Michael Pokorny
Abstract:With the rapid advancement of large language models, brain-language decoding has achieved remarkable progress. However, it remains unclear whether decoded content genuinely reflects neural representations or is largely reconstructed by the language model itself. This ambiguity limits interpretability and hinders the investigation of intrinsic brain-language correspondence. To address this challenge, we propose MD-SigLIP. This margin-regularized structured semantic alignment framework directly aligns brain embeddings with text embeddings in a shared semantic space, enabling retrieval-based decoding. This formulation enables explicit modeling of the correspondence between neural representations and language semantics. Building upon duplicate-aware sigmoid contrastive learning, we introduce a listwise margin-regularized term that enforces structured ranking constraints between positive semantic clusters and negative samples. By modeling multi-positive semantic structure and margin-based ordering simultaneously, the method captures the manifold organization of language embeddings reflected in neural signals. Experiments demonstrate state-of-the-art retrieval performance under both full-vocabulary and subset evaluation settings.
Abstract:Text-Image-to-Video (TI2V) models are an emerging unified architecture, where a single model simultaneously supports text-to-video (T2V) and image-to-video (I2V) generation. Given a high-quality first frame or a detailed textual prompt, TI2V models unlock substantially better visual quality than their T2V mode, raising a natural question: can the capability elicited by such privileged conditions be internalized into the model's own base generation ability? A common approach toward this goal is model self-distillation. However, the most straightforward solution, supervised fine-tuning, follows an off-policy strategy: its supervision is confined to teacher-generated endpoints from a fixed offline distribution rather than student-visited states, lacking precise correction tailored to the evolving policy. Recent on-policy distillation methods instead suffer from condition-state mismatch, where supervision is steered toward the given first frame instead of the student's actual content, misleading the correction. To achieve self-distillation that absorbs the teacher's privileged prior while retaining precise policy correction, in this work, we propose Hybrid-Policy Self-Distillation (HPSD), a novel self-distillation framework where a single TI2V model acts as both teacher and student under different conditions: the teacher operates in TI2V mode with a high-quality first frame and an enhanced prompt, while the student runs in the base T2V mode with only the vanilla prompt. Specifically, the student inherits off-policy teacher trajectory points as anchors, locally refines them toward its own policy, and finally receives velocity-level supervision on these self-generated roll-outs. Extensive experiments demonstrate that HPSD significantly improves T2V performance while also delivering notable TI2V gains, effectively strengthening the model's base generation ability.
Abstract:Rejection sampling fine-tuning (RFT) is widely used to train code agents by generating trajectories on verifiable software engineering tasks, retaining those that pass the tests, and fine-tuning on the successful rollouts. However, even strong code agents repeatedly fail on a substantial fraction of such tasks, and standard RFT simply discards these failures. The discarded samples are precisely the hardest and most informative ones, drawn from verifiable instances that are costly to curate. Stronger base models may reduce the number of failures, but the remaining hard cases still define the frontier for further improvement. We propose FailForge, an agentic framework that converts failed rollouts into training signal. For each failed instance, an agent diagnoses the failure from error feedback and execution traces, distills the diagnosis into a concise and actionable skill, and injects the skill into the agent context for a guided second attempt. Trajectories that succeed under skill guidance are folded back into the RFT corpus. Crucially, the skill is removed at training time, so the model internalizes the recovered behavior rather than relying on external hints at inference. FailForge recovers over 26% of previously failed instances at marginal additional cost, and training Qwen3.5-4B on the augmented corpus improves the SWE-bench Verified resolve rate by 6.6 points over a strong RFT baseline, with gains concentrated on the hardest problems.
Abstract:Epitopes determine where antibodies bind antigens and shape downstream therapeutic properties such as functional blockade and escape resistance, making epitope understanding central to antibody drug discovery. Although large language models (LLMs) have shown strong biomedical reasoning ability, it remains unclear whether they can infer epitope information directly from antigen and antibody sequences. Existing epitope resources typically focus on isolated prediction tasks or rely on specialized structural settings, while general protein benchmarks do not evaluate epitope-centered decisions across the antibody development workflow. To address this gap, we introduce EpiBench, a closed-book, sequence-based, and automatically scorable benchmark for evaluating epitope reasoning in LLMs. EpiBench contains 1,609 curated samples grounded in structural antibody--antigen contacts, curated functional B-cell assays, and deep mutational scanning escape measurements. It covers five connected tasks: targetable region discovery, antibody-conditioned epitope identification, epitope binning, functional epitope assessment, and antibody escape assessment, with controlled sampling to reduce shortcut-based evaluation artifacts. We evaluate nine general-purpose LLMs and analyze their behavior through task-specific baselines, antigen length stratification, explicit-reasoning comparison, and failure-mode inspection. The results show that current LLMs capture partial epitope-related signals but remain limited in antibody-specific sequence grounding, long-context residue localization, and biologically grounded reasoning. Therefore, EpiBench provides a diagnostic testbed for measuring and improving sequence-aware biomedical LLMs toward reliable LLM-assisted antibody discovery.
Abstract:Deep search agents tackle challenging questions through long-horizon web interactions, a process that is both complex and fragile: small reasoning errors may propagate through long, noisy trajectories into fluent but incorrect answers. Diagnosing such failures is difficult, requiring the manual inspection of extremely long execution traces, which could be beyond human capacity. We therefore introduce SearchAuditBench, a benchmark that evaluates whether LLM auditors can localize, attribute, and repair these failures, thereby reducing the human burden. SearchAuditBench comprises 1,243 failed trajectories, averaging 73.1 messages and 65.1K tokens, collected from eight open-weight models on five deep-search benchmarks, each expert-annotated with the critical error step, a search-specific root cause, and a reference repair with grading rubrics. We further propose SearchAuditor, a multi-perspective auditing framework that effectively localizes, attributes, and repairs search-agent failures through evidence-grounded adjudication. Experimental results show that even the strongest baseline, when powered by a frontier model like GPT-5.5, attains only a 26.6% end-to-end pass rate. In contrast, our SearchAuditor consistently outperforms all baselines across different frontier models, achieving an end-to-end pass rate of 32.3%, and resuming failed runs with its repairs enables agents to better recover from errors.
Abstract:Training LLM-based search agents requires high-quality search data: tasks that demand genuine multi-hop retrieval and trajectories that use search tools effectively. Existing pipelines often depend on human-written tasks, expert demonstrations, or stronger teacher models. We present SearchMaster, a self-play framework that trains a single LLM from search tasks it generates, solves, and verifies in a local search environment. The key challenge is that self-generated tasks and rollouts can yield misleading signals: pseudo multi-hop questions, success-rate difficulty estimates that ignore search depth, and rollouts with excessive opening but little targeted evidence acquisition. SearchMaster addresses these failure modes with three controls. An Evidence-Chain Generator (ECG) grounds task generation in explicit cross-document evidence chains to reduce pseudo multi-hop questions. A Search-Depth Reward (SDR) scores task difficulty by the search depth of successful rollouts rather than success rate alone, keeping retained tasks search-intensive. An Over-Opening Penalty (OOP) regulates tool use by discouraging excessive document opening, avoiding long but shallow browsing. Verified Proposer and Solver rollouts are then jointly optimized with GRPO. Across six deep-search benchmarks, SearchMaster improves a Qwen3.5-9B backbone from 38.19% to 51.52% average accuracy, with a 30.1-point gain on BrowseComp-Plus. These results show that grounded and regulated self-play can provide effective search-agent training data without human-labeled QA pairs or expert demonstrations. The code is available at https://github.com/WentaoTan/SearchMaster.
Abstract:Modern predictive systems are expected to adapt their behavior to the specific situation they are facing. A clinical model should not treat every patient the same; a retrieval-augmented model should change its answer when given different evidence; a mixture-of-experts model should route different inputs to different experts. We call this capability context-adaptive inference: before predicting, the system uses information about the current context to specialize its parameters or computation for that instance. This article provides a unified view of context-adaptive inference across three traditions that are usually treated separately: (i) explicit adaptation in statistics (e.g. varying-coefficient models, local regression, hierarchical sharing), (ii) rapid task-specific adaptation in meta-learning and transfer, and (iii) implicit adaptation in large foundation models via prompting, retrieval, and expert routing. We formalize these approaches under a common objective: to map context $c$ to adapted parameters $θ(c)$, then to predict via $f(x; θ(c))$. Under squared loss, linear prediction heads, and fixed features, we prove that explicit parameter adaptation and implicit routing are mathematically equivalent to kernel ridge regression on joint features of inputs and context. Building on this bridge, we propose practical design principles and evaluation metrics including adaptation-efficiency, routing stability, and context-specific robustness to guide when to specialize, how to constrain that specialization, and how to audit context-adaptive models in deployment. Finally, we identify open problems in identifiability, robustness under distribution shift, and efficient large-scale adaptation, outlining design principles for methods that are scalable, reliable, and transparent in real-world settings.
Abstract:AI reasoning has become a central focus in contemporary artificial intelligence, largely driven by the success of large language models. However, mathematical research, which is characterized by non-linear derivation paths, rigorous logical requirements, and protracted exploration cycles, poses severe challenges for existing reasoning systems. To overcome these limitations, we present the MechMath Agent Team (MMAT), which is a large language model driven agent designed to serve as a co-pilot throughout the full cycle of mathematical research. We design a tripartite Harness Architecture that decouples system responsibilities into Control, Execution, and Augmentation planes, thereby reconciling rigorous logical control with the agility demanded by open-ended research. Building upon this framework, we instantiate three specialized agents: a Knowledge Base Manager, a Natural Language Prover, and a Formal Language Prover, all operating in a closed loop to produce formally certified mathematical proofs. We evaluate MMAT on open problems in Number Theory, Algebraic Complexity Theory, Differential Algebra, Operator Algebra, and Inequalities. Across a two-month deployment, 11 problems have been solved, demonstrating its capacity to act as a co-pilot throughout the entire research cycle. The contributions are threefold: a general decoupled Harness Architecture for multi-agent mathematical reasoning, its concrete instantiation in the MMAT system, and empirical validation on a diverse suite of open problems.
Abstract:On-policy distillation (OPD) offers superior capacity transfer by supervising student-sampled trajectories with dense token-level signals. To furnish high-quality supervision sources and thereby elevate the performance frontier of distillation, an intuitive direction is to infuse privileged information to either teacher or student itself. However, this additional input induces a potential failure mode we dub privilege illusion: a pattern that conflates the transferable capability gap that students are meant to close, and the information asymmetry gap that can only be mimicked but never replicated. This issue is further amplified by the inherent non-uniformity of token-level supervision, where only a small subset of tokens carries pivotal capability-bearing signals. To this end, we propose DOPD, an advantage-aware dual distillation paradigm that dynamically routes token-level supervision between privileged teacher and privileged student policies based on their advantage gap and relative probabilities. Each token receives supervision of different strength, objective, and strategy from either teacher or student itself, which transfers credible capability while simultaneously receiving auxiliary signals, to alleviate privilege illusion. Extensive experiments on both large language model (LLM) and vision-language model (VLM) settings demonstrate that DOPD consistently outperforms Vanilla OPD and other counterparts. Further results on stability, robustness, continual learning, and out-of-distribution tasks validate its superiority.
Abstract:Deploying multimodal foundation models as closed-loop policies increasingly requires conditioning actions on observations that are no longer visible. However, existing benchmarks either expose the full state, conflate hidden-state reconstruction with other agent skills, or test recall only after an episode has ended. We introduce RNG-Bench (Reconstructive Non-Markov Games), a benchmark suite designed to isolate a base model's ability to reconstruct past observations and act on them during multi-step interaction. RNG-Bench includes two complementary games: Matching Pairs, where card identities briefly revealed at specific locations must later be recalled, and 3D Maze, where egocentric views must be integrated into a spatial map. Both games are evaluated under a unified harness with three controlled difficulty axes: grid size, visual pattern, and observation modality. The benchmark further introduces a head-to-head duel protocol to control for instance-level variance and a Memory Gap metric that disentangles forgetting from poor action selection. The hardest configurations require contexts of roughly 128K tokens and 350 image inputs per episode, and remain far from saturated by frontier MLLMs. Memory Gap analysis shows that most residual errors stem from forgetting earlier observations rather than from suboptimal decision making. Finally, fine-tuning Qwen3.5-9B on optimal-policy rollouts and filtered model demonstrations improves performance on RNG-Bench and transfers to existing benchmarks without degrading general multimodal capability.