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scMEDAL for the interpretable analysis of single-cell transcriptomics data with batch effect visualization using a deep mixed effects autoencoder

arXiv:2411.06635v4 Announce Type: replace Abstract: Single-cell RNA sequencing enables high-resolution analysis of cellular heterogeneity, yet disentangling biological signal from batch effects remains a major challenge. Existing batch-correction algorithms suppress or discard batch-related variation rather than modeling it. We propose scMEDAL,…

Multimodal Cancer Modeling in the Age of Foundation Model Embeddings

arXiv:2505.07683v3 Announce Type: replace Abstract: The Cancer Genome Atlas (TCGA) has enabled novel discoveries and served as a large-scale reference dataset in cancer through its harmonized genomics, clinical, and imaging data. Numerous prior studies have developed bespoke deep learning models…

How do Transformers Learn Implicit Reasoning?

arXiv:2505.23653v2 Announce Type: replace Abstract: Recent work suggests that large language models (LLMs) can perform multi-hop reasoning implicitly — producing correct answers without explicitly verbalizing intermediate steps — but the underlying mechanisms remain poorly understood. In this paper, we study…

Communication Efficient LLM Pre-training with SparseLoCo

arXiv:2508.15706v2 Announce Type: replace Abstract: Communication-efficient distributed training algorithms have received considerable interest recently due to their benefits for training Large Language Models (LLMs) in bandwidth-constrained settings, such as across datacenters and over the internet. Despite reducing communication frequency, these…

PETRA: Pretrained Evolutionary Transformer for SARS-CoV-2 Mutation Prediction

arXiv:2511.03976v1 Announce Type: new Abstract: Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine development. While large-scale generative pre-trained transformers…

HyperAdapt: Simple High-Rank Adaptation

arXiv:2509.18629v2 Announce Type: replace Abstract: Foundation models excel across diverse tasks, but adapting them to specialized applications often requires fine-tuning, an approach that is memory and compute-intensive. Parameter-efficient fine-tuning (PEFT) methods mitigate this by updating only a small subset of…