Nikhil Naik

Erik Nijkamp, Jeffrey Ruffolo, Eli N. Weinstein et al.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Bram Wallace, Meihua Dang, Rafael Rafailov et al.

Large language models (LLMs) are fine-tuned using human comparison data with Reinforcement Learning from Human Feedback (RLHF) methods to make them better aligned with users' preferences. In contrast to LLMs, human preference learning has not been widely explored in text-to-image diffusion models; the best existing approach is to fine-tune a pretrained model using carefully curated high quality images and captions to improve visual appeal and text alignment. We propose Diffusion-DPO, a method to align diffusion models to human preferences by directly optimizing on human comparison data. Diffusion-DPO is adapted from the recently developed Direct Preference Optimization (DPO), a simpler alternative to RLHF which directly optimizes a policy that best satisfies human preferences under a classification objective. We re-formulate DPO to account for a diffusion model notion of likelihood, utilizing the evidence lower bound to derive a differentiable objective. Using the Pick-a-Pic dataset of 851K crowdsourced pairwise preferences, we fine-tune the base model of the state-of-the-art Stable Diffusion XL (SDXL)-1.0 model with Diffusion-DPO. Our fine-tuned base model significantly outperforms both base SDXL-1.0 and the larger SDXL-1.0 model consisting of an additional refinement model in human evaluation, improving visual appeal and prompt alignment. We also develop a variant that uses AI feedback and has comparable performance to training on human preferences, opening the door for scaling of diffusion model alignment methods.

Aman Shrivastava, Ramprasaath R. Selvaraju, Nikhil Naik et al.

We propose CLIP-Lite, an information efficient method for visual representation learning by feature alignment with textual annotations. Compared to the previously proposed CLIP model, CLIP-Lite requires only one negative image-text sample pair for every positive image-text sample during the optimization of its contrastive learning objective. We accomplish this by taking advantage of an information efficient lower-bound to maximize the mutual information between the two input modalities. This allows CLIP-Lite to be trained with significantly reduced amounts of data and batch sizes while obtaining better performance than CLIP at the same scale. We evaluate CLIP-Lite by pretraining on the COCO-Captions dataset and testing transfer learning to other datasets. CLIP-Lite obtains a +14.0% mAP absolute gain in performance on Pascal VOC classification, and a +22.1% top-1 accuracy gain on ImageNet, while being comparable or superior to other, more complex, text-supervised models. CLIP-Lite is also superior to CLIP on image and text retrieval, zero-shot classification, and visual grounding. Finally, we show that CLIP-Lite can leverage language semantics to encourage bias-free visual representations that can be used in downstream tasks. Implementation: https://github.com/4m4n5/CLIP-Lite

Mingfei Gao, Zeyuan Chen, Nikhil Naik et al.

We propose a novel framework to conduct field extraction from forms with unlabeled data. To bootstrap the training process, we develop a rule-based method for mining noisy pseudo-labels from unlabeled forms. Using the supervisory signal from the pseudo-labels, we extract a discriminative token representation from a transformer-based model by modeling the interaction between text in the form. To prevent the model from overfitting to label noise, we introduce a refinement module based on a progressive pseudo-label ensemble. Experimental results demonstrate the effectiveness of our framework.

Alvin Chan, Ali Madani, Ben Krause et al.

Attribute extrapolation in sample generation is challenging for deep neural networks operating beyond the training distribution. We formulate a new task for extrapolation in sequence generation, focusing on natural language and proteins, and propose GENhance, a generative framework that enhances attributes through a learned latent space. Trained on movie reviews and a computed protein stability dataset, GENhance can generate strongly-positive text reviews and highly stable protein sequences without being exposed to similar data during training. We release our benchmark tasks and models to contribute to the study of generative modeling extrapolation and data-driven design in biology and chemistry.

Ali Madani, Bryan McCann, Nikhil Naik et al.

Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the exponentially growing set of proteins that lack costly, structural annotations. We train a 1.2B-parameter language model, ProGen, on ~280M protein sequences conditioned on taxonomic and keyword tags such as molecular function and cellular component. This provides ProGen with an unprecedented range of evolutionary sequence diversity and allows it to generate with fine-grained control as demonstrated by metrics based on primary sequence similarity, secondary structure accuracy, and conformational energy.