Vijay Sadashivaiah

Vijay Sadashivaiah, Georgios Dasoulas, Judith Mueller et al.

Training stable biological foundation models requires rethinking attention mechanisms: we find that using sigmoid attention as a drop in replacement for softmax attention a) produces better learned representations: on six diverse single-cell datasets, sigmoid achieves 25% higher cell-type separation, better cell-type cohesion metrics, and lower validation loss, b) faster training, models with sigmoid attention train up to 10% faster than their softmax counterparts, and c) more stable training by eliminating inherent sources of instability in softmax attention. We establish that sigmoid attention has globally bounded derivatives ($\leq 0.25$) as opposed to softmax, and a diagonal Jacobian structure in contrast with softmax's dense coupling, which together help alleviate training instabilities. In stress tests on 160M-parameter bidirectional attention models trained without gradient clipping on 8K-token sequences, softmax diverges catastrophically, with gradients exploding by four orders of magnitude, while sigmoid remains stable. Finally, we implement and open-source TritonSigmoid, an efficient GPU kernel that achieves 515 TFLOPS on H100 GPUs, outperforming both FlashAttention-2 and FlashSigmoid, with native padding support, which is essential for biological sequences. Our results establish sigmoid attention as both theoretically grounded and empirically superior for biological foundation models. Code is available at https://github.com/MSDLLCpapers/triton-sigmoid

Keerthiram Murugesan, Vijay Sadashivaiah, Ronny Luss et al.

Knowledge transfer between heterogeneous source and target networks and tasks has received a lot of attention in recent times as large amounts of quality labeled data can be difficult to obtain in many applications. Existing approaches typically constrain the target deep neural network (DNN) feature representations to be close to the source DNNs feature representations, which can be limiting. We, in this paper, propose a novel adversarial multi-armed bandit approach that automatically learns to route source representations to appropriate target representations following which they are combined in meaningful ways to produce accurate target models. We see upwards of 5\% accuracy improvements compared with the state-of-the-art knowledge transfer methods on four benchmark (target) image datasets CUB200, Stanford Dogs, MIT67, and Stanford40 where the source dataset is ImageNet. We qualitatively analyze the goodness of our transfer scheme by showing individual examples of the important features focused on by our target network at different layers compared with the (closest) competitors. We also observe that our improvement over other methods is higher for smaller target datasets making it an effective tool for small data applications that may benefit from transfer learning.