FMAdapt


Recent Readings for Adaptation of Foundation Models (since 2022) (Index of Posts):

No. Read Date Title and Information We Read @
1 2025, Mar, 17 Agent - In Healthcare 2025-S4
2 2025, Mar, 10 Extra - BioLLM 2025-S4
3 2025, Feb, 5 advanced LLM - Math reasoning 2025-S4
4 2025, Feb, 3 advanced LLM - for code reasoning 2025-S4
5 2025, Jan, 29 Survey - FMs in Robotics 2025-S3
6 2025, Jan, 27 Survey - FMs in healthcare 2025-S3
7 2025, Jan, 22 Survey - BioScience LLMs 2025-S2
8 2024, Apr, 23 LLM fine tuning 2024-S25
9 2024, Apr, 16 MultiAgent LLMs 2024-S23
10 2024, Apr, 11 LLM Agents 2024-S22
11 2024, Apr, 9 Self-exam LLM and reasoning 2024-S21
12 2024, Apr, 4 Prompt Engineering 2024-S20
13 2024, Mar, 26 Model editing and Disgorgement 2024-S17
14 2024, Mar, 21 Domain Centered FMs 2024-S16
15 2024, Mar, 14 Knowledge Augmented FMs 2024-S14
16 2022, Jun, 3 Decision Transformers 2022-W3
17 2022, May, 3 A Generalist Agent + offline RL + UniMask 2022-W1


Here is a detailed list of posts!



[1]: Agent - In Healthcare


Applications

In this session, our readings cover:

Required Readings:

The rise of agentic AI teammates in medicine

  • Perspectives Digital medicine Volume 405, Issue 10477 vp457 February 08, 2025
  • James Zou jamesz@stanford.edu ∙ Eric J Topol
  • Medicine is in the dawn of a fundamental shift from using artificial intelligence (AI) as tools to deploying AI as agents. When used as a tool, AI is passive and reactive. Even powerful medical AI foundation models today remain tools that depend on human users to provide input and context, interpret their output, and take follow-up steps. To fully unlock AI’s potential in medicine, clinicians need to make the key conceptual shift from using AI as sophisticated calculators to embracing AI as health-care teammates.

Lab-in-the-loop therapeutic antibody design with deep learning

  • https://doi.org/10.1101/2025.02.19.639050
  • Therapeutic antibody design is a complex multi-property optimization problem that traditionally relies on expensive search through sequence space. Here, we introduce “Lab-in-the-loop,” a paradigm shift for antibody design that orchestrates generative machine learning models, multi-task property predictors, active learning ranking and selection, and in vitro experimentation in a semiautonomous, iterative optimization loop. By automating the design of antibody variants, property prediction, ranking and selection of designs to assay in the lab, and ingestion of in vitro data, we enable a holistic, end-to-end approach to antibody optimization. We apply lab-in-the-loop to four clinically relevant antigen targets: EGFR, IL-6, HER2, and OSM. Over 1,800 unique antibody variants are designed and tested, derived from lead molecule candidates obtained via animal immunization and state-of-the-art immune repertoire mining techniques. Four lead candidate and four design crystal structures are solved to reveal mechanistic insights into the effects of mutations. We perform four rounds of iterative optimization and report 3–100× better binding variants for every target and ten candidate lead molecules, with the best binders in a therapeutically relevant 100 pM range.
  • All authors are or were employees of Genentech Inc. (a member of the Roche Group) or Roche, and may hold Roche stock or related interests.

From Medprompt to o1: Exploration of Run-Time Strategies for Medical Challenge Problems and Beyond

  • Harsha Nori, Naoto Usuyama, Nicholas King, Scott Mayer McKinney, Xavier Fernandes, Sheng Zhang, Eric Horvitz
  • Run-time steering strategies like Medprompt are valuable for guiding large language models (LLMs) to top performance on challenging tasks. Medprompt demonstrates that a general LLM can be focused to deliver state-of-the-art performance on specialized domains like medicine by using a prompt to elicit a run-time strategy involving chain of thought reasoning and ensembling. OpenAI’s o1-preview model represents a new paradigm, where a model is designed to do run-time reasoning before generating final responses. We seek to understand the behavior of o1-preview on a diverse set of medical challenge problem benchmarks. Following on the Medprompt study with GPT-4, we systematically evaluate the o1-preview model across various medical benchmarks. Notably, even without prompting techniques, o1-preview largely outperforms the GPT-4 series with Medprompt. We further systematically study the efficacy of classic prompt engineering strategies, as represented by Medprompt, within the new paradigm of reasoning models. We found that few-shot prompting hinders o1’s performance, suggesting that in-context learning may no longer be an effective steering approach for reasoning-native models. While ensembling remains viable, it is resource-intensive and requires careful cost-performance optimization. Our cost and accuracy analysis across run-time strategies reveals a Pareto frontier, with GPT-4o representing a more affordable option and o1-preview achieving state-of-the-art performance at higher cost. Although o1-preview offers top performance, GPT-4o with steering strategies like Medprompt retains value in specific contexts. Moreover, we note that the o1-preview model has reached near-saturation on many existing medical benchmarks, underscoring the need for new, challenging benchmarks. We close with reflections on general directions for inference-time computation with LLMs.

A Survey on Medical Large Language Models: Technology, Application, Trustworthiness, and Future Directions

  • Lei Liu, Xiaoyan Yang, Junchi Lei, Yue Shen, Jian Wang, Peng Wei, Zhixuan Chu, Zhan Qin, Kui Ren
  • With the advent of Large Language Models (LLMs), medical artificial intelligence (AI) has experienced substantial technological progress and paradigm shifts, highlighting the potential of LLMs to streamline healthcare delivery and improve patient outcomes. Considering this rapid technical progress, in this survey, we trace the recent advances of Medical Large Language Models (Med-LLMs), including the background, key findings, and mainstream techniques, especially for the evolution from general-purpose models to medical-specialized applications. Firstly, we delve into the foundational technology of Med-LLMs, indicating how general models can be progressively adapted and refined for the complicated medical tasks. Secondly, the wide-ranging applications of Med-LLMs are investigated across various healthcare domains, as well as an up-to-date review of existing Med-LLMs. The transformative impact of these models on daily medical practice is evident through their ability to assist clinicians, educators, and patients. Recognizing the importance of responsible innovation, we discuss the challenges associated with ensuring fairness, accountability, privacy, and robustness. Ethical considerations, rigorous evaluation methodologies, and the establishment of regulatory frameworks are crucial for building trustworthiness in the real-world system. We emphasize the need for ongoing scrutiny and development to maintain high standards of safety and reliability. Finally, we anticipate possible future trajectories for Med-LLMs, identifying key avenues for prudent expansion. By consolidating these insights, our review aims to provide professionals and researchers with a thorough understanding of the strengths and limitations of Med-LLMs, fostering a balanced and ethical approach to their integration into the healthcare ecosystem.

A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics

  • Kai He, Rui Mao, Qika Lin, Yucheng Ruan, Xiang Lan, Mengling Feng, Erik Cambria
  • The utilization of large language models (LLMs) in the Healthcare domain has generated both excitement and concern due to their ability to effectively respond to freetext queries with certain professional knowledge. This survey outlines the capabilities of the currently developed LLMs for Healthcare and explicates their development process, with the aim of providing an overview of the development roadmap from traditional Pretrained Language Models (PLMs) to LLMs. Specifically, we first explore the potential of LLMs to enhance the efficiency and effectiveness of various Healthcare applications highlighting both the strengths and limitations. Secondly, we conduct a comparison between the previous PLMs and the latest LLMs, as well as comparing various LLMs with each other. Then we summarize related Healthcare training data, training methods, optimization strategies, and usage. Finally, the unique concerns associated with deploying LLMs in Healthcare settings are investigated, particularly regarding fairness, accountability, transparency and ethics. Our survey provide a comprehensive investigation from perspectives of both computer science and Healthcare specialty. Besides the discussion about Healthcare concerns, we supports the computer science community by compiling a collection of open source resources, such as accessible datasets, the latest methodologies, code implementations, and evaluation benchmarks in the Github. Summarily, we contend that a significant paradigm shift is underway, transitioning from PLMs to LLMs. This shift encompasses a move from discriminative AI approaches to generative AI approaches, as well as a shift from model-centered methodologies to data-centered methodologies. Also, we determine that the biggest obstacle of using LLMs in Healthcare are fairness, accountability, transparency and ethics.

More Readings:

MEDEC: A Benchmark for Medical Error Detection and Correction in Clinical Notes

  • Asma Ben Abacha, Wen-wai Yim, Yujuan Fu, Zhaoyi Sun, Meliha Yetisgen, Fei Xia, Thomas Lin
  • [Submitted on 26 Dec 2024 (v1), last revised 2 Jan 2025 (this version, v2)]
  • Several studies showed that Large Language Models (LLMs) can answer medical questions correctly, even outperforming the average human score in some medical exams. However, to our knowledge, no study has been conducted to assess the ability of language models to validate existing or generated medical text for correctness and consistency. In this paper, we introduce MEDEC (this https URL), the first publicly available benchmark for medical error detection and correction in clinical notes, covering five types of errors (Diagnosis, Management, Treatment, Pharmacotherapy, and Causal Organism). MEDEC consists of 3,848 clinical texts, including 488 clinical notes from three US hospital systems that were not previously seen by any LLM. The dataset has been used for the MEDIQA-CORR shared task to evaluate seventeen participating systems [Ben Abacha et al., 2024]. In this paper, we describe the data creation methods and we evaluate recent LLMs (e.g., o1-preview, GPT-4, Claude 3.5 Sonnet, and Gemini 2.0 Flash) for the tasks of detecting and correcting medical errors requiring both medical knowledge and reasoning capabilities. We also conducted a comparative study where two medical doctors performed the same task on the MEDEC test set. The results showed that MEDEC is a sufficiently challenging benchmark to assess the ability of models to validate existing or generated notes and to correct medical errors. We also found that although recent LLMs have a good performance in error detection and correction, they are still outperformed by medical doctors in these tasks. We discuss the potential factors behind this gap, the insights from our experiments, the limitations of current evaluation metrics, and share potential pointers for future research.

A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery

  • Yu Zhang, Xiusi Chen, Bowen Jin, Sheng Wang, Shuiwang Ji, Wei Wang, Jiawei Han
  • In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at this https URL.

[2]: Extra - BioLLM


Applications

In this session, our readings cover:

Required Readings:

Genome modeling and design across all domains of life with Evo 2

  • Garyk Brixi, Matthew G. Durrant, Jerome Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel A. Gonzalez, Samuel H. King, David B. Li, View ORCID ProfileAditi T. Merchant, Mohsen Naghipourfar, Eric Nguyen, Chiara Ricci-Tam, David W. Romero, Gwanggyu Sun, Ali Taghibakshi, Anton Vorontsov, Brandon Yang, Myra Deng, Liv Gorton, Nam Nguyen, Nicholas K. Wang, Etowah Adams, Stephen A. Baccus, Steven Dillmann, Stefano Ermon, Daniel Guo, Rajesh Ilango, Ken Janik, Amy X. Lu, Reshma Mehta, View ORCID ProfileMohammad R.K. Mofrad, Madelena Y. Ng, Jaspreet Pannu, Christopher Ré, Jonathan C. Schmok, John St. John, Jeremy Sullivan, Kevin Zhu, Greg Zynda, Daniel Balsam, Patrick Collison, Anthony B. Costa, Tina Hernandez-Boussard, Eric Ho, Ming-Yu Liu, Thomas McGrath, Kimberly Powell, Dave P. Burke, View ORCID ProfileHani Goodarzi, View ORCID ProfilePatrick D. Hsu, View ORCID ProfileBrian L. Hie
  • doi: https://doi.org/10.1101/2025.02.18.638918
  • All of life encodes information with DNA. While tools for sequencing, synthesis, and editing of genomic code have transformed biological research, intelligently composing new biological systems would also require a deep understanding of the immense complexity encoded by genomes. We introduce Evo 2, a biological foundation model trained on 9.3 trillion DNA base pairs from a highly curated genomic atlas spanning all domains of life. We train Evo 2 with 7B and 40B parameters to have an unprecedented 1 million token context window with single-nucleotide resolution. Evo 2 learns from DNA sequence alone to accurately predict the functional impacts of genetic variation—from noncoding pathogenic mutations to clinically significant BRCA1 variants—without task-specific finetuning. Applying mechanistic interpretability analyses, we reveal that Evo 2 autonomously learns a breadth of biological features, including exon–intron boundaries, transcription factor binding sites, protein structural elements, and prophage genomic regions. Beyond its predictive capabilities, Evo 2 generates mitochondrial, prokaryotic, and eukaryotic sequences at genome scale with greater naturalness and coherence than previous methods. Guiding Evo 2 via inference-time search enables controllable generation of epigenomic structure, for which we demonstrate the first inference-time scaling results in biology. We make Evo 2 fully open, including model parameters, training code, inference code, and the OpenGenome2 dataset, to accelerate the exploration and design of biological complexity.

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

  • Jesse Zhang, Airol A Ubas, Richard de Borja, Valentine Svensson, Nicole Thomas, Neha Thakar, Ian Lai, Aidan Winters, Umair Khan, Matthew G. Jones, Vuong Tran, Joseph Pangallo, Efthymia Papalexi, Ajay Sapre, Hoai Nguyen, Oliver Sanderson, Maria Nigos, Olivia Kaplan, Sarah Schroeder, Bryan Hariadi, Simone Marrujo, Crina Curca Alec Salvino, Guillermo Gallareta Olivares, Ryan Koehler, Gary Geiss, Alexander Rosenberg, Charles Roco, Daniele Merico, Nima Alidoust, View ORCID ProfileHani Goodarzi, View ORCID ProfileJohnny Yu
  • doi: https://doi.org/10.1101/2025.02.20.639398
  • Building predictive models of the cell requires systematically mapping how perturbations reshape each cell’s state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas of 100 million transcriptomic profiles measuring how each of 1,100 small-molecule perturbations impact cells across 50 cancer cell lines. Our high-throughput Mosaic platform, composed of a highly diverse and optimally balanced “cell village”, reduces batch effects and enables parallel profiling of thousands of conditions at single-cell resolution at an unprecedented scale. As the largest single-cell dataset to date, Tahoe-100M enables artificial-intelligence (AI)-driven models to learn context-dependent functions, capturing fundamental principles of gene regulation and network dynamics. Although we leverage cancer models and pharmacological compounds to create this resource, Tahoe-100M is fundamentally designed as a broadly applicable perturbation atlas and supports deeper insights into cell biology across multiple tissues and contexts. By publicly releasing this atlas, we aim to accelerate the creation and development of robust AI frameworks for systems biology, ultimately improving our ability to predict and manipulate cellular behaviors across a wide range of applications.

More Readings:

Structure-based drug design with geometric deep learning

  • https://doi.org/10.1016/j.sbi.2023.102548
  • Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine learning, has been applied to macromolecular structures. This review provides an overview of the recent applications of geometric deep learning in bioorganic and medicinal chemistry, highlighting its potential for structure-based drug discovery and design. Emphasis is placed on molecular property prediction, ligand binding site and pose prediction, and structure-based de novo molecular design. The current challenges and opportunities are highlighted, and a forecast of the future of geometric deep learning for drug discovery is presented. Questions answered in this article

  • Structure-based drug design is based on methods that leverage three-dimensional (3D) structures of macromolecular targets, such as proteins and nucleic acids, for decision-making in medicinal chemistry [1,2]. Structure-based modeling is well established throughout the drug discovery process, aiming to rationalize non-covalent interactions between ligands and their target macromolecule(s) [3]. The questions addressed with structure-based approaches include molecular property prediction, ligand binding site recognition, binding pose estimation, as well as de novo design [4, 5, 6, 7]. For such tasks, detailed knowledge of the 3D structure of the investigated macromolecular surfaces and ligand–receptor interfaces is essential. Recently, an emerging concept of neural-network-based “artificial intelligence”, geometric deep learning, has been introduced to solve numerous problems in the molecular sciences, including structure-based drug discovery and design [8].

Generative models for molecular discovery: Recent advances and challenges

  • Camille Bilodeau, Wengong Jin, Tommi Jaakkola, Regina Barzilay, Klavs F. Jensen
  • 05 March 2022 https://doi.org/10.1002/wcms.1608Citations
  • Development of new products often relies on the discovery of novel molecules. While conventional molecular design involves using human expertise to propose, synthesize, and test new molecules, this process can be cost and time intensive, limiting the number of molecules that can be reasonably tested. Generative modeling provides an alternative approach to molecular discovery by reformulating molecular design as an inverse design problem. Here, we review the recent advances in the state-of-the-art of generative molecular design and discusses the considerations for integrating these models into real molecular discovery campaigns. We first review the model design choices required to develop and train a generative model including common 1D, 2D, and 3D representations of molecules and typical generative modeling neural network architectures. We then describe different problem statements for molecular discovery applications and explore the benchmarks used to evaluate models based on those problem statements. Finally, we discuss the important factors that play a role in integrating generative models into experimental workflows. Our aim is that this review will equip the reader with the information and context necessary to utilize generative modeling within their domain.

DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

  • [Submitted on 4 Oct 2022 (v1), last revised 11 Feb 2023 (this version, v2)]
  • Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi Jaakkola
  • Predicting the binding structure of a small molecule ligand to a protein – a task known as molecular docking – is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.
  • Comments: International Conference on Learning Representations (ICLR 2023)

Highly accurate protein structure prediction with AlphaFold

  • Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1,2,3,4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10,11,12,13,14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm.

Evolutionary-scale prediction of atomic-level protein structure with a language model

  • Speedy structures from single sequences: Machine learning methods for protein structure prediction have taken advantage of the evolutionary information present in multiple sequence alignments to derive accurate structural information, but predicting structure accurately from a single sequence is much more difficult. Lin et al. trained transformer protein language models with up to 15 billion parameters on experimental and high-quality predicted structures and found that information about atomic-level structure emerged in the model as it was scaled up. They created ESMFold, a sequence-to-structure predictor that is nearly as accurate as alignment-based methods and considerably faster. The increased speed permitted the generation of a database, the ESM Metagenomic Atlas, containing more than 600 million metagenomic proteins. —MAF
  • Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large language model. As language models of protein sequences are scaled up to 15 billion parameters, an atomic-resolution picture of protein structure emerges in the learned representations. This results in an order-of-magnitude acceleration of high-resolution structure prediction, which enables large-scale structural characterization of metagenomic proteins. We apply this capability to construct the ESM Metagenomic Atlas by predicting structures for >617 million metagenomic protein sequences, including >225 million that are predicted with high confidence, which gives a view into the vast breadth and diversity of natural proteins.

Accurate prediction of protein structures and interactions using a three-track neural network

  • Science 19 Aug 2021
  • Deep learning takes on protein folding: In 1972, Anfinsen won a Nobel prize for demonstrating a connection between a protein’s amino acid sequence and its three-dimensional structure. Since 1994, scientists have competed in the biannual Critical Assessment of Structure Prediction (CASP) protein-folding challenge. Deep learning methods took center stage at CASP14, with DeepMind’s Alphafold2 achieving remarkable accuracy. Baek et al. explored network architectures based on the DeepMind framework. They used a three-track network to process sequence, distance, and coordinate information simultaneously and achieved accuracies approaching those of DeepMind. The method, RoseTTA fold, can solve challenging x-ray crystallography and cryo–electron microscopy modeling problems and generate accurate models of protein-protein complexes. —VV

  • DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

Transformer protein language models are unsupervised structure learners

  • https://doi.org/10.1101/2020.12.15.422761
  • Unsupervised contact prediction is central to uncovering physical, structural, and functional constraints for protein structure determination and design. For decades, the predominant approach has been to infer evolutionary constraints from a set of related sequences. In the past year, protein language models have emerged as a potential alternative, but performance has fallen short of state-of-the-art approaches in bioinformatics. In this paper we demonstrate that Transformer attention maps learn contacts from the unsupervised language modeling objective. We find the highest capacity models that have been trained to date already outperform a state-of-the-art unsupervised contact prediction pipeline, suggesting these pipelines can be replaced with a single forward pass of an end-to-end model.1

PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

  • [Submitted on 5 Jun 2022 (v1), last revised 19 Sep 2022 (this version, v2)]
  • Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
  • We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at this https URL Comments: Accepted by NeurIPS 2022 Dataset and Benchmark Track. a

[3]: advanced LLM - Math reasoning


Reasoning

In this session, our readings cover:

Required Readings:

Solving olympiad geometry without human demonstrations

  • Trieu H. Trinh, Yuhuai Wu, Quoc V. Le, He He & Thang Luong
  • Nature volume 625, pages476–482 (2024)Cite this article
  • Published: 17 January 2024
  • https://www.nature.com/articles/s41586-023-06747-5
  • Proving mathematical theorems at the olympiad level represents a notable milestone in human-level automated reasoning1,2,3,4, owing to their reputed difficulty among the world’s best talents in pre-university mathematics. Current machine-learning approaches, however, are not applicable to most mathematical domains owing to the high cost of translating human proofs into machine-verifiable format. The problem is even worse for geometry because of its unique translation challenges1,5, resulting in severe scarcity of training data. We propose AlphaGeometry, a theorem prover for Euclidean plane geometry that sidesteps the need for human demonstrations by synthesizing millions of theorems and proofs across different levels of complexity. AlphaGeometry is a neuro-symbolic system that uses a neural language model, trained from scratch on our large-scale synthetic data, to guide a symbolic deduction engine through infinite branching points in challenging problems. On a test set of 30 latest olympiad-level problems, AlphaGeometry solves 25, outperforming the previous best method that only solves ten problems and approaching the performance of an average International Mathematical Olympiad (IMO) gold medallist. Notably, AlphaGeometry produces human-readable proofs, solves all geometry problems in the IMO 2000 and 2015 under human expert evaluation and discovers a generalized version of a translated IMO theorem in 2004.

Mathematical discoveries from program search with large language models

  • Published: 14 December 2023
  • Bernardino Romera-Paredes, Mohammadamin Barekatain, Alexander Novikov, Matej Balog, M. Pawan Kumar, Emilien Dupont, Francisco J. R. Ruiz, Jordan S. Ellenberg, Pengming Wang, Omar Fawzi, Pushmeet Kohli & Alhussein Fawzi
  • Nature https://www.nature.com/articles/s41586-023-06924-6#auth-Bernardino-Romera_Paredes-Aff1
  • Large language models (LLMs) have demonstrated tremendous capabilities in solving complex tasks, from quantitative reasoning to understanding natural language. However, LLMs sometimes suffer from confabulations (or hallucinations), which can result in them making plausible but incorrect statements1,2. This hinders the use of current large models in scientific discovery. Here we introduce FunSearch (short for searching in the function space), an evolutionary procedure based on pairing a pretrained LLM with a systematic evaluator. We demonstrate the effectiveness of this approach to surpass the best-known results in important problems, pushing the boundary of existing LLM-based approaches3. Applying FunSearch to a central problem in extremal combinatorics—the cap set problem—we discover new constructions of large cap sets going beyond the best-known ones, both in finite dimensional and asymptotic cases. This shows that it is possible to make discoveries for established open problems using LLMs. We showcase the generality of FunSearch by applying it to an algorithmic problem, online bin packing, finding new heuristics that improve on widely used baselines. In contrast to most computer search approaches, FunSearch searches for programs that describe how to solve a problem, rather than what the solution is. Beyond being an effective and scalable strategy, discovered programs tend to be more interpretable than raw solutions, enabling feedback loops between domain experts and FunSearch, and the deployment of such programs in real-world applications.

DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

  • Zhihong Shao, Peiyi Wang, Qihao Zhu, Runxin Xu, Junxiao Song, Xiao Bi, Haowei Zhang, Mingchuan Zhang, Y.K. Li, Y. Wu, Daya Guo
  • Mathematical reasoning poses a significant challenge for language models due to its complex and structured nature. In this paper, we introduce DeepSeekMath 7B, which continues pre-training DeepSeek-Coder-Base-v1.5 7B with 120B math-related tokens sourced from Common Crawl, together with natural language and code data. DeepSeekMath 7B has achieved an impressive score of 51.7% on the competition-level MATH benchmark without relying on external toolkits and voting techniques, approaching the performance level of Gemini-Ultra and GPT-4. Self-consistency over 64 samples from DeepSeekMath 7B achieves 60.9% on MATH. The mathematical reasoning capability of DeepSeekMath is attributed to two key factors: First, we harness the significant potential of publicly available web data through a meticulously engineered data selection pipeline. Second, we introduce Group Relative Policy Optimization (GRPO), a variant of Proximal Policy Optimization (PPO), that enhances mathematical reasoning abilities while concurrently optimizing the memory usage of PPO.
  • Elements:
    • Both Deepseek and Qwen use GRPO in post-training! Group Relative Policy Optimization or GRPO was introduced in the DeepSeekMath Paper last year to improve mathematical reasoning capabilities with less memory consumption, but is now used in an online way also to improve Truthfulness, Helpfulness, Conciseness…
    • Generate multiple outputs for each input question using the current Policy
    • Score these outputs using a reward model
    • Average the rewards and use it as a baseline to compute the advantages
    • Update the Policy to maximize the GRPO objective, which includes the advantages and a KL term
  • Insights:
    • Doesn’t need value function model, reducing memory and complexity
    • Adds KL term directly to the loss rather than in the reward
    • Works with rule-based Reward Models and Generative/Score based RM
    • Looks similar to RLOO method
    • DS 3 improved coding, math, writing, role-playing, and question answering

DeepSeek-V3 Technical Report

  • DeepSeek-AI, (100 additional authors not shown)
  • We present DeepSeek-V3, a strong Mixture-of-Experts (MoE) language model with 671B total parameters with 37B activated for each token. To achieve efficient inference and cost-effective training, DeepSeek-V3 adopts Multi-head Latent Attention (MLA) and DeepSeekMoE architectures, which were thoroughly validated in DeepSeek-V2. Furthermore, DeepSeek-V3 pioneers an auxiliary-loss-free strategy for load balancing and sets a multi-token prediction training objective for stronger performance. We pre-train DeepSeek-V3 on 14.8 trillion diverse and high-quality tokens, followed by Supervised Fine-Tuning and Reinforcement Learning stages to fully harness its capabilities. Comprehensive evaluations reveal that DeepSeek-V3 outperforms other open-source models and achieves performance comparable to leading closed-source models. Despite its excellent performance, DeepSeek-V3 requires only 2.788M H800 GPU hours for its full training. In addition, its training process is remarkably stable. Throughout the entire training process, we did not experience any irrecoverable loss spikes or perform any rollbacks. The model checkpoints are available at this https URL.

More Readings:

Large Language Models for Mathematical Reasoning: Progresses and Challenges

  • Janice Ahn, Rishu Verma, Renze Lou, Di Liu, Rui Zhang, Wenpeng Yin
  • [Submitted on 31 Jan 2024 (v1), last revised 16 Sep 2024 (this version, v4)]
  • Mathematical reasoning serves as a cornerstone for assessing the fundamental cognitive capabilities of human intelligence. In recent times, there has been a notable surge in the development of Large Language Models (LLMs) geared towards the automated resolution of mathematical problems. However, the landscape of mathematical problem types is vast and varied, with LLM-oriented techniques undergoing evaluation across diverse datasets and settings. This diversity makes it challenging to discern the true advancements and obstacles within this burgeoning field. This survey endeavors to address four pivotal dimensions: i) a comprehensive exploration of the various mathematical problems and their corresponding datasets that have been investigated; ii) an examination of the spectrum of LLM-oriented techniques that have been proposed for mathematical problem-solving; iii) an overview of factors and concerns affecting LLMs in solving math; and iv) an elucidation of the persisting challenges within this domain. To the best of our knowledge, this survey stands as one of the first extensive examinations of the landscape of LLMs in the realm of mathematics, providing a holistic perspective on the current state, accomplishments, and future challenges in this rapidly evolving field.

A Survey of Deep Learning for Mathematical Reasoning

  • Pan Lu, Liang Qiu, Wenhao Yu, Sean Welleck, Kai-Wei Chang
  • [Submitted on 20 Dec 2022 (v1), last revised 22 Jun 2023 (this version, v2)]
  • Mathematical reasoning is a fundamental aspect of human intelligence and is applicable in various fields, including science, engineering, finance, and everyday life. The development of artificial intelligence (AI) systems capable of solving math problems and proving theorems has garnered significant interest in the fields of machine learning and natural language processing. For example, mathematics serves as a testbed for aspects of reasoning that are challenging for powerful deep learning models, driving new algorithmic and modeling advances. On the other hand, recent advances in large-scale neural language models have opened up new benchmarks and opportunities to use deep learning for mathematical reasoning. In this survey paper, we review the key tasks, datasets, and methods at the intersection of mathematical reasoning and deep learning over the past decade. We also evaluate existing benchmarks and methods, and discuss future research directions in this domain.

AI Capabilities Can Be Significantly Improved Without Expensive Retraining

  • https://epoch.ai/blog/ai-capabilities-can-be-significantly-improved-without-expensive-retraining

[4]: advanced LLM - for code reasoning


Reasoning

In this session, our readings cover:

Required Readings:

Agent for software engineering

  • https://www.phontron.com/slides/neubig24softwareagents.pdf

Language Models for Code Optimization: Survey, Challenges and Future Directions

  • https://arxiv.org/abs/2501.01277
  • [Submitted on 2 Jan 2025 (v1), last revised 3 Jan 2025 (this version, v2)]
  • Jingzhi Gong, Vardan Voskanyan, Paul Brookes, Fan Wu, Wei Jie, Jie Xu, Rafail Giavrimis, Mike Basios, Leslie Kanthan, Zheng Wang
  • Language models (LMs) built upon deep neural networks (DNNs) have recently demonstrated breakthrough effectiveness in software engineering tasks such as code generation, completion, and repair. This has paved the way for the emergence of LM-based code optimization techniques, which are crucial for enhancing the performance of existing programs, such as accelerating program execution time. However, a comprehensive survey dedicated to this specific application has been lacking. To fill this gap, we present a systematic literature review of over 50 primary studies, identifying emerging trends and addressing 11 specialized questions. Our findings reveal five critical open challenges, such as balancing model complexity with practical usability, cross-language/performance generalizability, and building trust in AI-driven solutions. Furthermore, we provide eight future research directions to facilitate more efficient, robust, and reliable LM-based code optimization. Thereby, this study aims to provide actionable insights and foundational references for both researchers and practitioners in this rapidly evolving field.

DeepSeek-Coder-V2: Breaking the Barrier of Closed-Source Models in Code Intelligence

  • https://arxiv.org/abs/2406.11931
  • DeepSeek-AI, Qihao Zhu, Daya Guo, Zhihong Shao, Dejian Yang, Peiyi Wang, Runxin Xu, Y. Wu, + Yukun Li, Huazuo Gao, Shirong Ma, Wangding Zeng, Xiao Bi, Zihui Gu, Hanwei Xu, Damai Dai, Kai Dong, Liyue Zhang, Yishi Piao, Zhibin Gou, Zhenda Xie, Zhewen Hao, Bingxuan Wang, Junxiao Song, Deli Chen, Xin Xie, Kang Guan, Yuxiang You, Aixin Liu, Qiushi Du, Wenjun Gao, Xuan Lu, Qinyu Chen, Yaohui Wang, Chengqi Deng, Jiashi Li, Chenggang Zhao, Chong Ruan, Fuli Luo, Wenfeng Liang
  • We present DeepSeek-Coder-V2, an open-source Mixture-of-Experts (MoE) code language model that achieves performance comparable to GPT4-Turbo in code-specific tasks. Specifically, DeepSeek-Coder-V2 is further pre-trained from an intermediate checkpoint of DeepSeek-V2 with additional 6 trillion tokens. Through this continued pre-training, DeepSeek-Coder-V2 substantially enhances the coding and mathematical reasoning capabilities of DeepSeek-V2, while maintaining comparable performance in general language tasks. Compared to DeepSeek-Coder-33B, DeepSeek-Coder-V2 demonstrates significant advancements in various aspects of code-related tasks, as well as reasoning and general capabilities. Additionally, DeepSeek-Coder-V2 expands its support for programming languages from 86 to 338, while extending the context length from 16K to 128K. In standard benchmark evaluations, DeepSeek-Coder-V2 achieves superior performance compared to closed-source models such as GPT4-Turbo, Claude 3 Opus, and Gemini 1.5 Pro in coding and math benchmarks.

Iterative Refinement of Project-Level Code Context for Precise Code Generation with Compiler Feedback

  • [Submitted on 25 Mar 2024 (v1), last revised 11 Jun 2024 (this version, v3)]
  • Zhangqian Bi, Yao Wan, Zheng Wang, Hongyu Zhang, Batu Guan, Fangxin Lu, Zili Zhang, Yulei Sui, Hai Jin, Xuanhua Shi
  • Large Language Models (LLMs) have shown remarkable progress in automated code generation. Yet, LLM-generated code may contain errors in API usage, class, data structure, or missing project-specific information. As much of this project-specific context cannot fit into the prompts of LLMs, we must find ways to allow the model to explore the project-level code context. We present CoCoGen, a new code generation approach that uses compiler feedback to improve the LLM-generated code. CoCoGen first leverages static analysis to identify mismatches between the generated code and the project’s context. It then iteratively aligns and fixes the identified errors using information extracted from the code repository. We integrate CoCoGen with two representative LLMs, i.e., GPT-3.5-Turbo and Code Llama (13B), and apply it to Python code generation. Experimental results show that CoCoGen significantly improves the vanilla LLMs by over 80% in generating code dependent on the project context and consistently outperforms the existing retrieval-based code generation baselines.

More Readings:


[5]: Survey - FMs in Robotics


Applications

In this session, our readings cover:

Required Readings:

A Survey on Integration of Large Language Models with Intelligent Robots

  • [Submitted on 14 Apr 2024 (v1), last revised 15 Aug 2024 (this version, v5)]
  • Yeseung Kim, Dohyun Kim, Jieun Choi, Jisang Park, Nayoung Oh, Daehyung Park
  • In recent years, the integration of large language models (LLMs) has revolutionized the field of robotics, enabling robots to communicate, understand, and reason with human-like proficiency. This paper explores the multifaceted impact of LLMs on robotics, addressing key challenges and opportunities for leveraging these models across various domains. By categorizing and analyzing LLM applications within core robotics elements – communication, perception, planning, and control – we aim to provide actionable insights for researchers seeking to integrate LLMs into their robotic systems. Our investigation focuses on LLMs developed post-GPT-3.5, primarily in text-based modalities while also considering multimodal approaches for perception and control. We offer comprehensive guidelines and examples for prompt engineering, facilitating beginners’ access to LLM-based robotics solutions. Through tutorial-level examples and structured prompt construction, we illustrate how LLM-guided enhancements can be seamlessly integrated into robotics applications. This survey serves as a roadmap for researchers navigating the evolving landscape of LLM-driven robotics, offering a comprehensive overview and practical guidance for harnessing the power of language models in robotics development.

Large Language Models for Robotics: Opportunities, Challenges, and Perspectives

  • Jiaqi Wang, Zihao Wu, Yiwei Li, Hanqi Jiang, Peng Shu, Enze Shi, Huawen Hu, Chong Ma, Yiheng Liu, Xuhui Wang, Yincheng Yao, Xuan Liu, Huaqin Zhao, Zhengliang Liu, Haixing Dai, Lin Zhao, Bao Ge, Xiang Li, Tianming Liu, Shu Zhang
  • Large language models (LLMs) have undergone significant expansion and have been increasingly integrated across various domains. Notably, in the realm of robot task planning, LLMs harness their advanced reasoning and language comprehension capabilities to formulate precise and efficient action plans based on natural language instructions. However, for embodied tasks, where robots interact with complex environments, text-only LLMs often face challenges due to a lack of compatibility with robotic visual perception. This study provides a comprehensive overview of the emerging integration of LLMs and multimodal LLMs into various robotic tasks. Additionally, we propose a framework that utilizes multimodal GPT-4V to enhance embodied task planning through the combination of natural language instructions and robot visual perceptions. Our results, based on diverse datasets, indicate that GPT-4V effectively enhances robot performance in embodied tasks. This extensive survey and evaluation of LLMs and multimodal LLMs across a variety of robotic tasks enriches the understanding of LLM-centric embodied intelligence and provides forward-looking insights toward bridging the gap in Human-Robot-Environment interaction.

A Survey of Robot Intelligence with Large Language Models

  • https://doi.org/10.3390/app14198868
  • Submission received: 6 September 2024 / Revised: 24 September 2024 / Accepted: 25 September 2024 / Published: 2 October 2024
  • (This article belongs to the Special Issue Advancements in Intelligent Systems: The Confluence of AI, Machine Learning, and Robotics)
  • Since the emergence of ChatGPT, research on large language models (LLMs) has actively progressed across various fields. LLMs, pre-trained on vast text datasets, have exhibited exceptional abilities in understanding natural language and planning tasks. These abilities of LLMs are promising in robotics. In general, traditional supervised learning-based robot intelligence systems have a significant lack of adaptability to dynamically changing environments. However, LLMs help a robot intelligence system to improve its generalization ability in dynamic and complex real-world environments. Indeed, findings from ongoing robotics studies indicate that LLMs can significantly improve robots’ behavior planning and execution capabilities. Additionally, vision-language models (VLMs), trained on extensive visual and linguistic data for the vision question answering (VQA) problem, excel at integrating computer vision with natural language processing. VLMs can comprehend visual contexts and execute actions through natural language. They also provide descriptions of scenes in natural language. Several studies have explored the enhancement of robot intelligence using multimodal data, including object recognition and description by VLMs, along with the execution of language-driven commands integrated with visual information. This review paper thoroughly investigates how foundation models such as LLMs and VLMs have been employed to boost robot intelligence. For clarity, the research areas are categorized into five topics: reward design in reinforcement learning, low-level control, high-level planning, manipulation, and scene understanding. This review also summarizes studies that show how foundation models, such as the Eureka model for automating reward function design in reinforcement learning, RT-2 for integrating visual data, language, and robot actions in vision-language-action models, and AutoRT for generating feasible tasks and executing robot behavior policies via LLMs, have improved robot intelligence. Keywords: embodied intelligence; foundation model; large language model (LLM); vision-language model (VLM); vision-language-action (VLA) model; robotics

More Readings:


[6]: Survey - FMs in healthcare


Applications

In this session, our readings cover:

Required Readings:

A Comprehensive Survey of Foundation Models in Medicine

  • Khan, Wasif, Seowung Leem, Kyle B. See, Joshua K. Wong, Shaoting Zhang, and Ruogu Fang. “A Comprehensive Survey of Foundation Models in Medicine.” arXiv, January 16, 2025. https://doi.org/10.48550/arXiv.2406.10729.

  • URL
  • Wasif Khan, Seowung Leem, Kyle B. See, Joshua K. Wong, Shaoting Zhang, Ruogu Fang
  • Foundation models (FMs) are large-scale deep-learning models trained on extensive datasets using self-supervised techniques. These models serve as a base for various downstream tasks, including healthcare. FMs have been adopted with great success across various domains within healthcare, including natural language processing (NLP), computer vision, graph learning, biology, and omics. Existing healthcare-based surveys have not yet included all of these domains. Therefore, this survey provides a comprehensive overview of FMs in healthcare. We focus on the history, learning strategies, flagship models, applications, and challenges of FMs. We explore how FMs such as the BERT and GPT families are reshaping various healthcare domains, including clinical large language models, medical image analysis, and omics data. Furthermore, we provide a detailed taxonomy of healthcare applications facilitated by FMs, such as clinical NLP, medical computer vision, graph learning, and other biology-related tasks. Despite the promising opportunities FMs provide, they also have several associated challenges, which are explained in detail. We also outline potential future directions to provide researchers and practitioners with insights into the potential and limitations of FMs in healthcare to advance their deployment and mitigate associated risks.

Foundation Model for Advancing Healthcare: Challenges, Opportunities and Future Directions

  • He, Yuting, Fuxiang Huang, Xinrui Jiang, Yuxiang Nie, Minghao Wang, Jiguang Wang, and Hao Chen. “Foundation Model for Advancing Healthcare: Challenges, Opportunities and Future Directions.” IEEE Reviews in Biomedical Engineering PP (November 12, 2024). https://doi.org/10.1109/RBME.2024.3496744.

  • https://github.com/YutingHe-list/Awesome-Foundation-Models-for-Advancing-Healthcare

  • Abstract: Foundation model, trained on a diverse range of data and adaptable to a myriad of tasks, is advancing healthcare. It fosters the development of healthcare artificial intelligence (AI) models tailored to the intricacies of the medical field, bridging the gap between limited AI models and the varied nature of healthcare practices. The advancement of a healthcare foundation model (HFM) brings forth tremendous potential to augment intelligent healthcare services across a broad spectrum of scenarios. However, despite the imminent widespread deployment of HFMs, there is currently a lack of clear understanding regarding their operation in the healthcare field, their existing challenges, and their future trajectory. To answer these critical inquiries, we present a comprehensive and in-depth examination that delves into the landscape of HFMs. It begins with a comprehensive overview of HFMs, encompassing their methods, data, and applications, to provide a quick understanding of the current progress. Subsequently, it delves into a thorough exploration of the challenges associated with data, algorithms, and computing infrastructures in constructing and widely applying foundation models in healthcare. Furthermore, this survey identifies promising directions for future development in this field. We believe that this survey will enhance the community’s understanding of the current progress of HFMs and serve as a valuable source of guidance for future advancements in this domain. For the latest HFM papers and related resources, please refer to our website.

A Multi-Center Study on the Adaptability of a Shared Foundation Model for Electronic Health Records.

  • Guo, Lin Lawrence, Jason Fries, Ethan Steinberg, Scott Lanyon Fleming, Keith Morse, Catherine Aftandilian, Jose Posada, Nigam Shah, and Lillian Sung. “” Npj Digital Medicine 7, no. 1 (June 27, 2024): 1–9. https://doi.org/10.1038/s41746-024-01166-w.

  • Foundation models are transforming artificial intelligence (AI) in healthcare by providing modular components adaptable for various downstream tasks, making AI development more scalable and cost-effective. Foundation models for structured electronic health records (EHR), trained on coded medical records from millions of patients, demonstrated benefits including increased performance with fewer training labels, and improved robustness to distribution shifts. However, questions remain on the feasibility of sharing these models across hospitals and their performance in local tasks. This multi-center study examined the adaptability of a publicly accessible structured EHR foundation model (FMSM), trained on 2.57 M patient records from Stanford Medicine. Experiments used EHR data from The Hospital for Sick Children (SickKids) and Medical Information Mart for Intensive Care (MIMIC-IV). We assessed both adaptability via continued pretraining on local data, and task adaptability compared to baselines of locally training models from scratch, including a local foundation model. Evaluations on 8 clinical prediction tasks showed that adapting the off-the-shelf FMSM matched the performance of gradient boosting machines (GBM) locally trained on all data while providing a 13% improvement in settings with few task-specific training labels. Continued pretraining on local data showed FMSM required fewer than 1% of training examples to match the fully trained GBM’s performance, and was 60 to 90% more sample-efficient than training local foundation models from scratch. Our findings demonstrate that adapting EHR foundation models across hospitals provides improved prediction performance at less cost, underscoring the utility of base foundation models as modular components to streamline the development of healthcare AI.


[7]: Survey - BioScience LLMs


Applications

In this session, our readings cover:

Required Readings:

Scientific Large Language Models: A Survey on Biological & Chemical Domains

  • https://arxiv.org/abs/2401.14656
  • Qiang Zhang, Keyang Ding, Tianwen Lyv, Xinda Wang, Qingyu Yin, Yiwen Zhang, Jing Yu, Yuhao Wang, Xiaotong Li, Zhuoyi Xiang, Kehua Feng, Xiang Zhuang, Zeyuan Wang, Ming Qin, Mengyao Zhang, Jinlu Zhang, Jiyu Cui, Tao Huang, Pengju Yan, Renjun Xu, Hongyang Chen, Xiaolin Li, Xiaohui Fan, Huabin Xing, Huajun Chen
  • Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of “scientific language”, whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

Computational Protein Science in the Era of Large Language Models (LLMs)

  • https://arxiv.org/abs/2501.10282
  • Wenqi Fan, Yi Zhou, Shijie Wang, Yuyao Yan, Hui Liu, Qian Zhao, Le Song, Qing Li
  • Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In the last few decades, Artificial Intelligence (AI) has made significant impacts in computational protein science, leading to notable successes in specific protein modeling tasks. However, those previous AI models still meet limitations, such as the difficulty in comprehending the semantics of protein sequences, and the inability to generalize across a wide range of protein modeling tasks. Recently, LLMs have emerged as a milestone in AI due to their unprecedented language processing & generalization capability. They can promote comprehensive progress in fields rather than solving individual tasks. As a result, researchers have actively introduced LLM techniques in computational protein science, developing protein Language Models (pLMs) that skillfully grasp the foundational knowledge of proteins and can be effectively generalized to solve a diversity of sequence-structure-function reasoning problems. While witnessing prosperous developments, it’s necessary to present a systematic overview of computational protein science empowered by LLM techniques. First, we summarize existing pLMs into categories based on their mastered protein knowledge, i.e., underlying sequence patterns, explicit structural and functional information, and external scientific languages. Second, we introduce the utilization and adaptation of pLMs, highlighting their remarkable achievements in promoting protein structure prediction, protein function prediction, and protein design studies. Then, we describe the practical application of pLMs in antibody design, enzyme design, and drug discovery. Finally, we specifically discuss the promising future directions in this fast-growing field.

Extra Readings:


[8]: LLM fine tuning


Alignment

In this session, our readings cover:

Required Readings:

Recent Large Language Models Reshaping the Open-Source Arena

  • https://deci.ai/blog/list-of-large-language-models-in-open-source/
  • The release of Meta’s Llama model and the subsequent release of Llama 2 in 2023 kickstarted an explosion of open-source language models, with better and more innovative models being released on what seems like a daily basis. With new open-source models being released on a daily basis, here we dove into the ocean of open-source possibilities to curate a select list of the most intriguing and influential models making waves in recent months, inlcuding Qwen1.5/ Yi/ Smaug/ Mixtral-8x7B-v0.1/ DBRX/ SOLAR-10.7B-v1.0 / Tulu 2 / WizardLM/ Starling 7B/ OLMo-7B/ Gemma and DeciLM-7B.
  • Plus the newly avaiable DBRX model https://www.databricks.com/blog/introducing-dbrx-new-state-art-open-llm

Instruction Tuning for Large Language Models: A Survey

  • https://arxiv.org/abs/2308.10792
  • Shengyu Zhang, Linfeng Dong, Xiaoya Li, Sen Zhang, Xiaofei Sun, Shuhe Wang, Jiwei Li, Runyi Hu, Tianwei Zhang, Fei Wu, Guoyin Wang
  • This paper surveys research works in the quickly advancing field of instruction tuning (IT), a crucial technique to enhance the capabilities and controllability of large language models (LLMs). Instruction tuning refers to the process of further training LLMs on a dataset consisting of \textsc{(instruction, output)} pairs in a supervised fashion, which bridges the gap between the next-word prediction objective of LLMs and the users’ objective of having LLMs adhere to human instructions. In this work, we make a systematic review of the literature, including the general methodology of IT, the construction of IT datasets, the training of IT models, and applications to different modalities, domains and applications, along with an analysis on aspects that influence the outcome of IT (e.g., generation of instruction outputs, size of the instruction dataset, etc). We also review the potential pitfalls of IT along with criticism against it, along with efforts pointing out current deficiencies of existing strategies and suggest some avenues for fruitful research. Project page: this http URL

Delta tuning: A comprehensive study of parameter efficient methods for pre-trained language models

  • https://arxiv.org/abs/2203.06904
  • Despite the success, the process of fine-tuning large-scale PLMs brings prohibitive adaptation costs. In fact, fine-tuning all the parameters of a colossal model and retaining separate instances for different tasks are practically infeasible. This necessitates a new branch of research focusing on the parameter-efficient adaptation of PLMs, dubbed as delta tuning in this paper. In contrast with the standard fine-tuning, delta tuning only fine-tunes a small portion of the model parameters while keeping the rest untouched, largely reducing both the computation and storage costs. Recent studies have demonstrated that a series of delta tuning methods with distinct tuned parameter selection could achieve performance on a par with full-parameter fine-tuning, suggesting a new promising way of stimulating large-scale PLMs. In this paper, we first formally describe the problem of delta tuning and then comprehensively review recent delta tuning approaches. We also propose a unified categorization criterion that divide existing delta tuning methods into three groups: addition-based, specification-based, and reparameterization-based methods. Though initially proposed as an efficient method to steer large models, we believe that some of the fascinating evidence discovered along with delta tuning could help further reveal the mechanisms of PLMs and even deep neural networks. To this end, we discuss the theoretical principles underlying the effectiveness of delta tuning and propose frameworks to interpret delta tuning from the perspective of optimization and optimal control, respectively. Furthermore, we provide a holistic empirical study of representative methods, where results on over 100 NLP tasks demonstrate a comprehensive performance comparison of different approaches. The experimental results also cover the analysis of combinatorial, scaling and transferable properties of delta tuning.

More readings

Gemini: A Family of Highly Capable Multimodal Models

  • https://arxiv.org/abs/2312.11805
  • This report introduces a new family of multimodal models, Gemini, that exhibit remarkable capabilities across image, audio, video, and text understanding. The Gemini family consists of Ultra, Pro, and Nano sizes, suitable for applications ranging from complex reasoning tasks to on-device memory-constrained use-cases. Evaluation on a broad range of benchmarks shows that our most-capable Gemini Ultra model advances the state of the art in 30 of 32 of these benchmarks - notably being the first model to achieve human-expert performance on the well-studied exam benchmark MMLU, and improving the state of the art in every one of the 20 multimodal benchmarks we examined. We believe that the new capabilities of Gemini models in cross-modal reasoning and language understanding will enable a wide variety of use cases and we discuss our approach toward deploying them responsibly to users.

QLoRA: Efficient Finetuning of Quantized LLMs

  • Tim Dettmers, Artidoro Pagnoni, Ari Holtzman, Luke Zettlemoyer We present QLoRA, an efficient finetuning approach that reduces memory usage enough to finetune a 65B parameter model on a single 48GB GPU while preserving full 16-bit finetuning task performance. QLoRA backpropagates gradients through a frozen, 4-bit quantized pretrained language model into Low Rank Adapters~(LoRA). Our best model family, which we name Guanaco, outperforms all previous openly released models on the Vicuna benchmark, reaching 99.3% of the performance level of ChatGPT while only requiring 24 hours of finetuning on a single GPU. QLoRA introduces a number of innovations to save memory without sacrificing performance: (a) 4-bit NormalFloat (NF4), a new data type that is information theoretically optimal for normally distributed weights (b) double quantization to reduce the average memory footprint by quantizing the quantization constants, and (c) paged optimziers to manage memory spikes. We use QLoRA to finetune more than 1,000 models, providing a detailed analysis of instruction following and chatbot performance across 8 instruction datasets, multiple model types (LLaMA, T5), and model scales that would be infeasible to run with regular finetuning (e.g. 33B and 65B parameter models). Our results show that QLoRA finetuning on a small high-quality dataset leads to state-of-the-art results, even when using smaller models than the previous SoTA. We provide a detailed analysis of chatbot performance based on both human and GPT-4 evaluations showing that GPT-4 evaluations are a cheap and reasonable alternative to human evaluation. Furthermore, we find that current chatbot benchmarks are not trustworthy to accurately evaluate the performance levels of chatbots. A lemon-picked analysis demonstrates where Guanaco fails compared to ChatGPT. We release all of our models and code, including CUDA kernels for 4-bit training.
  • https://arxiv.org/abs/2106.09685
  • An important paradigm of natural language processing consists of large-scale pre-training on general domain data and adaptation to particular tasks or domains. As we pre-train larger models, full fine-tuning, which retrains all model parameters, becomes less feasible. Using GPT-3 175B as an example – deploying independent instances of fine-tuned models, each with 175B parameters, is prohibitively expensive. We propose Low-Rank Adaptation, or LoRA, which freezes the pre-trained model weights and injects trainable rank decomposition matrices into each layer of the Transformer architecture, greatly reducing the number of trainable parameters for downstream tasks. Compared to GPT-3 175B fine-tuned with Adam, LoRA can reduce the number of trainable parameters by 10,000 times and the GPU memory requirement by 3 times. LoRA performs on-par or better than fine-tuning in model quality on RoBERTa, DeBERTa, GPT-2, and GPT-3, despite having fewer trainable parameters, a higher training throughput, and, unlike adapters, no additional inference latency. We also provide an empirical investigation into rank-deficiency in language model adaptation, which sheds light on the efficacy of LoRA. We release a package that facilitates the integration of LoRA with PyTorch models and provide our implementations and model checkpoints for RoBERTa, DeBERTa, and GPT-2 at this https URL.

Astraios: Parameter-Efficient Instruction Tuning Code Large Language Models

  • https://arxiv.org/abs/2401.00788
  • Terry Yue Zhuo, Armel Zebaze, Nitchakarn Suppattarachai, Leandro von Werra, Harm de Vries, Qian Liu, Niklas Muennighoff
  • The high cost of full-parameter fine-tuning (FFT) of Large Language Models (LLMs) has led to a series of parameter-efficient fine-tuning (PEFT) methods. However, it remains unclear which methods provide the best cost-performance trade-off at different model scales. We introduce Astraios, a suite of 28 instruction-tuned OctoCoder models using 7 tuning methods and 4 model sizes up to 16 billion parameters. Through investigations across 5 tasks and 8 different datasets encompassing both code comprehension and code generation tasks, we find that FFT generally leads to the best downstream performance across all scales, and PEFT methods differ significantly in their efficacy based on the model scale. LoRA usually offers the most favorable trade-off between cost and performance. Further investigation into the effects of these methods on both model robustness and code security reveals that larger models tend to demonstrate reduced robustness and less security. At last, we explore the relationships among updated parameters, cross-entropy loss, and task performance. We find that the tuning effectiveness observed in small models generalizes well to larger models, and the validation loss in instruction tuning can be a reliable indicator of overall downstream performance.

This site was built using GitHub Pages.


[9]: MultiAgent LLMs


Agent

In this session, our readings cover:

Required Readings:

Large Language Model based Multi-Agents: A Survey of Progress and Challenges

  • Taicheng Guo, Xiuying Chen, Yaqi Wang, Ruidi Chang, Shichao Pei, Nitesh V. Chawla, Olaf Wiest, Xiangliang Zhang
  • Large Language Models (LLMs) have achieved remarkable success across a wide array of tasks. Due to the impressive planning and reasoning abilities of LLMs, they have been used as autonomous agents to do many tasks automatically. Recently, based on the development of using one LLM as a single planning or decision-making agent, LLM-based multi-agent systems have achieved considerable progress in complex problem-solving and world simulation. To provide the community with an overview of this dynamic field, we present this survey to offer an in-depth discussion on the essential aspects of multi-agent systems based on LLMs, as well as the challenges. Our goal is for readers to gain substantial insights on the following questions: What domains and environments do LLM-based multi-agents simulate? How are these agents profiled and how do they communicate? What mechanisms contribute to the growth of agents’ capacities? For those interested in delving into this field of study, we also summarize the commonly used datasets or benchmarks for them to have convenient access. To keep researchers updated on the latest studies, we maintain an open-source GitHub repository, dedicated to outlining the research on LLM-based multi-agent systems.

More Readings:

Understanding the planning of LLM agents: A survey

  • https://arxiv.org/abs/2402.02716
  • As Large Language Models (LLMs) have shown significant intelligence, the progress to leverage LLMs as planning modules of autonomous agents has attracted more attention. This survey provides the first systematic view of LLM-based agents planning, covering recent works aiming to improve planning ability. We provide a taxonomy of existing works on LLM-Agent planning, which can be categorized into Task Decomposition, Plan Selection, External Module, Reflection and Memory. Comprehensive analyses are conducted for each direction, and further challenges for the field of research are discussed.

LLM Agents can Autonomously Hack Websites

  • Richard Fang, Rohan Bindu, Akul Gupta, Qiusi Zhan, Daniel Kang
  • In recent years, large language models (LLMs) have become increasingly capable and can now interact with tools (i.e., call functions), read documents, and recursively call themselves. As a result, these LLMs can now function autonomously as agents. With the rise in capabilities of these agents, recent work has speculated on how LLM agents would affect cybersecurity. However, not much is known about the offensive capabilities of LLM agents. In this work, we show that LLM agents can autonomously hack websites, performing tasks as complex as blind database schema extraction and SQL injections without human feedback. Importantly, the agent does not need to know the vulnerability beforehand. This capability is uniquely enabled by frontier models that are highly capable of tool use and leveraging extended context. Namely, we show that GPT-4 is capable of such hacks, but existing open-source models are not. Finally, we show that GPT-4 is capable of autonomously finding vulnerabilities in websites in the wild. Our findings raise questions about the widespread deployment of LLMs.

Agent-FLAN: Designing Data and Methods of Effective Agent Tuning for Large Language Models

  • Zehui Chen, Kuikun Liu, Qiuchen Wang, Wenwei Zhang, Jiangning Liu, Dahua Lin, Kai Chen, Feng Zhao
  • Open-sourced Large Language Models (LLMs) have achieved great success in various NLP tasks, however, they are still far inferior to API-based models when acting as agents. How to integrate agent ability into general LLMs becomes a crucial and urgent problem. This paper first delivers three key observations: (1) the current agent training corpus is entangled with both formats following and agent reasoning, which significantly shifts from the distribution of its pre-training data; (2) LLMs exhibit different learning speeds on the capabilities required by agent tasks; and (3) current approaches have side-effects when improving agent abilities by introducing hallucinations. Based on the above findings, we propose Agent-FLAN to effectively Fine-tune LANguage models for Agents. Through careful decomposition and redesign of the training corpus, Agent-FLAN enables Llama2-7B to outperform prior best works by 3.5\% across various agent evaluation datasets. With comprehensively constructed negative samples, Agent-FLAN greatly alleviates the hallucination issues based on our established evaluation benchmark. Besides, it consistently improves the agent capability of LLMs when scaling model sizes while slightly enhancing the general capability of LLMs. The code will be available at this https URL.

Humanoid Locomotion as Next Token Prediction

  • Ilija Radosavovic, Bike Zhang, Baifeng Shi, Jathushan Rajasegaran, Sarthak Kamat, Trevor Darrell, Koushil Sreenath, Jitendra Malik
  • We cast real-world humanoid control as a next token prediction problem, akin to predicting the next word in language. Our model is a causal transformer trained via autoregressive prediction of sensorimotor trajectories. To account for the multi-modal nature of the data, we perform prediction in a modality-aligned way, and for each input token predict the next token from the same modality. This general formulation enables us to leverage data with missing modalities, like video trajectories without actions. We train our model on a collection of simulated trajectories coming from prior neural network policies, model-based controllers, motion capture data, and YouTube videos of humans. We show that our model enables a full-sized humanoid to walk in San Francisco zero-shot. Our model can transfer to the real world even when trained on only 27 hours of walking data, and can generalize to commands not seen during training like walking backward. These findings suggest a promising path toward learning challenging real-world control tasks by generative modeling of sensorimotor trajectories.

[10]: LLM Agents


Agent

Required Readings:

A Survey on Large Language Model based Autonomous Agents

  • https://arxiv.org/abs/2308.11432
  • Autonomous agents have long been a prominent research focus in both academic and industry communities. Previous research in this field often focuses on training agents with limited knowledge within isolated environments, which diverges significantly from human learning processes, and thus makes the agents hard to achieve human-like decisions. Recently, through the acquisition of vast amounts of web knowledge, large language models (LLMs) have demonstrated remarkable potential in achieving human-level intelligence. This has sparked an upsurge in studies investigating LLM-based autonomous agents. In this paper, we present a comprehensive survey of these studies, delivering a systematic review of the field of LLM-based autonomous agents from a holistic perspective. More specifically, we first discuss the construction of LLM-based autonomous agents, for which we propose a unified framework that encompasses a majority of the previous work. Then, we present a comprehensive overview of the diverse applications of LLM-based autonomous agents in the fields of social science, natural science, and engineering. Finally, we delve into the evaluation strategies commonly used for LLM-based autonomous agents. Based on the previous studies, we also present several challenges and future directions in this field. To keep track of this field and continuously update our survey, we maintain a repository of relevant references at this https URL.

More Readings:

Position Paper: Agent AI Towards a Holistic Intelligence

  • https://arxiv.org/abs/2403.00833
  • Qiuyuan Huang, Naoki Wake, Bidipta Sarkar, Zane Durante, Ran Gong, Rohan Taori, Yusuke Noda, Demetri Terzopoulos, Noboru Kuno, Ade Famoti, Ashley Llorens, John Langford, Hoi Vo, Li Fei-Fei, Katsu Ikeuchi, Jianfeng Gao
  • Recent advancements in large foundation models have remarkably enhanced our understanding of sensory information in open-world environments. In leveraging the power of foundation models, it is crucial for AI research to pivot away from excessive reductionism and toward an emphasis on systems that function as cohesive wholes. Specifically, we emphasize developing Agent AI – an embodied system that integrates large foundation models into agent actions. The emerging field of Agent AI spans a wide range of existing embodied and agent-based multimodal interactions, including robotics, gaming, and healthcare systems, etc. In this paper, we propose a novel large action model to achieve embodied intelligent behavior, the Agent Foundation Model. On top of this idea, we discuss how agent AI exhibits remarkable capabilities across a variety of domains and tasks, challenging our understanding of learning and cognition. Furthermore, we discuss the potential of Agent AI from an interdisciplinary perspective, underscoring AI cognition and consciousness within scientific discourse. We believe that those discussions serve as a basis for future research directions and encourage broader societal engagement.

Tool Use in LLMs

  • https://zorazrw.github.io/files/WhatAreToolsAnyway.pdf
  • an overview of tool use in LLMs, including a formal definition of the tool-use paradigm, scenarios where LLMs leverage tool usage, and for which tasks this approach works well; it also provides an analysis of complex tool usage and summarize testbeds and evaluation metrics across LM tooling works

Practices for Governing Agentic AI Systems

  • https://cdn.openai.com/papers/practices-for-governing-agentic-ai-systems.pdf
  • Agentic AI systems—AI systems that can pursue complex goals with limited direct supervision— are likely to be broadly useful if we can integrate them responsibly into our society. While such systems have substantial potential to help people more efficiently and effectively achieve their own goals, they also create risks of harm. In this white paper, we suggest a definition of agentic AI systems and the parties in the agentic AI system life-cycle, and highlight the importance of agreeing on a set of baseline responsibilities and safety best practices for each of these parties. As our primary contribution, we offer an initial set of practices for keeping agents’ operations safe and accountable, which we hope can serve as building blocks in the development of agreed baseline best practices. We enumerate the questions and uncertainties around operationalizing each of these practices that must be addressed before such practices can be codified. We then highlight categories of indirect impacts from the wide-scale adoption of agentic AI systems, which are likely to necessitate additional governance frameworks.

Emergent autonomous scientific research capabilities of large language models

  • https://arxiv.org/abs/2304.05332
  • Transformer-based large language models are rapidly advancing in the field of machine learning research, with applications spanning natural language, biology, chemistry, and computer programming. Extreme scaling and reinforcement learning from human feedback have significantly improved the quality of generated text, enabling these models to perform various tasks and reason about their choices. In this paper, we present an Intelligent Agent system that combines multiple large language models for autonomous design, planning, and execution of scientific experiments. We showcase the Agent’s scientific research capabilities with three distinct examples, with the most complex being the successful performance of catalyzed cross-coupling reactions. Finally, we discuss the safety implications of such systems and propose measures to prevent their misuse.

What Makes a Dialog Agent Useful?

  • https://huggingface.co/blog/dialog-agents

[11]: Self-exam LLM and reasoning


Reasoning

In this session, our readings cover:

Required Readings:

Augmented Language Models: a Survey

  • Grégoire Mialon, Roberto Dessì, Maria Lomeli, Christoforos Nalmpantis, Ram Pasunuru, Roberta Raileanu, Baptiste Rozière, Timo Schick, Jane Dwivedi-Yu, Asli Celikyilmaz, Edouard Grave, Yann LeCun, Thomas Scialom
  • This survey reviews works in which language models (LMs) are augmented with reasoning skills and the ability to use tools. The former is defined as decomposing a potentially complex task into simpler subtasks while the latter consists in calling external modules such as a code interpreter. LMs can leverage these augmentations separately or in combination via heuristics, or learn to do so from demonstrations. While adhering to a standard missing tokens prediction objective, such augmented LMs can use various, possibly non-parametric external modules to expand their context processing ability, thus departing from the pure language modeling paradigm. We therefore refer to them as Augmented Language Models (ALMs). The missing token objective allows ALMs to learn to reason, use tools, and even act, while still performing standard natural language tasks and even outperforming most regular LMs on several benchmarks. In this work, after reviewing current advance in ALMs, we conclude that this new research direction has the potential to address common limitations of traditional LMs such as interpretability,

Self-Consistency Improves Chain of Thought Reasoning in Language Models

  • https://arxiv.org/abs/2203.11171
  • Chain-of-thought prompting combined with pre-trained large language models has achieved encouraging results on complex reasoning tasks. In this paper, we propose a new decoding strategy, self-consistency, to replace the naive greedy decoding used in chain-of-thought prompting. It first samples a diverse set of reasoning paths instead of only taking the greedy one, and then selects the most consistent answer by marginalizing out the sampled reasoning paths. Self-consistency leverages the intuition that a complex reasoning problem typically admits multiple different ways of thinking leading to its unique correct answer. Our extensive empirical evaluation shows that self-consistency boosts the performance of chain-of-thought prompting with a striking margin on a range of popular arithmetic and commonsense reasoning benchmarks, including GSM8K (+17.9%), SVAMP (+11.0%), AQuA (+12.2%), StrategyQA (+6.4%) and ARC-challenge (+3.9%).

If LLM Is the Wizard, Then Code Is the Wand: A Survey on How Code Empowers Large Language Models to Serve as Intelligent Agents

  • https://arxiv.org/abs/2401.00812
  • Ke Yang, Jiateng Liu, John Wu, Chaoqi Yang, Yi R. Fung, Sha Li, Zixuan Huang, Xu Cao, Xingyao Wang, Yiquan Wang, Heng Ji, Chengxiang Zhai
  • The prominent large language models (LLMs) of today differ from past language models not only in size, but also in the fact that they are trained on a combination of natural language and formal language (code). As a medium between humans and computers, code translates high-level goals into executable steps, featuring standard syntax, logical consistency, abstraction, and modularity. In this survey, we present an overview of the various benefits of integrating code into LLMs’ training data. Specifically, beyond enhancing LLMs in code generation, we observe that these unique properties of code help (i) unlock the reasoning ability of LLMs, enabling their applications to a range of more complex natural language tasks; (ii) steer LLMs to produce structured and precise intermediate steps, which can then be connected to external execution ends through function calls; and (iii) take advantage of code compilation and execution environment, which also provides diverse feedback for model improvement. In addition, we trace how these profound capabilities of LLMs, brought by code, have led to their emergence as intelligent agents (IAs) in situations where the ability to understand instructions, decompose goals, plan and execute actions, and refine from feedback are crucial to their success on downstream tasks. Finally, we present several key challenges and future directions of empowering LLMs with code.

More Readings:

ReAct: Synergizing Reasoning and Acting in Language Models

  • Shunyu Yao, Jeffrey Zhao, Dian Yu, Nan Du, Izhak Shafran, Karthik Narasimhan, Yuan Cao
  • While large language models (LLMs) have demonstrated impressive capabilities across tasks in language understanding and interactive decision making, their abilities for reasoning (e.g. chain-of-thought prompting) and acting (e.g. action plan generation) have primarily been studied as separate topics. In this paper, we explore the use of LLMs to generate both reasoning traces and task-specific actions in an interleaved manner, allowing for greater synergy between the two: reasoning traces help the model induce, track, and update action plans as well as handle exceptions, while actions allow it to interface with external sources, such as knowledge bases or environments, to gather additional information. We apply our approach, named ReAct, to a diverse set of language and decision making tasks and demonstrate its effectiveness over state-of-the-art baselines, as well as improved human interpretability and trustworthiness over methods without reasoning or acting components. Concretely, on question answering (HotpotQA) and fact verification (Fever), ReAct overcomes issues of hallucination and error propagation prevalent in chain-of-thought reasoning by interacting with a simple Wikipedia API, and generates human-like task-solving trajectories that are more interpretable than baselines without reasoning traces. On two interactive decision making benchmarks (ALFWorld and WebShop), ReAct outperforms imitation and reinforcement learning methods by an absolute success rate of 34% and 10% respectively, while being prompted with only one or two in-context examples. Project site with code: this https URL
  • Comments: v3 is the ICLR camera ready version with some typos fixed. Project site with code: this https URL

Towards Reasoning in Large Language Models: A Survey

  • Jie Huang, Kevin Chen-Chuan Chang
  • Reasoning is a fundamental aspect of human intelligence that plays a crucial role in activities such as problem solving, decision making, and critical thinking. In recent years, large language models (LLMs) have made significant progress in natural language processing, and there is observation that these models may exhibit reasoning abilities when they are sufficiently large. However, it is not yet clear to what extent LLMs are capable of reasoning. This paper provides a comprehensive overview of the current state of knowledge on reasoning in LLMs, including techniques for improving and eliciting reasoning in these models, methods and benchmarks for evaluating reasoning abilities, findings and implications of previous research in this field, and suggestions on future directions. Our aim is to provide a detailed and up-to-date review of this topic and stimulate meaningful discussion and future work. Comments: ACL 2023 Findings, 15 pages

Large Language Models Can Self-Improve

  • Jiaxin Huang, Shixiang Shane Gu, Le Hou, Yuexin Wu, Xuezhi Wang, Hongkun Yu, Jiawei Han / Large Language Models (LLMs) have achieved excellent performances in various tasks. However, fine-tuning an LLM requires extensive supervision. Human, on the other hand, may improve their reasoning abilities by self-thinking without external inputs. In this work, we demonstrate that an LLM is also capable of self-improving with only unlabeled datasets. We use a pre-trained LLM to generate “high-confidence” rationale-augmented answers for unlabeled questions using Chain-of-Thought prompting and self-consistency, and fine-tune the LLM using those self-generated solutions as target outputs. We show that our approach improves the general reasoning ability of a 540B-parameter LLM (74.4%->82.1% on GSM8K, 78.2%->83.0% on DROP, 90.0%->94.4% on OpenBookQA, and 63.4%->67.9% on ANLI-A3) and achieves state-of-the-art-level performance, without any ground truth label. We conduct ablation studies and show that fine-tuning on reasoning is critical for self-improvement.
  • https://arxiv.org/abs/2210.11610

Orca 2: Teaching Small Language Models How to Reason /

  • https://arxiv.org/abs/2311.11045
  • Orca 1 learns from rich signals, such as explanation traces, allowing it to outperform conventional instruction-tuned models on benchmarks like BigBench Hard and AGIEval. In Orca 2, we continue exploring how improved training signals can enhance smaller LMs’ reasoning abilities. Research on training small LMs has often relied on imitation learning to replicate the output of more capable models. We contend that excessive emphasis on imitation may restrict the potential of smaller models. We seek to teach small LMs to employ different solution strategies for different tasks, potentially different from the one used by the larger model. For example, while larger models might provide a direct answer to a complex task, smaller models may not have the same capacity. In Orca 2, we teach the model various reasoning techniques (step-by-step, recall then generate, recall-reason-generate, direct answer, etc.). More crucially, we aim to help the model learn to determine the most effective solution strategy for each task. We evaluate Orca 2 using a comprehensive set of 15 diverse benchmarks (corresponding to approximately 100 tasks and over 36,000 unique prompts). Orca 2 significantly surpasses models of similar size and attains performance levels similar or better to those of models 5-10x larger, as assessed on complex tasks that test advanced reasoning abilities in zero-shot settings. make Orca 2 weights publicly available at this http URL to support research on the development, evaluation, and alignment of smaller LMs

[12]: Prompt Engineering


Prompting

In this session, our readings cover:

Required Readings:

Unleashing the potential of prompt engineering in Large Language Models: a comprehensive review

  • https://arxiv.org/abs/2310.14735
  • Banghao Chen, Zhaofeng Zhang, Nicolas Langrené, Shengxin Zhu / This paper delves into the pivotal role of prompt engineering in unleashing the capabilities of Large Language Models (LLMs). Prompt engineering is the process of structuring input text for LLMs and is a technique integral to optimizing the efficacy of LLMs. This survey elucidates foundational principles of prompt engineering, such as role-prompting, one-shot, and few-shot prompting, as well as more advanced methodologies such as the chain-of-thought and tree-of-thoughts prompting. The paper sheds light on how external assistance in the form of plugins can assist in this task, and reduce machine hallucination by retrieving external knowledge. We subsequently delineate prospective directions in prompt engineering research, emphasizing the need for a deeper understanding of structures and the role of agents in Artificial Intelligence-Generated Content (AIGC) tools. We discuss how to assess the efficacy of prompt methods from different perspectives and using different methods. Finally, we gather information about the application of prompt engineering in such fields as education and programming, showing its transformative potential. This comprehensive survey aims to serve as a friendly guide for anyone venturing through the big world of LLMs and prompt engineering.

More Readings:

Skeleton-of-Thought: Large Language Models Can Do Parallel Decoding

  • This work aims at decreasing the end-to-end generation latency of large language models (LLMs). One of the major causes of the high generation latency is the sequential decoding approach adopted by almost all state-of-the-art LLMs. In this work, motivated by the thinking and writing process of humans, we propose Skeleton-of-Thought (SoT), which first guides LLMs to generate the skeleton of the answer, and then conducts parallel API calls or batched decoding to complete the contents of each skeleton point in parallel. Not only does SoT provide considerable speed-ups across 12 LLMs, but it can also potentially improve the answer quality on several question categories. SoT is an initial attempt at data-centric optimization for inference efficiency, and further underscores the potential of pushing LLMs to think more like a human for answer quality.

Topologies of Reasoning: Demystifying Chains, Trees, and Graphs of Thoughts

  • The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models’ (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM’s capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

[13]: Model editing and Disgorgement


ModelEdit

In this session, our readings cover:

Required Readings:

Editing Large Language Models: Problems, Methods, and Opportunities

  • https://arxiv.org/abs/2305.13172
  • Yunzhi Yao, Peng Wang, Bozhong Tian, Siyuan Cheng, Zhoubo Li, Shumin Deng, Huajun Chen, Ningyu Zhang Despite the ability to train capable LLMs, the methodology for maintaining their relevancy and rectifying errors remains elusive. To this end, the past few years have witnessed a surge in techniques for editing LLMs, the objective of which is to efficiently alter the behavior of LLMs within a specific domain without negatively impacting performance across other inputs. This paper embarks on a deep exploration of the problems, methods, and opportunities related to model editing for LLMs. In particular, we provide an exhaustive overview of the task definition and challenges associated with model editing, along with an in-depth empirical analysis of the most progressive methods currently at our disposal. We also build a new benchmark dataset to facilitate a more robust evaluation and pinpoint enduring issues intrinsic to existing techniques. Our objective is to provide valuable insights into the effectiveness and feasibility of each editing technique, thereby assisting the community in making informed decisions on the selection of the most appropriate method for a specific task or context. Code and datasets are available at this https URL. Comments: EMNLP 2023. Updated with new experiments

More Readings:

Tuning Language Models by Proxy

  • Alisa Liu, Xiaochuang Han, Yizhong Wang, Yulia Tsvetkov, Yejin Choi, Noah A. Smith
  • Submitted on 16 Jan 2024]
  • Despite the general capabilities of large pretrained language models, they consistently benefit from further adaptation to better achieve desired behaviors. However, tuning these models has become increasingly resource-intensive, or impossible when model weights are private. We introduce proxy-tuning, a lightweight decoding-time algorithm that operates on top of black-box LMs to achieve the result of directly tuning the model, but by accessing only its prediction over the output vocabulary. Our method instead tunes a smaller LM, then applies the difference between the predictions of the small tuned and untuned LMs to shift the original predictions of the base model in the direction of tuning, while retaining the benefits of larger scale pretraining. In experiments, when we apply proxy-tuning to Llama2-70B using proxies of only 7B size, we can close 88% of the gap between Llama2-70B and its truly-tuned chat version, when evaluated across knowledge, reasoning, and safety benchmarks. Interestingly, when tested on TruthfulQA, proxy-tuned models are actually more truthful than directly tuned models, possibly because decoding-time guidance better retains the model’s factual knowledge. We then demonstrate the generality of proxy-tuning by applying it for domain adaptation on code, and task-specific finetuning on question-answering and math problems. Our work demonstrates the promise of using small tuned LMs to efficiently customize large, potentially proprietary LMs through decoding-time guidance.

A Survey of Machine Unlearning

  • https://arxiv.org/abs/2209.02299
  • Today, computer systems hold large amounts of personal data. Yet while such an abundance of data allows breakthroughs in artificial intelligence, and especially machine learning (ML), its existence can be a threat to user privacy, and it can weaken the bonds of trust between humans and AI. Recent regulations now require that, on request, private information about a user must be removed from both computer systems and from ML models, i.e. ``the right to be forgotten’’). While removing data from back-end databases should be straightforward, it is not sufficient in the AI context as ML models often `remember’ the old data. Contemporary adversarial attacks on trained models have proven that we can learn whether an instance or an attribute belonged to the training data. This phenomenon calls for a new paradigm, namely machine unlearning, to make ML models forget about particular data. It turns out that recent works on machine unlearning have not been able to completely solve the problem due to the lack of common frameworks and resources. Therefore, this paper aspires to present a comprehensive examination of machine unlearning’s concepts, scenarios, methods, and applications. Specifically, as a category collection of cutting-edge studies, the intention behind this article is to serve as a comprehensive resource for researchers and practitioners seeking an introduction to machine unlearning and its formulations, design criteria, removal requests, algorithms, and applications. In addition, we aim to highlight the key findings, current trends, and new research areas that have not yet featured the use of machine unlearning but could benefit greatly from it. We hope this survey serves as a valuable resource for ML researchers and those seeking to innovate privacy technologies. Our resources are publicly available at this https URL.

AI Model Disgorgement: Methods and Choices

  • https://arxiv.org/abs/2304.03545
  • Alessandro Achille, Michael Kearns, Carson Klingenberg, Stefano Soatto Responsible use of data is an indispensable part of any machine learning (ML) implementation. ML developers must carefully collect and curate their datasets, and document their provenance. They must also make sure to respect intellectual property rights, preserve individual privacy, and use data in an ethical way. Over the past few years, ML models have significantly increased in size and complexity. These models require a very large amount of data and compute capacity to train, to the extent that any defects in the training corpus cannot be trivially remedied by retraining the model from scratch. Despite sophisticated controls on training data and a significant amount of effort dedicated to ensuring that training corpora are properly composed, the sheer volume of data required for the models makes it challenging to manually inspect each datum comprising a training corpus. One potential fix for training corpus data defects is model disgorgement – the elimination of not just the improperly used data, but also the effects of improperly used data on any component of an ML model. Model disgorgement techniques can be used to address a wide range of issues, such as reducing bias or toxicity, increasing fidelity, and ensuring responsible usage of intellectual property. In this paper, we introduce a taxonomy of possible disgorgement methods that are applicable to modern ML systems. In particular, we investigate the meaning of “removing the effects” of data in the trained model in a way that does not require retraining from scratch.

[14]: Domain Centered FMs


DomainAdapt

In this session, our readings cover:

Required Readings:

Large Language Models for Software Engineering: A Systematic Literature Review

  • Large Language Models (LLMs) have significantly impacted numerous domains, including Software Engineering (SE). Many recent publications have explored LLMs applied to various SE tasks. Nevertheless, a comprehensive understanding of the application, effects, and possible limitations of LLMs on SE is still in its early stages. To bridge this gap, we conducted a systematic literature review on LLM4SE, with a particular focus on understanding how LLMs can be exploited to optimize processes and outcomes. We collect and analyze 229 research papers from 2017 to 2023 to answer four key research questions (RQs). In RQ1, we categorize different LLMs that have been employed in SE tasks, characterizing their distinctive features and uses. In RQ2, we analyze the methods used in data collection, preprocessing, and application highlighting the role of well-curated datasets for successful LLM for SE implementation. RQ3 investigates the strategies employed to optimize and evaluate the performance of LLMs in SE. Finally, RQ4 examines the specific SE tasks where LLMs have shown success to date, illustrating their practical contributions to the field. From the answers to these RQs, we discuss the current state-of-the-art and trends, identifying gaps in existing research, and flagging promising areas for future study.

More Readings:

Large language models generate functional protein sequences across diverse families

  • https://pubmed.ncbi.nlm.nih.gov/36702895/
  • Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

Large Language Models in Law: A Survey

  • https://arxiv.org/abs/2312.03718
  • The advent of artificial intelligence (AI) has significantly impacted the traditional judicial industry. Moreover, recently, with the development of AI-generated content (AIGC), AI and law have found applications in various domains, including image recognition, automatic text generation, and interactive chat. With the rapid emergence and growing popularity of large models, it is evident that AI will drive transformation in the traditional judicial industry. However, the application of legal large language models (LLMs) is still in its nascent stage. Several challenges need to be addressed. In this paper, we aim to provide a comprehensive survey of legal LLMs. We not only conduct an extensive survey of LLMs, but also expose their applications in the judicial system. We first provide an overview of AI technologies in the legal field and showcase the recent research in LLMs. Then, we discuss the practical implementation presented by legal LLMs, such as providing legal advice to users and assisting judges during trials. In addition, we explore the limitations of legal LLMs, including data, algorithms, and judicial practice. Finally, we summarize practical recommendations and propose future development directions to address these challenges.

ChemLLM: A Chemical Large Language Model

  • https://arxiv.org/abs/2402.06852
  • Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model’s ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model traini…

FunSearch: Making new discoveries in mathematical sciences using Large Language Models

  • https://deepmind.google/discover/blog/funsearch-making-new-discoveries-in-mathematical-sciences-using-large-language-models/

Transforming the future of music creation

  • https://deepmind.google/discover/blog/transforming-the-future-of-music-creation/

Segment Anything

  • https://arxiv.org/abs/2304.02643
  • We introduce the Segment Anything (SA) project: a new task, model, and dataset for image segmentation. Using our efficient model in a data collection loop, we built the largest segmentation dataset to date (by far), with over 1 billion masks on 11M licensed and privacy respecting images. The model is designed and trained to be promptable, so it can transfer zero-shot to new image distributions and tasks. We evaluate its capabilities on numerous tasks and find that its zero-shot performance is impressive – often competitive with or even superior to prior fully supervised results. We are releasing the Segment Anything Model (SAM) and corresponding dataset (SA-1B) of 1B masks and 11M images at this https URL to foster research into foundation models for computer vision.

EMO: Emote Portrait Alive - Generating Expressive Portrait Videos with Audio2Video Diffusion Model under Weak Conditions

  • In this work, we tackle the challenge of enhancing the realism and expressiveness in talking head video generation by focusing on the dynamic and nuanced relationship between audio cues and facial movements. We identify the limitations of traditional techniques that often fail to capture the full spectrum of human expressions and the uniqueness of individual facial styles. To address these issues, we propose EMO, a novel framework that utilizes a direct audio-to-video synthesis approach, bypassing the need for intermediate 3D models or facial landmarks. Our method ensures seamless frame transitions and consistent identity preservation throughout the video, resulting in highly expressive and lifelike animations. Experimental results demonsrate that EMO is able to produce not only convincing speaking videos but also singing videos in various styles, significantly outperforming existing state-of-the-art methodologies in terms of expressiveness and realism.

Sora: A Review on Background, Technology, Limitations, and Opportunities of Large Vision Models

  • Yixin Liu, Kai Zhang, Yuan Li, Zhiling Yan, Chujie Gao, Ruoxi Chen, Zhengqing Yuan, Yue Huang, Hanchi Sun, Jianfeng Gao, Lifang He, Lichao Sun
  • Sora is a text-to-video generative AI model, released by OpenAI in February 2024. The model is trained to generate videos of realistic or imaginative scenes from text instructions and show potential in simulating the physical world. Based on public technical reports and reverse engineering, this paper presents a comprehensive review of the model’s background, related technologies, applications, remaining challenges, and future directions of text-to-video AI models. We first trace Sora’s development and investigate the underlying technologies used to build this “world simulator”. Then, we describe in detail the applications and potential impact of Sora in multiple industries ranging from film-making and education to marketing. We discuss the main challenges and limitations that need to be addressed to widely deploy Sora, such as ensuring safe and unbiased video generation. Lastly, we discuss the future development of Sora and video generation models in general, and how advancements in the field could enable new ways of human-AI interaction, boosting productivity and creativity of video generation.

BloombergGPT: A Large Language Model for Finance

  • https://arxiv.org/abs/2303.17564
  • The use of NLP in the realm of financial technology is broad and complex, with applications ranging from sentiment analysis and named entity recognition to question answering. Large Language Models (LLMs) have been shown to be effective on a variety of tasks; however, no LLM specialized for the financial domain has been reported in literature. In this work, we present BloombergGPT, a 50 billion parameter language model that is trained on a wide range of financial data. We construct a 363 billion token dataset based on Bloomberg’s extensive data sources, perhaps the largest domain-specific dataset yet, augmented with 345 billion tokens from general purpose datasets. We validate BloombergGPT on standard LLM benchmarks, open financial benchmarks, and a suite of internal benchmarks that most accurately reflect our intended usage. Our mixed dataset training leads to a model that outperforms existing models on financial tasks by significant margins without sacrificing performance on general LLM benchmarks. Additionally, we explain our modeling choices, training process, and evaluation methodology. We release Training Chronicles (Appendix C) detailing our experience in training BloombergGPT.

Emu Video: Factorizing Text-to-Video Generation by Explicit Image Conditioning

  • https://arxiv.org/abs/2311.10709
  • We present Emu Video, a text-to-video generation model that factorizes the generation into two steps: first generating an image conditioned on the text, and then generating a video conditioned on the text and the generated image. We identify critical design decisions–adjusted noise schedules for diffusion, and multi-stage training–that enable us to directly generate high quality and high resolution videos, without requiring a deep cascade of models as in prior work. In human evaluations, our generated videos are strongly preferred in quality compared to all prior work–81% vs. Google’s Imagen Video, 90% vs. Nvidia’s PYOCO, and 96% vs. Meta’s Make-A-Video. Our model outperforms commercial solutions such as RunwayML’s Gen2 and Pika Labs. Finally, our factorizing approach naturally lends itself to animating images based on a user’s text prompt, where our generations are preferred 96% over prior work.

[15]: Knowledge Augmented FMs


RAG

In this session, our readings cover:

Required Readings:

Retrieval-Augmented Generation for AI-Generated Content: A Survey

  • https://arxiv.org/abs/2402.19473v1
  • The development of Artificial Intelligence Generated Content (AIGC) has been facilitated by advancements in model algorithms, scalable foundation model architectures, and the availability of ample high-quality datasets. While AIGC has achieved remarkable performance, it still faces challenges, such as the difficulty of maintaining up-to-date and long-tail knowledge, the risk of data leakage, and the high costs associated with training and inference. Retrieval-Augmented Generation (RAG) has recently emerged as a paradigm to address such challenges. In particular, RAG introduces the information retrieval process, which enhances AIGC results by retrieving relevant objects from available data stores, leading to greater accuracy and robustness. In this paper, we comprehensively review existing efforts that integrate RAG technique into AIGC scenarios. We first classify RAG foundations according to how the retriever augments the generator. We distill the fundamental abstractions of the augmentation methodologies for various retrievers and generators. This unified perspective encompasses all RAG scenarios, illuminating advancements and pivotal technologies that help with potential future progress. We also summarize additional enhancements methods for RAG, facilitating effective engineering and implementation of RAG systems. Then from another view, we survey on practical applications of RAG across different modalities and tasks, offering valuable references for researchers and practitioners. Furthermore, we introduce the benchmarks for RAG, discuss the limitations of current RAG systems, and suggest potential directions for future research. Project: this https URL

Retrieval-Augmented Generation for Large Language Models: A Survey

  • https://arxiv.org/abs/2312.10997
  • Large language models (LLMs) demonstrate powerful capabilities, but they still face challenges in practical applications, such as hallucinations, slow knowledge updates, and lack of transparency in answers. Retrieval-Augmented Generation (RAG) refers to the retrieval of relevant information from external knowledge bases before answering questions with LLMs. RAG has been demonstrated to significantly enhance answer accuracy, reduce model hallucination, particularly for knowledge-intensive tasks. By citing sources, users can verify the accuracy of answers and increase trust in model outputs. It also facilitates knowledge updates and the introduction of domain-specific knowledge. RAG effectively combines the parameterized knowledge of LLMs with non-parameterized external knowledge bases, making it one of the most important methods for implementing large language models. This paper outlines the development paradigms of RAG in the era of LLMs, summarizing three paradigms: Naive RAG, Advanced RAG, and Modular RAG. It then provides a summary and organization of the three main components of RAG: retriever, generator, and augmentation methods, along with key technologies in each component. Furthermore, it discusses how to evaluate the effectiveness of RAG models, introducing two evaluation methods for RAG, emphasizing key metrics and abilities for evaluation, and presenting the latest automatic evaluation framework. Finally, potential future research directions are introduced from three aspects: vertical optimization, horizontal scalability, and the technical stack and ecosystem of RAG.

More Readings:

Sora: A Review on Background, Technology, Limitations, and Opportunities of Large Vision Models

  • Yixin Liu, Kai Zhang, Yuan Li, Zhiling Yan, Chujie Gao, Ruoxi Chen, Zhengqing Yuan, Yue Huang, Hanchi Sun, Jianfeng Gao, Lifang He, Lichao Sun
  • Sora is a text-to-video generative AI model, released by OpenAI in February 2024. The model is trained to generate videos of realistic or imaginative scenes from text instructions and show potential in simulating the physical world. Based on public technical reports and reverse engineering, this paper presents a comprehensive review of the model’s background, related technologies, applications, remaining challenges, and future directions of text-to-video AI models. We first trace Sora’s development and investigate the underlying technologies used to build this “world simulator”. Then, we describe in detail the applications and potential impact of Sora in multiple industries ranging from film-making and education to marketing. We discuss the main challenges and limitations that need to be addressed to widely deploy Sora, such as ensuring safe and unbiased video generation. Lastly, we discuss the future development of Sora and video generation models in general, and how advancements in the field could enable new ways of human-AI interaction, boosting productivity and creativity of video generation.

A Comprehensive Study of Knowledge Editing for Large Language Models

  • https://arxiv.org/abs/2401.01286
  • Large Language Models (LLMs) have shown extraordinary capabilities in understanding and generating text that closely mirrors human communication. However, a primary limitation lies in the significant computational demands during training, arising from their extensive parameterization. This challenge is further intensified by the dynamic nature of the world, necessitating frequent updates to LLMs to correct outdated information or integrate new knowledge, thereby ensuring their continued relevance. Note that many applications demand continual model adjustments post-training to address deficiencies or undesirable behaviors. There is an increasing interest in efficient, lightweight methods for on-the-fly model modifications. To this end, recent years have seen a burgeoning in the techniques of knowledge editing for LLMs, which aim to efficiently modify LLMs’ behaviors within specific domains while preserving overall performance across various inputs. In this paper, we first define the knowledge editing problem and then provide a comprehensive review of cutting-edge approaches. Drawing inspiration from educational and cognitive research theories, we propose a unified categorization criterion that classifies knowledge editing methods into three groups: resorting to external knowledge, merging knowledge into the model, and editing intrinsic knowledge. Furthermore, we introduce a new benchmark, KnowEdit, for a comprehensive empirical evaluation of representative knowledge editing approaches. Additionally, we provide an in-depth analysis of knowledge location, which can give a deeper understanding of the knowledge structures inherent within LLMs. Finally, we discuss several potential applications of knowledge editing, outlining its broad and impactful implications.

Even More

A Survey of Table Reasoning with Large Language Models

  • Xuanliang Zhang, Dingzirui Wang, Longxu Dou, Qingfu Zhu, Wanxiang Che
  • https://arxiv.org/abs/2402.08259
  • Table reasoning, which aims to generate the corresponding answer to the question following the user requirement according to the provided table, and optionally a text description of the table, effectively improving the efficiency of obtaining information. Recently, using Large Language Models (LLMs) has become the mainstream method for table reasoning, because it not only significantly reduces the annotation cost but also exceeds the performance of previous methods. However, existing research still lacks a summary of LLM-based table reasoning works. Due to the existing lack of research, questions about which techniques can improve table reasoning performance in the era of LLMs, why LLMs excel at table reasoning, and how to enhance table reasoning abilities in the future, remain largely unexplored. This gap significantly limits progress in research. To answer the above questions and advance table reasoning research with LLMs, we present this survey to analyze existing research, inspiring future work. In this paper, we analyze the mainstream techniques used to improve table reasoning performance in the LLM era, and the advantages of LLMs compared to pre-LLMs for solving table reasoning. We provide research directions from both the improvement of existing methods and the expansion of practical applications to inspire future research.

[16]: Decision Transformers


RL AGI

Decision Transformer: Reinforcement Learning via Sequence Modeling

  • Lili Chen, Kevin Lu, Aravind Rajeswaran, Kimin Lee, Aditya Grover, Michael Laskin, Pieter Abbeel, Aravind Srinivas, Igor Mordatch
  • https://arxiv.org/abs/2106.01345
  • We introduce a framework that abstracts Reinforcement Learning (RL) as a sequence modeling problem. This allows us to draw upon the simplicity and scalability of the Transformer architecture, and associated advances in language modeling such as GPT-x and BERT. In particular, we present Decision Transformer, an architecture that casts the problem of RL as conditional sequence modeling. Unlike prior approaches to RL that fit value functions or compute policy gradients, Decision Transformer simply outputs the optimal actions by leveraging a causally masked Transformer. By conditioning an autoregressive model on the desired return (reward), past states, and actions, our Decision Transformer model can generate future actions that achieve the desired return. Despite its simplicity, Decision Transformer matches or exceeds the performance of state-of-the-art model-free offline RL baselines on Atari, OpenAI Gym, and Key-to-Door tasks.

Prompting Decision Transformer for Few-Shot Policy Generalization

  • Mengdi Xu, Yikang Shen, Shun Zhang, Yuchen Lu, Ding Zhao, Joshua B. Tenenbaum, Chuang Gan
  • https://arxiv.org/abs/2206.13499
  • Humans can leverage prior experience and learn novel tasks from a handful of demonstrations. In contrast to offline meta-reinforcement learning, which aims to achieve quick adaptation through better algorithm design, we investigate the effect of architecture inductive bias on the few-shot learning capability. We propose a Prompt-based Decision Transformer (Prompt-DT), which leverages the sequential modeling ability of the Transformer architecture and the prompt framework to achieve few-shot adaptation in offline RL. We design the trajectory prompt, which contains segments of the few-shot demonstrations, and encodes task-specific information to guide policy generation. Our experiments in five MuJoCo control benchmarks show that Prompt-DT is a strong few-shot learner without any extra finetuning on unseen target tasks. Prompt-DT outperforms its variants and strong meta offline RL baselines by a large margin with a trajectory prompt containing only a few timesteps. Prompt-DT is also robust to prompt length changes and can generalize to out-of-distribution (OOD) environments.

[17]: A Generalist Agent + offline RL + UniMask


RL AGI
Papers Paper URL Abstract
A Generalist Agent URL Gato, works as a multi-modal, multi-task, multi-embodiment generalist policy. The same network with the same weights can play Atari, caption images, chat, stack blocks with a real robot arm and much more, deciding based on its context whether to output text, joint torques, button presses, or other tokens.
Why should we prefer offline reinforcement learning over behavioral cloning? ICLR 2022 URL natural to ask: when can an offline RL method outperform BC with an equal amount of expert data, even when BC is a natural choice?
Uni[MASK]: Unified Inference in Sequential Decision Problems URL show how sequential decision making tasks can be thought of in terms of corresponding input maskings, enabling the training of a single model to perform all tasks at once. applies naturally to sequential decision making, where many well-studied tasks like behavior cloning, offline RL, inverse dynamics, and waypoint conditioning correspond to different sequence maskings over a sequence of states, actions, and returns.



Here is a name list of posts!


Decision Transformers

1 minute read

Decision Transformer: Reinforcement Learning via Sequence Modeling Lili Chen, Kevin Lu, Aravind Rajeswaran, Kimin Lee, Aditya Grover, Michael Laskin, Piet...