Shrey Jain

Shrey Jain, Zoë Hitzig, Pamela Mishkin

Generative AI models perturb the foundations of effective human communication. They present new challenges to contextual confidence, disrupting participants' ability to identify the authentic context of communication and their ability to protect communication from reuse and recombination outside its intended context. In this paper, we describe strategies--tools, technologies and policies--that aim to stabilize communication in the face of these challenges. The strategies we discuss fall into two broad categories. Containment strategies aim to reassert context in environments where it is currently threatened--a reaction to the context-free expectations and norms established by the internet. Mobilization strategies, by contrast, view the rise of generative AI as an opportunity to proactively set new and higher expectations around privacy and authenticity in mediated communication.

Yasha Ektefaie, Leo Cui, Shrey Jain et al.

Phylogenetic trees are hybrid objects: branch lengths vary continuously, while topologies change discretely through edge contractions and expansions. Billera-Holmes-Vogtmann (BHV) tree space provides a canonical geometry for this structure, representing each resolved topology as a Euclidean orthant and topological changes as motion across shared lower-dimensional boundaries. We introduce PhylaFlow, a hybrid flow-matching model that learns posterior-basin transport in BHV tree space. PhylaFlow is trained on BHV geodesic paths from random starting trees to short-run posterior samples, coupling continuous branch-length motion within orthants with learned boundary events and discrete topology transitions. We evaluate the learned geometry operationally: if the flow reaches posterior-relevant regions, finite-budget Bayesian refinement initialized from, or guided by, its terminal trees should recover posterior-supported topologies more efficiently. Across DS1-DS8 phylogenetic posterior benchmarks, PhylaFlow substantially reduces initial Tree-KL relative to classical initializers. After finite-budget MrBayes refinement, direct PhylaFlow improves early and intermediate topology-recovery trajectories on most datasets, while split-guided PhylaFlow-MCMC obtains the strongest hard-case results. The best PhylaFlow variant outperforms short-warmup on seven of eight datasets and PhyloGFN on five of eight under the same refinement budget. In a joint sequence-conditioned experiment, sequence embeddings steer posterior split recovery, although exact posterior topology recovery remains preliminary. These results show that hybrid flow matching can learn actionable transport in BHV tree space and provide a geometry-aware proposal mechanism for Bayesian phylogenetic inference.

Aaditya Bhat, Shrey Jain

CLIP (Contrastive Language-Image Pre-training) models developed by OpenAI have achieved outstanding results on various image recognition and retrieval tasks, displaying strong zero-shot performance. This means that they are able to perform effectively on tasks for which they have not been explicitly trained. Inspired by the success of OpenAI CLIP, a new publicly available dataset called LAION-5B was collected which resulted in the development of open ViT-H/14, ViT-G/14 models that outperform the OpenAI L/14 model. The LAION-5B dataset also released an approximate nearest neighbor index, with a web interface for search & subset creation. In this paper, we evaluate the performance of various CLIP models as zero-shot face recognizers. Our findings show that CLIP models perform well on face recognition tasks, but increasing the size of the CLIP model does not necessarily lead to improved accuracy. Additionally, we investigate the robustness of CLIP models against data poisoning attacks by testing their performance on poisoned data. Through this analysis, we aim to understand the potential consequences and misuse of search engines built using CLIP models, which could potentially function as unintentional face recognition engines.

Shrey Jain, Camille Bruckmann, Chase McDougall

In this paper we investigate the correlation between NFT valuations and various features from three primary categories: public market data, NFT metadata, and social trends data.

Shrey Jain, Connor Spelliscy, Samuel Vance-Law et al.

AI-enabled tools have become sophisticated enough to allow a small number of individuals to run disinformation campaigns of an unprecedented scale. Privacy-preserving identity attestations can drastically reduce instances of impersonation and make disinformation easy to identify and potentially hinder. By understanding how identity attestations are positioned across the spectrum of decentralization, we can gain a better understanding of the costs and benefits of various attestations. In this paper, we discuss attestation types, including governmental, biometric, federated, and web of trust-based, and include examples such as e-Estonia, China's social credit system, Worldcoin, OAuth, X (formerly Twitter), Gitcoin Passport, and EAS. We believe that the most resilient systems create an identity that evolves and is connected to a network of similarly evolving identities that verify one another. In this type of system, each entity contributes its respective credibility to the attestation process, creating a larger, more comprehensive set of attestations. We believe these systems could be the best approach to authenticating identity and protecting against some of the threats to democracy that AI can pose in the hands of malicious actors. However, governments will likely attempt to mitigate these risks by implementing centralized identity authentication systems; these centralized systems could themselves pose risks to the democratic processes they are built to defend. We therefore recommend that policymakers support the development of standards-setting organizations for identity, provide legal clarity for builders of decentralized tooling, and fund research critical to effective identity authentication systems.

Jaiveer Gill, Ratul Chakraborty, Reetham Gubba et al.

The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for development with a new computational tool. We introduce various methods to detect and cluster chemical compounds based on their SMILES data. Our first method, analyzing the graphical structures of chemical compounds using embedding data, employs vector search to meet our threshold value. The results yielded pronounced, concentrated clusters, and the method produced favorable results in querying and understanding the compounds. We also used natural language description embeddings stored in a vector database with GPT3.5, which outperforms the base model. Thus, we introduce a similarity search and clustering algorithm to aid in searching for and interacting with molecules, enhancing efficiency in chemical exploration and enabling future development of emergent properties in molecular property prediction models.

Tobin South, Alexander Camuto, Shrey Jain et al. · mit

In a world of increasing closed-source commercial machine learning models, model evaluations from developers must be taken at face value. These benchmark results-whether over task accuracy, bias evaluations, or safety checks-are traditionally impossible to verify by a model end-user without the costly or impossible process of re-performing the benchmark on black-box model outputs. This work presents a method of verifiable model evaluation using model inference through zkSNARKs. The resulting zero-knowledge computational proofs of model outputs over datasets can be packaged into verifiable evaluation attestations showing that models with fixed private weights achieve stated performance or fairness metrics over public inputs. We present a flexible proving system that enables verifiable attestations to be performed on any standard neural network model with varying compute requirements. For the first time, we demonstrate this across a sample of real-world models and highlight key challenges and design solutions. This presents a new transparency paradigm in the verifiable evaluation of private models.

Cliff Wong, Sam Preston, Qianchu Liu et al. · microsoft-research

A significant fraction of real-world patient information resides in unstructured clinical text. Medical abstraction extracts and normalizes key structured attributes from free-text clinical notes, which is the prerequisite for a variety of important downstream applications, including registry curation, clinical trial operations, and real-world evidence generation. Prior medical abstraction methods typically resort to building attribute-specific models, each of which requires extensive manual effort such as rule creation or supervised label annotation for the individual attribute, thus limiting scalability. In this paper, we show that existing frontier models already possess the universal abstraction capability for scaling medical abstraction to a wide range of clinical attributes. We present UniMedAbstractor (UMA), a unifying framework for zero-shot medical abstraction with a modular, customizable prompt template and the selection of any frontier large language models. Given a new attribute for abstraction, users only need to conduct lightweight prompt adaptation in UMA to adjust the specification in natural languages. Compared to traditional methods, UMA eliminates the need for attribute-specific training labels or handcrafted rules, thus substantially reducing the development time and cost. We conducted a comprehensive evaluation of UMA in oncology using a wide range of marquee attributes representing the cancer patient journey. These include relatively simple attributes typically specified within a single clinical note (e.g. performance status), as well as complex attributes requiring sophisticated reasoning across multiple notes at various time points (e.g. tumor staging). Based on a single frontier model such as GPT-4o, UMA matched or even exceeded the performance of state-of-the-art attribute-specific methods, each of which was tailored to the individual attribute.

Alyssa Unell, Noel C. F. Codella, Sam Preston et al.

The National Comprehensive Cancer Network (NCCN) provides evidence-based guidelines for cancer treatment. Translating complex patient presentations into guideline-compliant treatment recommendations is time-intensive, requires specialized expertise, and is prone to error. Advances in large language model (LLM) capabilities promise to reduce the time required to generate treatment recommendations and improve accuracy. We present an LLM agent-based approach to automatically generate guideline-concordant treatment trajectories for patients with non-small cell lung cancer (NSCLC). Our contributions are threefold. First, we construct a novel longitudinal dataset of 121 cases of NSCLC patients that includes clinical encounters, diagnostic results, and medical histories, each expertly annotated with the corresponding NCCN guideline trajectories by board-certified oncologists. Second, we demonstrate that existing LLMs possess domain-specific knowledge that enables high-quality proxy benchmark generation for both model development and evaluation, achieving strong correlation (Spearman coefficient r=0.88, RMSE = 0.08) with expert-annotated benchmarks. Third, we develop a hybrid approach combining expensive human annotations with model consistency information to create both the agent framework that predicts the relevant guidelines for a patient, as well as a meta-classifier that verifies prediction accuracy with calibrated confidence scores for treatment recommendations (AUROC=0.800), a critical capability for communicating the accuracy of outputs, custom-tailoring tradeoffs in performance, and supporting regulatory compliance. This work establishes a framework for clinically viable LLM-based guideline adherence systems that balance accuracy, interpretability, and regulatory requirements while reducing annotation costs, providing a scalable pathway toward automated clinical decision support.

Matthias Blondeel, Noel Codella, Sam Preston et al.

Molecular Tumor Boards (MTBs) are multidisciplinary forums where oncology specialists collaboratively assess complex patient cases to determine optimal treatment strategies. A central element of this process is the patient summary, typically compiled by a medical oncologist, radiation oncologist, or surgeon, or their trained medical assistant, who distills heterogeneous medical records into a concise narrative to facilitate discussion. This manual approach is often labor-intensive, subjective, and prone to omissions of critical information. To address these limitations, we introduce the Healthcare Agent Orchestrator (HAO), a Large Language Model (LLM)-driven AI agent that coordinates a multi-agent clinical workflow to generate accurate and comprehensive patient summaries for MTBs. Evaluating predicted patient summaries against ground truth presents additional challenges due to stylistic variation, ordering, synonym usage, and phrasing differences, which complicate the measurement of both succinctness and completeness. To overcome these evaluation hurdles, we propose TBFact, a ``model-as-a-judge'' framework designed to assess the comprehensiveness and succinctness of generated summaries. Using a benchmark dataset derived from de-identified tumor board discussions, we applied TBFact to evaluate our Patient History agent. Results show that the agent captured 94% of high-importance information (including partial entailments) and achieved a TBFact recall of 0.84 under strict entailment criteria. We further demonstrate that TBFact enables a data-free evaluation framework that institutions can deploy locally without sharing sensitive clinical data. Together, HAO and TBFact establish a robust foundation for delivering reliable and scalable support to MTBs.