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Latent Collaboration in Multi-Agent Systems

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Jiaru Zou Princeton University University of Illinois Urbana-Champaign Co-Leadership Core Contributors, Xiyuan Yang University of Illinois Urbana-Champaign Co-Leadership Core Contributors, Ruizhong Qiu University of Illinois Urbana-Champaign Core Contributors, Gaotang Li University of Illinois Urbana-Champaign Core Contributors, Katherine Tieu University of Illinois Urbana-Champaign Core Contributors, Pan Lu Stanford University Core Contributors, Ke Shen Hanghang Tong University of Illinois Urbana-Champaign, Yejin Choi Stanford University, Jingrui He University of Illinois Urbana-Champaign, James Zou Stanford University, Mengdi Wang Princeton University, Ling Yang Princeton University
December 3, 2025
A new multi-agent system framework LatentMAS enables large language models (LLMs) to collaborate entirely in continuous latent space rather than text, achieving up to 14.6% higher accuracy, 4x faster inference, and ~70-84% reduction in token usage across diverse benchmarks including math, science, commonsense reasoning, and code generation; compared to conventional text-based multi-agent collaboration methods, LatentMAS provides lossless, more expressive, and computationally efficient cross-agent communication via shared latent working memory (KV caches) without additional training, offering a promising new paradigm for agentic AI systems relevant to portfolio companies like Anodot and Sequence that rely on advanced AI reasoning, or Ply and Simply that could benefit from more efficient multi-agent LLM collaboration frameworks.

An updated evolutionary classification of CRISPR–Cas systems including rare variants | Nature Microbiology

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Kira S. Makarova, Sergey A. Shmakov, Yuri I. Wolf, Pascal Mutz, Han Altae-Tran, Chase L. Beisel, Stan J. J. Brouns, Emmanuelle Charpentier, David Cheng, Jennifer Doudna, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Patrick Pausch, Rafael Pinilla-Redondo, Shiraz A. Shah, Virginijus Siksnys, Michael P. Terns, Jesse Tordoff, Česlovas Venclovas, Malcolm F. White, Alexander F. Yakunin, Feng Zhang, Eugene V. Koonin
November 17, 2025
A major update in the evolutionary classification of CRISPR–Cas systems expands the framework to 2 classes, 7 types, and 46 subtypes (from 6 types and 33 subtypes five years ago), incorporating newly identified rare variants—particularly multiple new class 1 subtypes (III-G, III-H, III-I) and a distinct type VII with Cas14 nuclease—reflecting a broad diversity mainly involved in prokaryotic adaptive immunity and defense against viruses and mobile genetic elements (MGEs). The analysis highlights extensive modular evolution, signaling pathway diversity (cOA and SAM–AMP second messengers in type III), and reveals frequent recruitment of CRISPR–Cas by transposons for RNA-guided transposition, plus repeated exaptation for non-defense functions. Distribution studies show CRISPR–Cas systems are highly prevalent in archaea (especially thermophiles) and bacteria, with class 1 systems generally dominating over class 2. Newly discovered rare variants contribute only about 0.3% of systems in sequenced genomes but emphasize a long tail of diversity needing further mining aided by AI and metagenomic data. For Aleph portfolio companies operating in AI, SaaS for data-driven products, and cybersecurity domains such as Anodot, Panorays, Ply, Sequence, and Superlegal, these insights indicate a rapidly evolving landscape of CRISPR-related molecular tools and defense mechanisms—highlighting potential areas for advanced genomic data analytics and biosecurity applications, and possibly informing innovative product development leveraging CRISPR technologies or their evolutionary dynamics.

AI Interview Series #1: Explain Some LLM Text Generation Strategies Used in LLMs - MarkTechPost

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Arham Islam
November 17, 2025
The article explains key large language model (LLM) text generation strategies—Greedy Search, Beam Search, Nucleus (Top-p) Sampling, and Temperature Sampling—highlighting their differing balance of focus, creativity, and coherence, relevant for Aleph portfolio companies using or developing LLM-based products like LawGeex (legal AI) and Superlegal (legal workflows), where precise vs. varied text generation matters. It also presents a detailed PyTorch implementation of a continual learning neural memory agent combining differentiable memory, experience replay, and meta-learning for adaptive AI systems, which could inform Aleph investments in AI infrastructure like NextSilicon or Grain Finance that may require stable continual learning models. Additionally, Kosmos—a new autonomous AI scientific discovery system running extensive research cycles using a structured long-term world model and multi-agent design—is described in depth; it reads thousands of papers and runs tens of thousands of lines of code to generate credible scientific reports with ~79% accuracy, reproducing known results and proposing novel mechanisms across domains including metabolomics, materials science, neuroscience, and genetics. This breakthrough in AI-augmented research demonstrates advanced LLM agent orchestration and reasoning capabilities with reproducibility and auditability, relevant to Aleph portfolio sectors like Windward (maritime AI leveraging complex data) and Fabric (supply chain automation), where integrating structured memory and multi-agent workflows can boost decision-making. Finally, the article surveys common memory architectures for multi-agent LLM systems, highlighting vector memory systems (e.g., vector retrieval augmented generation) as the dominant pattern for fast, scalable but limited memory suited for local or embedded queries, while noting their weaknesses on temporal, cross-session, or multi-hop relational tasks—insights critical for building robust AI agents like those in Sightful (sales intelligence) or Unit (embedded banking), where memory design impacts system reliability and user experience.

ReasoningBank: Scaling Agent Self-Evolving with Reasoning Memory

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Siru Ouyang, Jun Yan, I-Hung Hsu, Yanfei Chen, Ke Jiang, Zifeng Wang, Rujun Han, Long T. Le, Samira Daruki, Xiangru Tang, Vishy Tirumalashetty, George Lee, Mahsan Rofouei, Hangfei Lin, Jiawei Han, Chen-Yu Lee, Tomas Pfister
October 26, 2025
The paper introduces ReasoningBank, a novel memory framework for large language model (LLM) agents that distills transferable reasoning strategies from both successful and failed experiences to enable continuous self-improvement in persistent real-world tasks like web browsing and software engineering; combined with a new memory-aware test-time scaling method (MaTTS), it significantly outperforms existing memory mechanisms and scaling approaches in benchmarks, improving effectiveness and efficiency by leveraging rich, structured memories rather than just raw trajectories or successful workflows. This advancement is relevant for portfolio companies like Ply (ply.io) and Sequence (getsequence.io), which build agent-driven automation and workflow tools that could benefit from enhanced agent memory and scaling capabilities; it also impacts competitors and partners in the LLM agent ecosystem, such as those developing autonomous web or code agents (e.g., WebArena, BrowserGym environments). The synergy between memory and test-time compute scaling demonstrated by ReasoningBank and MaTTS illustrates a practical path toward adaptive, lifelong-learning AI agents with emergent reasoning strategies.

The astrocytic ensemble acts as a multiday trace to stabilize memory | Nature

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Ken-ichi Dewa, Kodai Kaseda, Aoi Kuwahara, Hideaki Kubotera, Ayato Yamasaki, Natsumi Awata, Atsuko Komori, Mika A. Holtz, Atsushi Kasai, Henrik Skibbe, Norio Takata, Tatsushi Yokoyama, Makoto Tsuda, Genri Numata, Shun Nakamura, Eiki Takimoto, Masayuki Sakamoto, Minako Ito, Takahiro Masuda & Jun Nagai
October 26, 2025
This comprehensive study published in Nature reveals that astrocytes form behaviorally relevant ensembles (BAEs) acting as multiday molecular traces critical for stabilizing emotionally salient, repeated fear memories, especially in the amygdala—a key region implicated in fear memory—by integrating local engram neuronal activity with long-range noradrenaline (NA) signaling. Using novel brain-wide astrocyte-specific Fos tagging combined with imaging and transcriptomics, the authors demonstrate that initial fear conditioning (FC) primes astrocytes by upregulating α1- and β1-adrenoreceptors over a day, enhancing their responsiveness to NA during fear recall (FR), which activates Fos and induces neuromodulatory IGFBP2 expression. Perturbation of astrocytic NA signaling or IGFBP2 impairs memory restabilization/reconsolidation, while astrocyte β1-adrenergic receptor overexpression amplifies astrocyte ensembles and leads to memory over-stabilization and generalization, as evidenced by increased reactivation of neuronal engram cells during recall. This astrocyte ensemble's slower timescale of activity contrasts with the rapid neuronal engrams and suggests astrocytes provide eligibility or stabilization traces over days to maintain memory precision, highlighting their integral role in memory circuits beyond neurons. These findings have implications for disorders with dysregulated noradrenergic signaling, such as PTSD, and open avenues for targeting astrocyte–neuron interactions in cognitive and neuropsychiatric therapeutics. Although none of Aleph’s portfolio companies are directly mentioned, the study’s insights into neural circuit stability, neuromodulation, and state-dependent molecular ensembles may be relevant in the broader neurotechnology and AI-driven cognitive analytics domains related to companies like Grain Finance (cognitive modeling of economic memory) or Sightful (interpreting nuanced human behavior), and intersect with AI and data analytics innovations in brain-inspired computing.

Efficient protein structure generation with sparse denoising models | Nature Machine Intelligence

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Michael Jendrusch, Jan O. Korbel
September 28, 2025
A new protein structure generative model family called "salad" (sparse all-atom denoising) offers significant advances for computational protein design, addressing major limitations in current diffusion-based models by enabling efficient, scalable generation of protein backbones up to 1,000 amino acids with improved runtime (19 seconds vs. >10 minutes for RFdiffusion on large proteins), reduced parameter count (~8M vs. 200M in Proteina), and comparable or better designability and diversity. Salad's sparse transformer architecture with invariant point attention reduces computational complexity from cubic to near-linear, enabling high-throughput design of large and complex proteins relevant for biotech, enzyme optimization, antibody and vaccine scaffold design. Notably, salad introduces a flexible structure editing sampling strategy that allows constraint enforcement (motif scaffolding, multi-state proteins, symmetric repeat proteins including screw symmetry) without retraining, outperforming or matching state-of-the-art models like Genie 2 and RFdiffusion on motif-scaffolding benchmarks and enabling multi-motif and multi-state protein design, a previously challenging task. While validated computationally via designability metrics using ProteinMPNN and AlphaFold/ESMFold predictions—with design success rates exceeding prior ML methods for multi-state design—experimental validation remains to be done. This modular, efficient approach advances protein generative modeling with potential impact on enzyme, antibody, biosensor, and vaccine design workflows, and offers a versatile, plug-and-play backbone generator that can integrate with sequence design and downstream experimental pipelines. The model's limitation includes training on PDB-only data without small molecules, suggesting future extension using AlphaFold DB and ligand complexes, which would enhance its applicability for enzyme and small-molecule binder design. Eden Shochat’s portfolio companies operating in biotech and AI-powered design, such as Anodot (AI analytics) or Windward (AI risk analytics), may find interest in similar efficiency and scalability gains in their computational pipelines; analogously, startups in synthetic biology or drug discovery could see salad’s approach as a competitor or collaborator in protein engineering tools.