Thailand

Language Models (LMs) excel in understanding textual descriptions of proteins, as evident in biomedical question-answering tasks. However, their capability falters with raw protein data, such as amino acid sequences, due to a deficit in pretraining on such data. Conversely, Protein Language Models (PLMs) can understand and convert protein data into high-quality representations, but struggle to process texts. To address their limitations, we introduce ProtT3, a framework for Protein-to-Text Generation for Text-based Protein Understanding. ProtT3 empowers an LM to understand protein sequences of amino acids by incorporating a PLM as its protein understanding module, enabling effective protein-to-text generation. This collaboration between PLM and LM is facilitated by a cross-modal projector (i.e., Q-Former) that bridges the modality gap between the PLM&#39;s representation space and the LM&#39;s input space. Unlike previous studies focusing on protein property prediction and protein-text retrieval, we delve into the largely unexplored field of protein-to-text generation. To facilitate comprehensive benchmarks and promote future research, we establish quantitative evaluations for protein-text modeling tasks, including protein captioning, protein question-answering, and protein-text retrieval. Our experiments show that ProtT3 substantially surpasses current baselines, with ablation studies further highlighting the efficacy of its core components. Our code is available at https://github.com/acharkq/ProtT3.

ACL 2024

ProtT3: Protein-to-Text Generation for Text-based Protein Understanding

protein-text retrieval

protein captioning

protein language model

protein-text modeling

large language model

Language Models (LMs) excel in understanding textual descriptions of proteins, as evident in biomedical question-answering tasks. However, their capability falters with raw protein data, such as amino acid sequences, due to a deficit in pretraining on such data. Conversely, Protein Language Models (PLMs) can understand and convert protein data into high-quality representations, but struggle to process texts. To address their limitations, we introduce ProtT3, a framework for Protein-to-Text Generation for Text-based Protein Understanding. ProtT3 empowers an LM to understand protein sequences of amino acids by incorporating a PLM as its protein understanding module, enabling effective protein-to-text generation. This collaboration between PLM and LM is facilitated by a cross-modal projector (i.e., Q-Former) that bridges the modality gap between the PLM's representation space and the LM's input space. Unlike previous studies focusing on protein property prediction and protein-text retrieval, we delve into the largely unexplored field of protein-to-text generation. To facilitate comprehensive benchmarks and promote future research, we establish quantitative evaluations for protein-text modeling tasks, including protein captioning, protein question-answering, and protein-text retrieval. Our experiments show that ProtT3 substantially surpasses current baselines, with ablation studies further highlighting the efficacy of its core components. Our code is available at https://github.com/acharkq/ProtT3.

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The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. More information will be announced soon.

Existing approaches on zero-shot event detection usually train models on datasets annotated with known event types, and prompt them with unseen event definitions. These approaches yield sporadic successes, yet generally fall short of expectations.
In this work, we aim to improve zero-shot event detection by training models to better follow event definitions. We hypothesize that a diverse set of event types and definitions are the key for models to learn to follow event definitions while existing event extraction datasets focus on annotating many high-quality examples for a few event types. 
To verify our hypothesis, we construct an automatically generated Diverse Event Definition (DivED) dataset and conduct comparative studies. Our experiments reveal that a large number of event types (200) and diverse event definitions can significantly boost event extraction performance; on the other hand, the performance does not scale with over ten examples per event type.
Beyond scaling, we incorporate event ontology information and hard-negative samples during training, further boosting the performance. 
Based on these findings, we fine-tuned a LLaMA-2-7B model on our DivED dataset, yielding performance that surpasses SOTA large language models like GPT-3.5 across three open benchmarks on zero-shot event detection.

Improving Event Definition Following For Zero-Shot Event Detection

When a teacher provides examples for a student to study, these examples must be informative, enabling a student to progress from their current state toward a target concept or skill. Good teachers must therefore simultaneously infer what students already know and adapt their teaching to students' changing state of knowledge. There is increasing interest in using computational models, particularly large language models, as pedagogical tools. As students, language models in particular have shown a remarkable ability to adapt to new tasks given small numbers of examples. But how effectively can these models adapt as teachers to students of different types? To study this question, we introduce a suite of models and evaluation methods we call AdapT. AdapT has two components: (1) a collection of simulated Bayesian student models that can be used for evaluation of automated teaching methods; (2) a platform for evaluation with human students, to characterize the real-world effectiveness of these methods. We additionally introduce (3) AToM, a new probabilistic method for adaptive teaching that jointly infers students' past beliefs and optimizes for the correctness of future beliefs. In evaluations of simulated students across three learning domains (fraction arithmetic, English morphology, function learning), AToM systematically outperforms LLM-based and standard Bayesian teaching methods. In human experiments, both AToM and LLMs outperform non-adaptive random example selection. Our results highlight both the difficulty of the adaptive teaching task and the potential of learned adaptive methods for solving it.

Toward In-Context Teaching: Adapting Examples to Students' Misconceptions

Recent studies demonstrated that large language models (LLMs) can excel in many tasks via in-context learning (ICL). However, recent
works show that ICL-prompted models tend to produce inaccurate results when presented with adversarial inputs. In this work, we investigate whether augmenting ICL with natural language explanations (NLEs) improves the robustness of LLMs on adversarial datasets covering natural language inference and paraphrasing identification. We prompt LLMs with a small set of human-generated NLEs to produce further NLEs, yielding more accurate results than both a zero-shot-ICL setting and using only human-generated NLEs. Our results on five popular LLMs (GPT3.5-turbo, Llama2, Vicuna, Zephyr, and Mistral) show that our approach yields over 6% improvement over baseline approaches for eight adversarial datasets: HANS, ISCS, NaN, ST, PICD, PISP, ANLI, and PAWS. Furthermore, previous studies have demonstrated that prompt selection strategies significantly enhance ICL on in-distribution test sets. However, our findings reveal that these strategies do not match the efficacy of our approach for robustness evaluations, resulting in an accuracy drop of 8% compared to the proposed approach.

Using Natural Language Explanations to Improve Robustness of In-context Learning

The upscaling of Large Language Models (LLMs) has yielded impressive advances in natural language processing, yet it also poses significant deployment challenges. Weight quantization has emerged as a widely embraced solution to reduce memory and computational demands. This paper introduces BitDistiller, a framework that synergizes Quantization-Aware Training (QAT) with Knowledge Distillation (KD) to boost the performance of LLMs at ultra-low precisions (sub-4-bit). Specifically, BitDistiller first incorporates a tailored asymmetric quantization and clipping technique to maximally preserve the fidelity of quantized weights, and then proposes a novel Confidence-Aware Kullback-Leibler Divergence (CAKLD) objective, which is employed in a self-distillation manner to enable faster convergence and superior model performance. Empirical evaluations demonstrate that BitDistiller significantly surpasses existing methods in both 3-bit and 2-bit configurations on general language understanding and complex reasoning benchmarks. Notably, BitDistiller is shown to be more cost-effective, demanding fewer data and training resources. The code is available at https://github.com/DD-DuDa/BitDistiller.

BitDistiller: Unleashing the Potential of Sub-4-Bit LLMs via Self-Distillation

While Large Language Models (LLMs) have found success in real-world applications, their underlying explanatory process is still poorly understood. This paper proposes \textit{IBE-Eval}, a framework inspired by philosophical accounts on \emph{Inference to the Best Explanation (IBE)} to advance the interpretation and evaluation of LLMs' explanations. \textit{IBE-Eval} estimates the plausibility of natural language explanations through a combination of explicit logical and linguistic features including: \emph{consistency}, \emph{parsimony}, \emph{coherence}, and \emph{uncertainty}. Extensive experiments are conducted on \emph{Causal Question Answering (CQA)}, where \textit{IBE-Eval} is tasked to select the most plausible causal explanation amongst competing ones generated by LLMs (i.e., GPT 3.5 and Llama 2). The experiments reveal that \textit{IBE-Eval} can successfully identify the best explanation with up to 77\% accuracy ($\approx 27\%$ above random), improving upon a GPT 3.5-as-a-Judge baseline ($\approx+17\%$) while being intrinsically more efficient and interpretable. Additional analyses suggest that, despite model-specific variances, LLM-generated explanations tend to conform to IBE criteria and that \textit{IBE-Eval} is significantly correlated with human judgment, opening up opportunities for future development of automated explanation verification tools.

Inference to the Best Explanation in Large Language Models

Recent advances in few-shot question answering (QA) mostly rely on the power of pre-trained large language models (LLMs) and fine-tuning in specific settings. Although the pre-training stage has already equipped LLMs with powerful reasoning capabilities, LLMs still need to be fine-tuned to adapt to specific domains to achieve the best results. In this paper, we propose to select the most informative data for fine-tuning, thereby improving the efficiency of the fine-tuning process with comparative or even better accuracy on the open-domain QA task. We present MinPrompt, a minimal data augmentation framework for open-domain QA based on an approximate graph algorithm and unsupervised question generation. We transform the raw text into a graph structure to build connections between different factual sentences, then apply graph algorithms to identify the minimal set of sentences needed to cover the most information in the raw text. We then generate QA pairs based on the identified sentence subset and train the model on the selected sentences to obtain the final model. Empirical results on several benchmark datasets and theoretical analysis show that MinPrompt is able to achieve comparable or better results than baselines with a high degree of efficiency, bringing consistent improvements in F-1 scores.

MinPrompt: Graph-based Minimal Prompt Data Augmentation for Few-shot Question Answering

This work aims to build a text embedder that can capture characteristics of texts specified by user instructions clarifying the similarity criterion. While previous methods improve general task awareness by injecting the instruction information into encoding, they fail to be sensitive to clearer criteria like "evaluate similarity based on emotion". We instead propose a different viewpoint, which treats the instruction as a "question" about the input text and encodes the expected answers to obtain the representation accordingly. Intuitively, texts with the same (implicit) semantics would share similar answers following the instruction, thus leading to more similar representations. Specifically, we propose InBedder that instantiates this learning-to-answer idea by only fine-tuning language models via abstractive question answering tasks. Despite its simplicity, InBedder demonstrates significantly improved instruction-following capabilities according to our proposed instruction awareness tests and instruction robustness tests, when applied to language models with large language models (LLMs) (e.g., llama-2-7b) and smaller encoder-based LMs (e.g., roberta-large). Additionally, our qualitative analysis of clustering outcomes, achieved by applying diverse instructions to the same unlabeled corpus, demonstrates a high degree of interpretability in the clusters formed.

Answer is All You Need: Instruction-following Text Embedding via Answering the Question

Large language models have demonstrated impressive performance on commonsense tasks; however, these tasks are often posed as multiple-choice questions, allowing models to exploit systematic biases. Commonsense is also inherently probabilistic with multiple correct answers. The purpose of “boiling water” could be making tea, cooking but also could be killing germs. Existing tasks do not capture the probabilistic nature of common sense. To this end, we present commonsense frame completion (CFC), a new generative task that evaluates common sense via multiple open-ended generations. We also propose a method of probabilistic evaluation that strongly correlates with human judgments. Humans drastically outperform strong language model baselines on our dataset, indicating this approach is both a challenging and useful evaluation of machine common sense.

Every Answer Matters: Evaluating Commonsense with Probabilistic Measures

While the introduction of contrastive learning frameworks in sentence representation learning has significantly contributed to advancements in the field, it still remains unclear whether state-of-the-art sentence embeddings can capture the fine-grained semantics of sentences, particularly when conditioned on specific perspectives.
In this paper, we introduce Hyper-CL, an efficient methodology that integrates hypernetworks with contrastive learning to compute conditioned sentence representations.
In our proposed approach, the hypernetwork is responsible for transforming pre-computed condition embeddings into corresponding projection layers. This enables the same sentence embeddings to be projected differently according to various conditions.
Evaluation on two representative conditioning benchmarks, namely conditional semantic text similarity and knowledge graph completion, demonstrates that Hyper-CL is effective in flexibly conditioning sentence representations, showcasing its computational efficiency at the same time.
We also provide a comprehensive analysis of the inner workings of our approach, leading to a better interpretation of its mechanisms.

Hyper-CL: Conditioning Sentence Representations with Hypernetworks

Active learning (AL) aims to lower the demand of annotation by selecting informative unannotated samples for the model building. In this paper, we explore the importance of conscious experimental design in the language documentation and description setting, particularly the distribution of the unannotated sample pool. We focus on the task of morphological inflection using a Transformer model. We propose context motivated benchmarks: a baseline and skyline. The baseline describes the frequency weighted distribution encountered in natural speech. We simulate this using Wikipedia texts. The skyline defines the more common approach, uniform sampling from a large, balanced corpus (UniMorph, in our case), which often yields mixed results. We note the unrealistic nature of this unannotated pool. When these factors are considered, our results show a clear benefit to targeted sampling.

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ProtT3: Protein-to-Text Generation for Text-based Protein Understanding

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Improving Event Definition Following For Zero-Shot Event Detection

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