Fast and scalable Wasserstein-1 neural optimal transport solver for single-cell perturbation prediction

Predicting single-cell perturbation responses requires mapping between two unpaired single-cell data distributions. Optimal transport (OT) theory provides a principled framework for constructing such mappings by minimizing transport cost. Recently, Wasserstein-2 ($W_2$) neural optimal transport solvers (\textit{e.g.}, CellOT) have been employed for this prediction task. However, $W_2$ OT relies on the general Kantorovich dual formulation, which involves optimizing over two conjugate functions, leading to a complex min-max optimization problem that converges slowly. To address these challenges, we propose a novel solver based on the Wasserstein-1 ($W_1$) dual formulation. Unlike $W_2$, the $W_1$ dual simplifies the optimization to a maximization problem over a single 1-Lipschitz function, thus eliminating the need for time-consuming min-max optimization. While solving the $W_1$ dual only reveals the transport direction and does not directly provide a unique optimal transport map, we incorporate an additional step using adversarial training to determine an appropriate transport step size, effectively recovering the transport map. Our experiments demonstrate that the proposed $W_1$ neural optimal transport solver can mimic the $W_2$ OT solvers in finding a unique and ``monotonic" map on 2D datasets. Moreover, the $W_1$ OT solver achieves performance on par with or surpasses $W_2$ OT solvers on real single-cell perturbation datasets. Furthermore, we show that $W_1$ OT solver achieves $25 \sim 45\times$ speedup, scales better on high dimensional transportation task, and can be directly applied on single-cell RNA-seq dataset with highly variable genes. Our implementation and experiments are open-sourced at \url{https://github.com/poseidonchan/w1ot}.

A Watermark for Order-Agnostic Language Models

Statistical watermarking techniques are well-established for sequentially decoded language models (LMs). However, these techniques cannot be directly applied to order-agnostic LMs, as the tokens in order-agnostic LMs are not generated sequentially. In this work, we introduce Pattern-mark, a pattern-based watermarking framework specifically designed for order-agnostic LMs. We develop a Markov-chain-based watermark generator that produces watermark key sequences with high-frequency key patterns. Correspondingly, we propose a statistical pattern-based detection algorithm that recovers the key sequence during detection and conducts statistical tests based on the count of high-frequency patterns. Our extensive evaluations on order-agnostic LMs, such as ProteinMPNN and CMLM, demonstrate Pattern-mark's enhanced detection efficiency, generation quality, and robustness, positioning it as a superior watermarking technique for order-agnostic LMs.

Distortion-free Watermarks are not Truly Distortion-free under Watermark Key Collisions

Language model (LM) watermarking techniques inject a statistical signal into LM-generated content by substituting the random sampling process with pseudo-random sampling, using watermark keys as the random seed. Among these statistical watermarking approaches, distortion-free watermarks are particularly crucial because they embed watermarks into LM-generated content without compromising generation quality. However, one notable limitation of pseudo-random sampling compared to true-random sampling is that, under the same watermark keys (i.e., key collision), the results of pseudo-random sampling exhibit correlations. This limitation could potentially undermine the distortion-free property. Our studies reveal that key collisions are inevitable due to the limited availability of watermark keys, and existing distortion-free watermarks exhibit a significant distribution bias toward the original LM distribution in the presence of key collisions. Moreover, achieving a perfect distortion-free watermark is impossible as no statistical signal can be embedded under key collisions. To reduce the distribution bias caused by key collisions, we introduce a new family of distortion-free watermarks--beta-watermark. Experimental results support that the beta-watermark can effectively reduce the distribution bias under key collisions.

GPT-4 Vision on Medical Image Classification -- A Case Study on COVID-19 Dataset

This technical report delves into the application of GPT-4 Vision (GPT-4V) in the nuanced realm of COVID-19 image classification, leveraging the transformative potential of in-context learning to enhance diagnostic processes.