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  1. Free, publicly-accessible full text available September 10, 2024
  2. Large language models have substantially advanced nuance and context understanding in natural language processing (NLP), further fueling the growth of intelligent conversational interfaces and virtual assistants. However, their hefty computational and memory demands make them potentially expensive to deploy on cloudless edge platforms with strict latency and energy requirements. For example, an inference pass using the state-of-the-art BERT-base model must serially traverse through 12 computationally intensive transformer layers, each layer containing 12 parallel attention heads whose outputs concatenate to drive a large feed-forward network. To reduce computation latency, several algorithmic optimizations have been proposed, e.g., a recent algorithm dynamically matches linguistic complexity with model sizes via entropy-based early exit. Deploying such transformer models on edge platforms requires careful co-design and optimizations from algorithms to circuits, where energy consumption is a key design consideration. 
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  3. Abstract Motivation

    Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for.


    Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood.

    Availability and implementation

    Our code and examples are available at:

    Supplementary information

    Supplementary data are available at Bioinformatics online.

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