Large Language Models (LLMs) face fundamental challenges in long-context reasoning: many documents exceed their finite context windows, while performance on texts that do fit degrades with sequence length, necessitating their augmentation with external memory frameworks. Current solutions, which have evolved from retrieval using semantic embeddings to more sophisticated structured knowledge graphs representations for improved sense-making and associativity, are tailored for fact-based retrieval and fail to build the space-time-anchored narrative representations required for tracking entities through episodic events. To bridge this gap, we propose the Generative Semantic Workspace (GSW), a neuro-inspired generative memory framework that builds structured, interpretable representations of evolving situations, enabling LLMs to reason over evolving roles, actions, and spatiotemporal contexts. Our framework comprises an Operator, which maps incoming observations to intermediate semantic structures, and a Reconciler, which integrates these into a persistent workspace that enforces temporal, spatial, and logical coherence. On the Episodic Memory Benchmark (EpBench) comprising corpora ranging from 100k to 1M tokens in length, GSW outperforms existing RAG based baselines by up to 20%. Furthermore, GSW is highly efficient, reducing query-time context tokens by 51% compared to the next most token-efficient baseline, reducing inference time costs considerably. More broadly, GSW offers a concrete blueprint for endowing LLMs with human-like episodic memory, paving the way for more capable agents that can reason over long horizons.

MOTIVATION: DNA sequence alignment, an important genomic task, involves assigning short DNA reads to the most probable locations on an extensive reference genome. Conventional methods tackle this challenge in two steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have encoded DNA sequences into vectors using Transformers and have shown promising results in tasks involving classification of short DNA sequences. Performance at sequence classification tasks does not, however, guarantee sequence alignment, where it is necessary to conduct a genome-wide search to align every read successfully, a significantly longer-range task by comparison. RESULTS: We bridge this gap by developing a "Embed-Search-Align" (ESA) framework, where a novel Reference-Free DNA Embedding (RDE) Transformer model generates vector embeddings of reads and fragments of the reference in a shared vector space; read-fragment distance metric is then used as a surrogate for sequence similarity. ESA introduces: (i) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (ii) a DNA vector store to enable search across fragments on a global scale. RDE is 99% accurate when aligning 250-length reads onto a human reference genome of 3 gigabases (single-haploid), rivaling conventional algorithmic sequence alignment methods such as Bowtie and BWA-Mem. RDE far exceeds the performance of six recent DNA-Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species. AVAILABILITY AND IMPLEMENTATION: Please see https://anonymous.4open.science/r/dna2vec-7E4E/readme.md.

News reports about emerging issues often include several conflicting story lines.Individual stories can be conceptualized as samples from an underlying mixture of competing narratives.The automated identification of these distinct narratives from unstructured text is a fundamental yet difficult task in Computational Linguistics since narratives are often intertwined and only implicitly conveyed in text.In this paper, we consider a more feasible proxy task: Identify the distinct sets of aligned story actors responsible for sustaining the issue-specific narratives.Discovering aligned actors, and the groups these alignments create, brings us closer to estimating the narrative that each group represents.With the help of Large Language Models (LLM), we address this task by: (i) Introducing a corpus of text segments rich in narrative content associated with six different current issues; (ii) Introducing a novel two-step graph-based framework that (a) identifies alignments between actors (INCANT) and (b) extracts aligned actor groups using the network structure (TAMPA).Amazon Mechanical Turk evaluations demonstrate the effectiveness of our framework.Across domains, alignment relationships from INCANT are accurate (macro F 1 ≥ 0.75) and actor groups from TAMPA are preferred over 2 non-trivial baseline models (ACC ≥ 0.75).

Pavan Holur, Tianyi Wang, Shadi Shahsavari, Timothy Tangherlini, Vwani Roychowdhury. Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2022.