Aayush Karan

Hi, I'm Aayush! I'm currently a PhD student in Computer Science at Harvard, advised by Prof. Sitan Chen and Prof. Yilun Du.

Broadly, I am interested in developing algorithmic techniques that enhance the capabilities of modern generative models. My research seeks principled algorithms that are empirically performant, often leveraging theoretical arguments in well-designed toy settings, to advance fundamentally intelligent behaviors such as reasoning, reward-optimization, and self-correction/failure prediction.

I graduated from Harvard in 2023 with an AB/SM in Physics, Mathematics, and Computer Science. As an undergrad, I explored research in a variety of fields across pure mathematics, computational biology, and theoretical physics.

Email  /  Google Scholar  /  Twitter

profile photo

Recent News

Oct 2025 RNA folding paper now out in Nature Methods!
July 2025 Presented Blink of an eye at ICML 2025 (Oral)!
June 2025 Joined the Kempner Institute at Harvard as a Grad Fellow!
June 2025 Presented A theory of loss prediction at FORC 2025!
May 2025 Started a Student Researcher position at Google DeepMind!
Dec 2024 Presented Unrolled denoising nets at NeurIPS 2024!
May 2024 Started a Research Intern position at Apple!
Research
Reasoning with Sampling:  Your Base Model is Smarter Than You Think
Aayush Karan, Yilun Du
arXiv preprint, 2025
blog post /  paper /  code /  tweet

We propose a sampling algorithm for base models that gives single-shot reasoning boosts on par with RL-posttraining, without compromising generation diversity and multi-shot (pass@k) performance. Crucially, our method is training-free, dataset-free, and verifier-free.


All-at-once RNA folding with 3D motif prediction framed by evolutionary information
Aayush Karan, Elena Rivas
Nature Methods, 2025
paper /  code /  tweet

The field of RNA structure prediction has long lacked a reliable, flexible, and self-contained method to detect the presence of key 3D building blocks in folded RNAs. We provide an algorithm that does exactly this, predicting a near exhaustive set of 3D configurations (everything), at any location (everywhere), fully end-to-end over multiple structural hierarchies (all-at-once).


ReGuidance:  A Simple Diffusion Wrapper for Boosting Sample Quality on Hard Inverse Problems
Aayush Karan, Kulin Shah, Sitan Chen
arXiv preprint, 2025
paper /  tweet

We discover that strong latent initializations in noise space offer a new axis for desiging inference-time algorithms that steer diffusion models towards reward functions. We propose a simple algorithm (ReGuidance) leveraging this insight and both empirically and theoretically demonstrate its superiority over prior techniques.


Blink of an eye:  a simple theory for feature localization in generative models
Marvin Li, Aayush Karan, Sitan Chen
ICML, 2025 (Oral, top 1% of submissions)
paper /  tweet

We present a unifying theory of LLMs and diffusion models explaining the sudden emergence of high-level semantic features during generation. We introduce the notion of critical windows for LLMs and empirically correlate them to reasoning failures.


When does a predictor know its own loss?
Aravind Gollakota, Parikshit Gopalan, Aayush Karan, Charlotte Peale, Udi Wieder
FORC, 2025
paper /  tweet

We present a theory of loss prediction in machine learning and establish an equivalence with algorithmic fairness. In particular, we prove that for binary classifiers, we can learn a nontrivial loss predictor only when the base model is not multicallibrated.


Unrolled denoising networks provably learn optimal Bayesian inference
Aayush Karan, Kulin Shah, Sitan Chen Yonina Eldar
NeurIPS, 2024
paper /  tweet

We propose a theory-inspired neural network architecture for solving inverse problems that provably learns optimal Bayesian inference. Our network mirrors diffusion models by learning noisy data priors and runs a Bayes-optimal algorithm on top. For the first time in the literature, we prove that the score-matching objective is learnable in one dimension.


Tridiagonal pairs of q-Serre type and their linear perturbations
Aayush Karan
Journal of Algebra, 2022
paper

We examine a pair of linear maps with a particular property (tridiagonal pairs) inspired from statistical physics, and we demonstrate that linear perturbations preserve this property under a very simple polynomial condition.


Generating set for nonzero determinant links under skein relation
Aayush Karan
Topology and its Applications, 2019
paper

We resolve an open problem proposed by David Mullins in 1993 regarding the recursive computability of crucial topological quantities known as nonzero determinant link invariants.