Generative protein language models are a natural way to design new proteins with desired functions.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families.

Position embedding is a core component of current Large Language Models (LLMs). Rotary position embedding (RoPE), a technique that encodes the position information with a rotation matrix, has been the de facto choice for position embedding in many LLMs, such as the Llama series. RoPE has been further utilized to extend long context capability, which is roughly based on adjusting the \textit{base} parameter of RoPE to mitigate out-of-distribution (OOD) problems in position embedding. However, in this paper, we find that LLMs may obtain a superficial long-context ability based on the OOD theory. We revisit the role of RoPE in LLMs and propose a novel property of long-term decay, we derive that the \textit{base of RoPE bounds context length}: there is an absolute lower bound for the base value to obtain certain context length capability. Our work reveals the relationship between context length and RoPE base both theoretically and empirically, which may shed light on future long context training.

Due to the recent remarkable advances in artificial intelligence, researchers have begun to consider challenging learning problems such as learning to generalize behavior from large offline datasets or learning online in non-Markovian environments. Meanwhile, recent advances in both of these areas have increasingly relied on conditioning policies on large context lengths. A natural question is if there is a limit to the performance benefits of increasing the context length if the computation needed is available. In this work, we establish a novel theoretical result that links the context length of a policy to the time needed to reliably evaluate its performance (i.e., its mixing time) in large scale partially observable reinforcement learning environments that exhibit latent sub-task structure. This analysis underscores a key tradeoff: when we extend the context length, our policy can more effectively model non-Markovian dependencies, but this comes at the cost of potentially slower policy evaluation and as a result slower downstream learning. Moreover, our empirical results highlight the relevance of this analysis when leveraging Transformer based neural networks. This perspective will become increasingly pertinent as the field scales towards larger and more realistic environments, opening up a number of potential future directions for improving the way we design learning agents.

While Transformers have shown remarkable success in natural language processing, their attention mechanism's large memory requirements have limited their ability to handle longer contexts. Prior approaches, such as recurrent memory or retrieval-based augmentation, have either compromised the random-access flexibility of attention (i.e., the capability to select any token in the entire context) or relied on separate mechanisms for relevant context retrieval, which may not be compatible with the model's attention. In this paper, we present a novel approach that allows access to the complete context while retaining random-access flexibility, closely resembling running attention on the entire context. Our method uses a landmark token to represent each block of the input and trains the attention to use it for selecting relevant blocks, enabling retrieval of blocks directly through the attention mechanism instead of by relying on a separate mechanism.

Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers or fixed k-mers to aggregate meaningful DNA units, losing single nucleotide resolution (i.e. DNA characters) where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity.

Large language models have an exceptional capability to incorporate new information in a contextual manner. However, the full potential of such an approach is often restrained due to a limitation in the effective context length. One solution to this issue is to endow an attention layer with access to an additional context, which comprises of (key, value) pairs. Yet, as the number of documents increases, the proportion of relevant keys to irrelevant ones decreases, leading the model to focus more on the irrelevant keys. We identify a significant challenge, dubbed the distraction issue, where keys linked to different semantic values might overlap, making them hard to distinguish.