arXiv subjects

Ishan Gaur

Publications and source records attributed to Ishan Gaur.

3 recordsLinked to original sources

arXiv2025

ProteinGuide: On-the-fly property guidance for protein sequence generative models

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

cs.LG↗

arXiv2024

ColorSwap: A Color and Word Order Dataset for Multimodal Evaluation

This paper introduces the ColorSwap dataset, designed to assess and improve the proficiency of multimodal models in matching objects with their colors. The dataset is comprised of 2,000 unique image-caption pairs, grouped into 1,000 examples. Each example includes a caption-image pair, along with a ``color-swapped'' pair. We follow the Winoground schema: the two captions in an example have the same words, but the color words have been rearranged to modify different objects. The dataset was created through a novel blend of automated caption and image generation with humans in the loop. We evaluate image-text matching (ITM) and visual language models (VLMs) and find that even the latest ones are still not robust at this task. GPT-4V and LLaVA score 72% and 42% on our main VLM metric, although they may improve with more advanced prompting techniques. On the main ITM metric, contrastive models such as CLIP and SigLIP perform close to chance (at 12% and 30%, respectively), although the non-contrastive BLIP ITM model is stronger (87%). We also find that finetuning on fewer than 2,000 examples yields significant performance gains on this out-of-distribution word-order understanding task. The dataset is here: https://github.com/Top34051/colorswap and here: https://huggingface.co/datasets/stanfordnlp/colorswap.

cs.CV↗

arXiv2022

Taurus: A Data Plane Architecture for Per-Packet ML

Emerging applications -- cloud computing, the internet of things, and augmented/virtual reality -- demand responsive, secure, and scalable datacenter networks. These networks currently implement simple, per-packet, data-plane heuristics (e.g., ECMP and sketches) under a slow, millisecond-latency control plane that runs data-driven performance and security policies. However, to meet applications' service-level objectives (SLOs) in a modern data center, networks must bridge the gap between line-rate, per-packet execution and complex decision making. In this work, we present the design and implementation of Taurus, a data plane for line-rate inference. Taurus adds custom hardware based on a flexible, parallel-patterns (MapReduce) abstraction to programmable network devices, such as switches and NICs; this new hardware uses pipelined SIMD parallelism to enable per-packet MapReduce operations (e.g., inference). Our evaluation of a Taurus switch ASIC -- supporting several real-world models -- shows that Taurus operates orders of magnitude faster than a server-based control plane while increasing area by 3.8% and latency for line-rate ML models by up to 221 ns. Furthermore, our Taurus FPGA prototype achieves full model accuracy and detects two orders of magnitude more events than a state-of-the-art control-plane anomaly-detection system.

cs.NI↗