This study explores the application of generative Large Language Models (LLMs) in DNA sequence analysis, highlighting their advantages over encoder-based models like DNABERT2 and Nucleotide Transformer. While encoder models excel in classification, they struggle to integrate external textual information. In contrast, generative LLMs can incorporate domain knowledge, such as BLASTn annotations, to improve classification accuracy even without fine-tuning. We evaluate this capability on antimicrobial resistance (AMR) gene classification, comparing generative LLMs with encoder-based baselines. Results show that LLMs significantly enhance classification when supplemented with textual information. Additionally, we demonstrate their potential in DNA sequence generation, further expanding their applicability. Our findings suggest that LLMs offer a novel paradigm for integrating biological sequences with external knowledge, bridging gaps in traditional classification methods.

As language models (LMs) become capable of handling a wide range of tasks, their evaluation is becoming as challenging as their development. Most generation benchmarks currently assess LMs using abstract evaluation criteria-like helpfulness and harmlessness-which often lack the flexibility and granularity of human assessment. Additionally, these benchmarks tend to focus disproportionately on specific capabilities such as instruction following, leading to coverage bias. To overcome these limitations, we introduce the BiGGen Bench, a principled generation benchmark designed to thoroughly evaluate nine distinct capabilities of LMs across 77 diverse tasks. A key feature of the BiGGen Bench is its use of instance-specific evaluation criteria, closely mirroring the nuanced discernment of human evaluation. We apply this benchmark to assess 100 frontier LMs using five evaluator LMs. Our code, data, and evaluation results are all publicly available at https://github.com/prometheus-eval/prometheus-eval.

Prompts used in recent large language model based applications are often fixed and lengthy, leading to significant computational overhead. To address this challenge, we propose Generative Prompt Internalization (GenPI), a lightweight method that employs a joint training approach. GenPI not only replicates the behavior of models with prompt inputs but also generates the content of the prompt along with reasons for why the model’s behavior should change accordingly. We demonstrate that our approach effectively internalizes complex prompts across various agent-based application scenarios. For effective training without interactions with the dedicated environments, we introduce a data synthesis technique that autonomously collects conversational datasets by swapping the roles of the agent and environment. This method is especially useful in scenarios where only a predefined prompt is available without a corresponding training dataset. By internalizing complex prompts, Generative Prompt Internalization enables high performance and efficient inference without the need for explicit prompts.

We introduce a new problem KTRL+F, a knowledge-augmented in-document search that necessitates real-time identification of all semantic targets within a document with the awareness of external sources through a single natural query. KTRL+F addresses following unique challenges for in-document search: 1) utilizing knowledge outside the document for extended use of additional information about targets, and 2) balancing between real-time applicability with the performance.We analyze various baselines in KTRL+F and find limitations of existing models, such as hallucinations, high latency, or difficulties in leveraging external knowledge. Therefore, we propose a Knowledge-Augmented Phrase Retrieval model that shows a promising balance between speed and performance by simply augmenting external knowledge in phrase embedding. We also conduct a user study to verify whether solving KTRL+F can enhance search experience for users. It demonstrates that even with our simple model, users can reduce the time for searching with less queries and reduced extra visits to other sources for collecting evidence. We encourage the research community to work on KTRL+F to enhance more efficient in-document information access.

The Situated Interactive Multi-Modal Conversations (SIMMC) 2.0 aims to create virtual shopping assistants that can accept complex multi-modal inputs, i.e. visual appearances of objects and user utterances. It consists of four subtasks, multi-modal disambiguation (MM-Disamb), multi-modal coreference resolution (MM-Coref), multi-modal dialog state tracking (MM-DST), and response retrieval and generation. While many task-oriented dialog systems usually tackle each subtask separately, we propose a jointly learned multi-modal encoder-decoder that incorporates visual inputs and performs all four subtasks at once for efficiency. This approach won the MM-Coref and response retrieval subtasks and nominated runner-up for the remaining subtasks using a single unified model at the 10th Dialog Systems Technology Challenge (DSTC10), setting a high bar for the novel task of multi-modal task-oriented dialog systems.