Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems. We evaluated six frontier LLMs on 137 small systems, and released a total of 350 systems at https://huggingface.co/datasets/h4duan/scigym-sbml. Our evaluation shows that while more capable models demonstrated superior performance, all models' performance declined significantly as system complexity increased, suggesting substantial room for improvement in the scientific capabilities of LLM agents.

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at [https://github.com/bowang-lab/BioReason](https://github.com/bowang-lab/BioReason).

Large language models (LLMs) are excellent in-context learners. However, the sensitivity of data contained in prompts raises privacy concerns. Our work first shows that these concerns are valid: we instantiate a simple but highly effective membership inference attack against the data used to prompt LLMs. To address this vulnerability, one could forego prompting and resort to fine-tuning LLMs with known algorithms for private gradient descent. However, this comes at the expense of the practicality and efficiency offered by prompting. Therefore, we propose to privately learn to prompt. We first show that soft prompts can be obtained privately through gradient descent on downstream data. However, this is not the case for discrete prompts. Thus, we orchestrate a noisy vote among an ensemble of LLMs presented with different prompts, i.e., a flock of stochastic parrots. The vote privately transfers the flock's knowledge into a single public prompt. We show that LLMs prompted with our private algorithms closely match the non-private baselines. For example, using GPT3 as the base model, we achieve a downstream accuracy of 92.7% on the sst2 dataset with $(\varepsilon=0.147, \delta=10^{-6})$-differential privacy vs. 95.2% for the non-private baseline. Through our experiments, we also show that our prompt-based approach is easily deployed with existing commercial~APIs.

Supervised learning can improve the design of state-of-the-art solvers for combinatorial problems, but labelling large numbers of combinatorial instances is often impractical due to exponential worst-case complexity. Inspired by the recent success of contrastive pre-training for images, we conduct a scientific study of the effect of augmentation design on contrastive pre-training for the Boolean satisfiability problem. While typical graph contrastive pre-training uses label-agnostic augmentations, our key insight is that many combinatorial problems have well-studied invariances, which allow for the design of label-preserving augmentations. We find that label-preserving augmentations are critical for the success of contrastive pre-training. We show that our representations are able to achieve comparable test accuracy to fully-supervised learning while using only 1% of the labels. We also demonstrate that our representations are more transferable to larger problems from unseen domains. Our code is available at https://github.com/h4duan/contrastive-sat.

Self-supervised models are increasingly prevalent in machine learning (ML) since they reduce the need for expensively labeled data. Because of their versatility in downstream applications, they are increasingly used as a service exposed via public APIs. At the same time, these encoder models are particularly vulnerable to model stealing attacks due to the high dimensionality of vector representations they output. Yet, encoders remain undefended: existing mitigation strategies for stealing attacks focus on supervised learning. We introduce a new dataset inference defense, which uses the private training set of the victim encoder model to attribute its ownership in the event of stealing. The intuition is that the log-likelihood of an encoder's output representations is higher on the victim's training data than on test data if it is stolen from the victim, but not if it is independently trained. We compute this log-likelihood using density estimation models. As part of our evaluation, we also propose measuring the fidelity of stolen encoders and quantifying the effectiveness of the theft detection without involving downstream tasks; instead, we leverage mutual information and distance measurements. Our extensive empirical results in the vision domain demonstrate that dataset inference is a promising direction for defending self-supervised models against model stealing.

In this paper, we present a Bayesian Moment Matching (BMM) based method aimed at solving the initialization problem in Boolean SAT solvers. The initialization problem can be stated as follows: given a SAT formula $\phi$, compute an initial order over the variables of $\phi$ and values/polarity for these variables such that the runtime of SAT solvers on input $\phi$ is minimized. At the start of a solver run, our BMM-based methods compute a posterior probability distribution for an assignment to the variables of the input formula after analyzing its clauses, which will then be used by the solver to initialize its search. We perform extensive experiments to evaluate the efficacy of our BMM-based heuristic against 4 other initialization methods (random, survey propagation, Jeroslow-Wang, and default) in state-of-the-art solvers, MapleCOMSPS and MapleLCMDistChronotBT over the SAT competition 2018 application benchmark, as well as the best-known solvers in the cryptographic category, namely, CryptoMiniSAT, Glucose, and MapleSAT. On the cryptographic benchmark, BMM-based solvers out-perform all other initialization methods. Further, the BMM-based MapleCOMSPS significantly out-perform the same solver using all other initialization methods by 12 additional instances solved and better average runtime, over the SAT 2018 competition benchmark.