The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible. Our codes can be found at https://github.com/HelloWorldLTY/Geneverse.

Instruction tuning is critical to improve LLMs but usually suffers from low-quality and redundant data. Data filtering for instruction tuning has proved important in improving both the efficiency and performance of the tuning process. But it also leads to extra cost and computation due to the involvement of LLMs in this process. To reduce the filtering cost, we study Superfiltering: Can we use a smaller and weaker model to select data for finetuning a larger and stronger model? Despite the performance gap between weak and strong language models, we find their highly consistent capability to perceive instruction difficulty and data selection results. This enables us to use a much smaller and more efficient model to filter the instruction data used to train a larger language model. Not only does it largely speed up the data filtering, but the filtered-data-finetuned LLM achieves even better performance on standard benchmarks. Extensive experiments validate the efficacy and efficiency of our approach.

Traditional supervised learning mostly works on individual tasks and requires training on a large set of task-specific examples. This paradigm seriously hinders the development of task generalization since preparing a task-specific example set is costly. To build a system that can quickly and easily generalize to new tasks, task instructions have been adopted as an emerging trend of supervision recently. These instructions give the model the definition of the task and allow the model to output the appropriate answer based on the instructions and inputs. However, task instructions are often expressed in different forms, which can be interpreted from two threads: first, some instructions are short sentences and are pretrained language model (PLM) oriented, such as prompts, while other instructions are paragraphs and are human-oriented, such as those in Amazon MTurk; second, different end-users very likely explain the same task with instructions of different textual expressions. A robust system for task generalization should be able to handle any new tasks regardless of the variability of instructions. However, the system robustness in dealing with instruction-driven task generalization is still unexplored. This work investigates the system robustness when the instructions of new tasks are (i) manipulated, (ii) paraphrased, or (iii) from different levels of conciseness. To our knowledge, this is the first work that systematically studies how robust a PLM is when it is supervised by instructions with different factors of variability.

Language models have been shown to perform remarkably well on a wide range of natural language processing tasks. In this paper, we propose LEAP, a novel system that uses language models to perform multi-step logical reasoning and incorporates explicit planning into the inference procedure. Explicit planning enables the system to make more informed reasoning decisions at each step by looking ahead into their future effects. Moreover, we propose a training strategy that safeguards the planning process from being led astray by spurious features. Our full system significantly outperforms other competing methods on multiple standard datasets. When using small T5 models as its core selection and deduction components, our system performs competitively compared to GPT-3 despite having only about 1B parameters (i.e., 175 times smaller than GPT-3). When using GPT-3.5, it significantly outperforms chain-of-thought prompting on the challenging PrOntoQA dataset. We have conducted extensive empirical studies to demonstrate that explicit planning plays a crucial role in the system’s performance.

Adapter-tuning is a paradigm that transfers a pretrained language model to downstream tasks by adding and tuning a small number of new parameters. Previously proposed adapter architectures are all feed-forward neural networks. In this paper, we investigate the effectiveness of using tiny-attention—i.e., attention with extremely small per-head dimensionality—as adapters. Our tiny-attention adapter learns to modify the hidden states at each position directly conditioned on the hidden states at all the other positions, which is missed by the previously proposed adapters. Moreover, we view its multiple attention heads as a mixture of experts and propose to average their weights during deployment, which further reduces its inference computation cost. On the GLUE benchmark, our tiny-attention adapter outperforms the other parameter-efficient transfer learning methods as well as full fine-tuning while only updating 0.05% of the parameters. On the FewGLUE benchmark, its performance is comparable to that of GPT-3 and PET.