Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Generative Retrieval introduces a new approach to Information Retrieval by reframing it as a constrained generation task, leveraging recent advancements in Autoregressive (AR) language models. However, AR-based Generative Retrieval methods suffer from high inference latency and cost compared to traditional dense retrieval techniques, limiting their practical applicability. This paper investigates fully Non-autoregressive (NAR) language models as a more efficient alternative for generative retrieval. While standard NAR models alleviate latency and cost concerns, they exhibit a significant drop in retrieval performance (compared to AR models) due to their inability to capture dependencies between target tokens. To address this, we question the conventional choice of limiting the target token space to solely words or sub-words. We propose PIXAR, a novel approach that expands the target vocabulary of NAR models to include multi-word entities and common phrases (up to 5 million tokens), thereby reducing token dependencies. PIXAR employs inference optimization strategies to maintain low inference latency despite the significantly larger vocabulary. Our results demonstrate that PIXAR achieves a relative improvement of 31.0% in MRR@10 on MS MARCO and 23.2% in Hits@5 on Natural Questions compared to standard NAR models with similar latency and cost.

Given unstructured text, Large Language Models (LLMs) are adept at answering simple (single-hop) questions. However, as the complexity of the questions increase, the performance of LLMs degrade. We believe this is due to the overhead associated with understanding the complex question followed by filtering and aggregating unstructured information in the raw text. Recent methods try to reduce this burden by integrating structured knowledge triples into the raw text, aiming to provide a structured overview that simplifies information processing. However, this simplistic approach is query-agnostic and the extracted facts are ambiguous as they lack context. To address these drawbacks and to enable LLMs to answer complex (multi-hop) questions with ease, we propose to use a knowledge graph (KG) that is context-aware and is distilled to contain query-relevant information. The use of our compressed distilled KG as input to the LLM results in our method utilizing up to $67\%$ fewer tokens to represent the query relevant information present in the supporting documents, compared to the state-of-the-art (SoTA) method. Our experiments show consistent improvements over the SoTA across several metrics (EM, F1, BERTScore, and Human Eval) on two popular benchmark datasets (HotpotQA and MuSiQue).

Virtual environments play a key role in benchmarking advances in complex planning and decision-making tasks but are expensive and complicated to build by hand. Can current language models themselves serve as world simulators, correctly predicting how actions change different world states, thus bypassing the need for extensive manual coding? Our goal is to answer this question in the context of text-based simulators. Our approach is to build and use a new benchmark, called ByteSized32-State-Prediction, containing a dataset of text game state transitions and accompanying game tasks. We use this to directly quantify, for the first time, how well LLMs can serve as text-based world simulators. We test GPT-4 on this dataset and find that, despite its impressive performance, it is still an unreliable world simulator without further innovations. This work thus contributes both new insights into current LLM's capabilities and weaknesses, as well as a novel benchmark to track future progress as new models appear.

We train a suite of multimodal foundation models (MMFM) using the popular LLaVA framework with the recently released Gemma family of large language models (LLMs). Of particular interest is the 2B parameter Gemma model, which provides opportunities to construct capable small-scale MMFMs. In line with findings from other papers in this space, we test the effect of ablating three design features: pretraining the connector, utilizing a more powerful image backbone, and increasing the size of the language backbone. The resulting models, which we call LLaVA-Gemma, exhibit moderate performance on an array of evaluations, but fail to improve past the current comparably sized SOTA models. Closer analysis of performance shows mixed effects; skipping pretraining tends to reduce performance, larger vision models sometimes improve performance, and increasing language model size has inconsistent effects. We publicly release training recipes, code and weights for our models for the LLaVA-Gemma models.

Recent advances have been improving the context windows of Large Language Models (LLMs). To quantify the real long-context capabilities of LLMs, evaluators such as the popular Needle in a Haystack have been developed to test LLMs over a large chunk of raw texts. While effective, current evaluations overlook the insight of how LLMs work with long-context code, i.e., repositories. To this end, we initiate the RepoQA benchmark to evaluate LLMs on long-context code understanding. Traditional needle testers ask LLMs to directly retrieve the answer from the context without necessary deep understanding. In RepoQA, we built our initial task, namely Searching Needle Function (SNF), which exercises LLMs to search functions given their natural-language description, i.e., LLMs cannot find the desired function if they cannot understand the description and code. RepoQA is multilingual and comprehensive: it includes 500 code search tasks gathered from 50 popular repositories across 5 modern programming languages. By evaluating 26 general and code-specific LLMs on RepoQA, we show (i) there is still a small gap between the best open and proprietary models; (ii) different models are good at different languages; and (iii) models may understand code better without comments.

With the proliferation of LLM-integrated applications such as GPT-s, millions are deployed, offering valuable services through proprietary instruction prompts. These systems, however, are prone to prompt extraction attacks through meticulously designed queries. To help mitigate this problem, we introduce the Raccoon benchmark which comprehensively evaluates a model's susceptibility to prompt extraction attacks. Our novel evaluation method assesses models under both defenseless and defended scenarios, employing a dual approach to evaluate the effectiveness of existing defenses and the resilience of the models. The benchmark encompasses 14 categories of prompt extraction attacks, with additional compounded attacks that closely mimic the strategies of potential attackers, alongside a diverse collection of defense templates. This array is, to our knowledge, the most extensive compilation of prompt theft attacks and defense mechanisms to date. Our findings highlight universal susceptibility to prompt theft in the absence of defenses, with OpenAI models demonstrating notable resilience when protected. This paper aims to establish a more systematic benchmark for assessing LLM robustness against prompt extraction attacks, offering insights into their causes and potential countermeasures. Resources of Raccoon are publicly available at https://github.com/M0gician/RaccoonBench.

Large multimodal language models have shown remarkable proficiency in understanding and editing images. However, a majority of these visually-tuned models struggle to comprehend the textual content embedded in images, primarily due to the limitation of training data. In this work, we introduce TRINS: a Text-Rich image INStruction dataset, with the objective of enhancing the reading ability of the multimodal large language model. TRINS is built upon LAION using hybrid data annotation strategies that include machine-assisted and human-assisted annotation processes. It contains 39,153 text-rich images, captions, and 102,437 questions. Specifically, we show that the number of words per annotation in TRINS is significantly longer than that of related datasets, providing new challenges. Furthermore, we introduce a simple and effective architecture, called a Language-vision Reading Assistant (LaRA), which is good at understanding textual content within images. LaRA outperforms existing state-of-the-art multimodal large language models on the TRINS dataset, as well as other classical benchmarks. Lastly, we conducted a comprehensive evaluation with TRINS on various text-rich image understanding and generation tasks, demonstrating its effectiveness.

The performance of deep learning-based natural language processing systems is based on large amounts of labeled training data which, in the clinical domain, are not easily available or affordable. Weak supervision and in-context learning offer partial solutions to this issue, particularly using large language models (LLMs), but their performance still trails traditional supervised methods with moderate amounts of gold-standard data. In particular, inferencing with LLMs is computationally heavy. We propose an approach leveraging fine-tuning LLMs and weak supervision with virtually no domain knowledge that still achieves consistently dominant performance. Using a prompt-based approach, the LLM is used to generate weakly-labeled data for training a downstream BERT model. The weakly supervised model is then further fine-tuned on small amounts of gold standard data. We evaluate this approach using Llama2 on three different n2c2 datasets. With no more than 10 gold standard notes, our final BERT models weakly supervised by fine-tuned Llama2-13B consistently outperformed out-of-the-box PubMedBERT by 4.7% to 47.9% in F1 scores. With only 50 gold standard notes, our models achieved close performance to fully fine-tuned systems.

As Large Language Models (LLMs) broaden their capabilities to manage thousands of API calls, they are confronted with complex data operations across vast datasets with significant overhead to the underlying system. In this work, we introduce LLM-dCache to optimize data accesses by treating cache operations as callable API functions exposed to the tool-augmented agent. We grant LLMs the autonomy to manage cache decisions via prompting, seamlessly integrating with existing function-calling mechanisms. Tested on an industry-scale massively parallel platform that spans hundreds of GPT endpoints and terabytes of imagery, our method improves Copilot times by an average of 1.24x across various LLMs and prompting techniques.