new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Jan 7

Evaluating Protein Transfer Learning with TAPE

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

  • 8 authors
·
Jun 19, 2019

Tapered Off-Policy REINFORCE: Stable and efficient reinforcement learning for LLMs

We propose a new algorithm for fine-tuning large language models using reinforcement learning. Tapered Off-Policy REINFORCE (TOPR) uses an asymmetric, tapered variant of importance sampling to speed up learning while maintaining stable learning dynamics, even without the use of KL regularization. TOPR can be applied in a fully offline fashion, allows the handling of positive and negative examples in a unified framework, and benefits from the implementational simplicity that is typical of Monte Carlo algorithms. We demonstrate the effectiveness of our approach with a series of experiments on the GSM8K and MATH reasoning benchmarks, finding performance gains for training both a model for solution generation and as a generative verifier. We show that properly leveraging positive and negative examples alike in the off-policy regime simultaneously increases test-time accuracy and training data efficiency, all the while avoiding the ``wasted inference'' that comes with discarding negative examples. We find that this advantage persists over multiple iterations of training and can be amplified by dataset curation techniques, enabling us to match 70B-parameter model performance with 8B language models. As a corollary to this work, we find that REINFORCE's baseline parameter plays an important and unexpected role in defining dataset composition in the presence of negative examples, and is consequently critical in driving off-policy performance.

  • 10 authors
·
Mar 18, 2025

Unveiling the Tapestry of Consistency in Large Vision-Language Models

Large vision-language models (LVLMs) have recently achieved rapid progress, exhibiting great perception and reasoning abilities concerning visual information. However, when faced with prompts in different sizes of solution spaces, LVLMs fail to always give consistent answers regarding the same knowledge point. This inconsistency of answers between different solution spaces is prevalent in LVLMs and erodes trust. To this end, we provide a multi-modal benchmark ConBench, to intuitively analyze how LVLMs perform when the solution space of a prompt revolves around a knowledge point. Based on the ConBench tool, we are the first to reveal the tapestry and get the following findings: (1) In the discriminate realm, the larger the solution space of the prompt, the lower the accuracy of the answers. (2) Establish the relationship between the discriminative and generative realms: the accuracy of the discriminative question type exhibits a strong positive correlation with its Consistency with the caption. (3) Compared to open-source models, closed-source models exhibit a pronounced bias advantage in terms of Consistency. Eventually, we ameliorate the consistency of LVLMs by trigger-based diagnostic refinement, indirectly improving the performance of their caption. We hope this paper will accelerate the research community in better evaluating their models and encourage future advancements in the consistency domain. The project is available at https://github.com/foundation-multimodal-models/ConBench.

  • 10 authors
·
May 23, 2024