End-to-end learnable discrete-continuous models are compositional, tend togeneralize better,and are more interpretable.

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Data contamination poses a significant challenge to reliable LLM evaluation, where models may achieve high performance by memorizing training data rather than demonstrating genuine reasoning capabilities. We introduce RADAR (Recall vs. Reasoning Detection through Activation Representation), a novel framework that leverages mechanistic interpretability to detect contamination by distinguishing recall-based from reasoning-based model responses. RADAR extracts 37 features spanning surface-level confidence trajectories and deep mechanistic properties including attention specialization, circuit dynamics, and activation flow patterns. Using an ensemble of classifiers trained on these features, RADAR achieves 93\% accuracy on a diverse evaluation set, with perfect performance on clear cases and 76.7\% accuracy on challenging ambiguous examples. This work demonstrates the potential of mechanistic interpretability for advancing LLM evaluation beyond traditional surface-level metrics.

Diverse language model responses are crucial for creative generation, open-ended tasks, and self-improvement training. We show that common diversity metrics, and even reward models used for preference optimization, systematically bias models toward shorter outputs, limiting expressiveness. To address this, we introduce Diverse, not Short (Diverse-NS), a length-controlled data selection strategy that improves response diversity while maintaining length parity. By generating and filtering preference data that balances diversity, quality, and length, Diverse-NS enables effective training using only 3,000 preference pairs. Applied to LLaMA-3.1-8B and the Olmo-2 family, Diverse-NS substantially enhances lexical and semantic diversity. We show consistent improvement in diversity with minor reduction or gains in response quality on four creative generation tasks: Divergent Associations, Persona Generation, Alternate Uses, and Creative Writing. Surprisingly, experiments with the Olmo-2 model family (7B, and 13B) show that smaller models like Olmo-2-7B can serve as effective "diversity teachers" for larger models. By explicitly addressing length bias, our method efficiently pushes models toward more diverse and expressive outputs.

This appendix contains further details regarding the theory and experiments.

As Large Language Models (LLMs) gain expertise across diverse domains and modalities, scalable oversight becomes increasingly challenging, particularly when their capabilities may surpass human evaluators. Debate has emerged as a promising mechanism for enabling such oversight. In this work, we extend the debate paradigm to a multimodal setting, exploring its potential for weaker models to supervise and enhance the performance of stronger models. We focus on visual question answering (VQA), where two "sighted" expert vision-language models debate an answer, while a "blind" (text-only) judge adjudicates based solely on the quality of the arguments. In our framework, the experts defend only answers aligned with their beliefs, thereby obviating the need for explicit role-playing and concentrating the debate on instances of expert disagreement. Experiments on several multimodal tasks demonstrate that the debate framework consistently outperforms individual expert models. Moreover, judgments from weaker LLMs can help instill reasoning capabilities in vision-language models through finetuning.

Pre-trained foundation models can be adapted for specific tasks using Low-Rank Adaptation (LoRA). However, the fairness properties of these adapted classifiers remain underexplored. Existing fairness-aware fine-tuning methods rely on direct access to sensitive attributes or their predictors, but in practice, these sensitive attributes are often held under strict consumer privacy controls, and neither the attributes nor their predictors are available to model developers, hampering the development of fair models. To address this issue, we introduce a set of LoRA-based fine-tuning methods that can be trained in a distributed fashion, where model developers and fairness auditors collaborate without sharing sensitive attributes or predictors. In this paper, we evaluate three such methods - sensitive unlearning, adversarial training, and orthogonality loss - against a fairness-unaware baseline, using experiments on the CelebA and UTK-Face datasets with an ImageNet pre-trained ViT-Base model. We find that orthogonality loss consistently reduces bias while maintaining or improving utility, whereas adversarial training improves False Positive Rate Parity and Demographic Parity in some cases, and sensitive unlearning provides no clear benefit. In tasks where significant biases are present, distributed fairness-aware fine-tuning methods can effectively eliminate bias without compromising consumer privacy and, in most cases, improve model utility.