, and ClinicalTrial), outperforming baselines by 4.5%, 8.5%, and 7.4%, respectively. It also improves interpretability by providing insights into the summarization rationale.

ILCiteR: Evidence-grounded Interpretable Local Citation Recommendation

Existing Machine Learning approaches for local citation recommendation directly map or translate a query, which is typically a claim or an entity mention, to citation-worthy research papers. Within such a formulation, it is challenging to pinpoint why one should cite a specific research paper for a particular query, leading to limited recommendation interpretability. To alleviate this, we introduce the evidence-grounded local citation recommendation task, where the target latent space comprises evidence spans for recommending specific papers. Using a distantly-supervised evidence retrieval and multi-step re-ranking framework, our proposed system, ILCiteR, recommends papers to cite for a query grounded on similar evidence spans extracted from the existing research literature. Unlike past formulations that simply output recommendations, ILCiteR retrieves ranked lists of evidence span and recommended paper pairs. Secondly, previously proposed neural models for citation recommendation require expensive training on massive labeled data, ideally after every significant update to the pool of candidate papers. In contrast, ILCiteR relies solely on distant supervision from a dynamic evidence database and pre-trained Transformer-based Language Models without any model training. We contribute a novel dataset for the evidence-grounded local citation recommendation task and demonstrate the efficacy of our proposed conditional neural rank-ensembling approach for re-ranking evidence spans.

Improving Retrieval in Theme-specific Applications using a Corpus Topical Taxonomy

Document retrieval has greatly benefited from the advancements of large-scale pre-trained language models (PLMs). However, their effectiveness is often limited in theme-specific applications for specialized areas or industries, due to unique terminologies, incomplete contexts of user queries, and specialized search intents. To capture the theme-specific information and improve retrieval, we propose to use a corpus topical taxonomy, which outlines the latent topic structure of the corpus while reflecting user-interested aspects. We introduce ToTER (Topical Taxonomy Enhanced Retrieval) framework, which identifies the central topics of queries and documents with the guidance of the taxonomy, and exploits their topical relatedness to supplement missing contexts. As a plug-and-play framework, ToTER can be flexibly employed to enhance various PLM-based retrievers. Through extensive quantitative, ablative, and exploratory experiments on two real-world datasets, we ascertain the benefits of using topical taxonomy for retrieval in theme-specific applications and demonstrate the effectiveness of ToTER.

TELEClass: Taxonomy Enrichment and LLM-Enhanced Hierarchical Text Classification with Minimal Supervision

Hierarchical text classification aims to categorize each document into a set of classes in a label taxonomy. Most earlier works focus on fully or semi-supervised methods that require a large amount of human annotated data which is costly and time-consuming to acquire. To alleviate human efforts, in this paper, we work on hierarchical text classification with the minimal amount of supervision: using the sole class name of each node as the only supervision. Recently, large language models (LLM) show competitive performance on various tasks through zero-shot prompting, but this method performs poorly in the hierarchical setting, because it is ineffective to include the large and structured label space in a prompt. On the other hand, previous weakly-supervised hierarchical text classification methods only utilize the raw taxonomy skeleton and ignore the rich information hidden in the text corpus that can serve as additional class-indicative features. To tackle the above challenges, we propose TELEClass, Taxonomy Enrichment and LLM-Enhanced weakly-supervised hierarchical text classification, which (1) automatically enriches the label taxonomy with class-indicative topical terms mined from the corpus to facilitate classifier training and (2) utilizes LLMs for both data annotation and creation tailored for the hierarchical label space. Experiments show that TELEClass can outperform previous weakly-supervised hierarchical text classification methods and LLM-based zero-shot prompting methods on two public datasets.

Multi-LoRA Composition for Image Generation

Low-Rank Adaptation (LoRA) is extensively utilized in text-to-image models for the accurate rendition of specific elements like distinct characters or unique styles in generated images. Nonetheless, existing methods face challenges in effectively composing multiple LoRAs, especially as the number of LoRAs to be integrated grows, thus hindering the creation of complex imagery. In this paper, we study multi-LoRA composition through a decoding-centric perspective. We present two training-free methods: LoRA Switch, which alternates between different LoRAs at each denoising step, and LoRA Composite, which simultaneously incorporates all LoRAs to guide more cohesive image synthesis. To evaluate the proposed approaches, we establish ComposLoRA, a new comprehensive testbed as part of this research. It features a diverse range of LoRA categories with 480 composition sets. Utilizing an evaluation framework based on GPT-4V, our findings demonstrate a clear improvement in performance with our methods over the prevalent baseline, particularly evident when increasing the number of LoRAs in a composition.

A Unified Taxonomy-Guided Instruction Tuning Framework for Entity Set Expansion and Taxonomy Expansion

Entity Set Expansion, Taxonomy Expansion, and Seed-Guided Taxonomy Construction are three representative tasks that can be used to automatically populate an existing taxonomy with new entities. However, previous approaches often address these tasks separately with heterogeneous techniques, lacking a unified perspective. To tackle this issue, in this paper, we identify the common key skills needed for these tasks from the view of taxonomy structures -- finding 'siblings' and finding 'parents' -- and propose a unified taxonomy-guided instruction tuning framework to jointly solve the three tasks. To be specific, by leveraging the existing taxonomy as a rich source of entity relationships, we utilize instruction tuning to fine-tune a large language model to generate parent and sibling entities. Extensive experiments on multiple benchmark datasets demonstrate the effectiveness of TaxoInstruct, which outperforms task-specific baselines across all three tasks.

Grasping the Essentials: Tailoring Large Language Models for Zero-Shot Relation Extraction

Relation extraction (RE), a crucial task in NLP, aims to identify semantic relationships between entities mentioned in texts. Despite significant advancements in this field, existing models typically rely on extensive annotated data for training, which can be both costly and time-consuming to acquire. Moreover, these models often struggle to adapt to new or unseen relationships. In contrast, few-shot learning settings, which aim to reduce annotation requirements, may offer incomplete and biased supervision for understanding target relation semantics, leading to degraded and unstable performance. To provide the model with accurate and explicit descriptions of the relations types and meanwhile minimize the annotation requirements, we study the definition only zero-shot RE setting where only relation definitions expressed in natural language are used to train a RE model. Motivated by the strong synthetic data generation power of LLMs, we propose a framework REPaL which consists of three stages: (1) We utilize LLMs to generate initial seed instances based on relation definitions and an unlabeled corpora. (2) We fine-tune a bidirectional Small Language Model (SLM) using these initial seeds to learn the relations for the target domain. (3) We enhance pattern coverage and mitigate bias resulting from the limited number of initial seeds by incorporating feedback acquired from SLM's predictions on unlabeled corpora. To accomplish this, we leverage the multi-turn conversation ability of LLMs to generate new instances in follow-up dialogues. Experiments on two datasets show REPaL achieves better zero-shot performance with large margins over baseline methods.

GenRES: Rethinking Evaluation for Generative Relation Extraction in the Era of Large Language Models

The field of relation extraction (RE) is experiencing a notable shift towards generative relation extraction (GRE), leveraging the capabilities of large language models (LLMs). However, we discovered that traditional relation extraction (RE) metrics like precision and recall fall short in evaluating GRE methods. This shortfall arises because these metrics rely on exact matching with human-annotated reference relations, while GRE methods often produce diverse and semantically accurate relations that differ from the references. To fill this gap, we introduce GenRES for a multi-dimensional assessment in terms of the topic similarity, uniqueness, granularity, factualness, and completeness of the GRE results. With GenRES, we empirically identified that (1) precision/recall fails to justify the performance of GRE methods; (2) human-annotated referential relations can be incomplete; (3) prompting LLMs with a fixed set of relations or entities can cause hallucinations. Next, we conducted a human evaluation of GRE methods that shows GenRES is consistent with human preferences for RE quality. Last, we made a comprehensive evaluation of fourteen leading LLMs using GenRES across document, bag, and sentence level RE datasets, respectively, to set the benchmark for future research in GRE