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Jul 29

HyPoradise: An Open Baseline for Generative Speech Recognition with Large Language Models

Advancements in deep neural networks have allowed automatic speech recognition (ASR) systems to attain human parity on several publicly available clean speech datasets. However, even state-of-the-art ASR systems experience performance degradation when confronted with adverse conditions, as a well-trained acoustic model is sensitive to variations in the speech domain, e.g., background noise. Intuitively, humans address this issue by relying on their linguistic knowledge: the meaning of ambiguous spoken terms is usually inferred from contextual cues thereby reducing the dependency on the auditory system. Inspired by this observation, we introduce the first open-source benchmark to utilize external large language models (LLMs) for ASR error correction, where N-best decoding hypotheses provide informative elements for true transcription prediction. This approach is a paradigm shift from the traditional language model rescoring strategy that can only select one candidate hypothesis as the output transcription. The proposed benchmark contains a novel dataset, HyPoradise (HP), encompassing more than 334,000 pairs of N-best hypotheses and corresponding accurate transcriptions across prevalent speech domains. Given this dataset, we examine three types of error correction techniques based on LLMs with varying amounts of labeled hypotheses-transcription pairs, which gains a significant word error rate (WER) reduction. Experimental evidence demonstrates the proposed technique achieves a breakthrough by surpassing the upper bound of traditional re-ranking based methods. More surprisingly, LLM with reasonable prompt and its generative capability can even correct those tokens that are missing in N-best list. We make our results publicly accessible for reproducible pipelines with released pre-trained models, thus providing a new evaluation paradigm for ASR error correction with LLMs.

  • 6 authors
·
Sep 27, 2023

Hypothesis Search: Inductive Reasoning with Language Models

Inductive reasoning is a core problem-solving capacity: humans can identify underlying principles from a few examples, which can then be robustly generalized to novel scenarios. Recent work has evaluated large language models (LLMs) on inductive reasoning tasks by directly prompting them yielding "in context learning." This can work well for straightforward inductive tasks, but performs very poorly on more complex tasks such as the Abstraction and Reasoning Corpus (ARC). In this work, we propose to improve the inductive reasoning ability of LLMs by generating explicit hypotheses at multiple levels of abstraction: we prompt the LLM to propose multiple abstract hypotheses about the problem, in natural language, then implement the natural language hypotheses as concrete Python programs. These programs can be directly verified by running on the observed examples and generalized to novel inputs. Because of the prohibitive cost of generation with state-of-the-art LLMs, we consider a middle step to filter the set of hypotheses that will be implemented into programs: we either ask the LLM to summarize into a smaller set of hypotheses, or ask human annotators to select a subset of the hypotheses. We verify our pipeline's effectiveness on the ARC visual inductive reasoning benchmark, its variant 1D-ARC, and string transformation dataset SyGuS. On a random 40-problem subset of ARC, our automated pipeline using LLM summaries achieves 27.5% accuracy, significantly outperforming the direct prompting baseline (accuracy of 12.5%). With the minimal human input of selecting from LLM-generated candidates, the performance is boosted to 37.5%. (And we argue this is a lower bound on the performance of our approach without filtering.) Our ablation studies show that abstract hypothesis generation and concrete program representations are both beneficial for LLMs to perform inductive reasoning tasks.

  • 6 authors
·
Sep 11, 2023

Sparks of Science: Hypothesis Generation Using Structured Paper Data

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of scientifically informed hypotheses. However, current foundation models often struggle to produce scientific ideas that are both novel and feasible. One reason is the lack of a dedicated dataset that frames Scientific Hypothesis Generation (SHG) as a Natural Language Generation (NLG) task. In this paper, we introduce HypoGen, the first dataset of approximately 5500 structured problem-hypothesis pairs extracted from top-tier computer science conferences structured with a Bit-Flip-Spark schema, where the Bit is the conventional assumption, the Spark is the key insight or conceptual leap, and the Flip is the resulting counterproposal. HypoGen uniquely integrates an explicit Chain-of-Reasoning component that reflects the intellectual process from Bit to Flip. We demonstrate that framing hypothesis generation as conditional language modelling, with the model fine-tuned on Bit-Flip-Spark and the Chain-of-Reasoning (and where, at inference, we only provide the Bit), leads to improvements in the overall quality of the hypotheses. Our evaluation employs automated metrics and LLM judge rankings for overall quality assessment. We show that by fine-tuning on our HypoGen dataset we improve the novelty, feasibility, and overall quality of the generated hypotheses. The HypoGen dataset is publicly available at huggingface.co/datasets/UniverseTBD/hypogen-dr1.

  • 7 authors
·
Apr 17, 2025

Conditional Hypothesis Generation for LLM-Based Text Analysis with Researcher-Specified Covariates

A core goal of computational social science is to discover interpretable differences in how language varies across outcomes of interest, such as political affiliation or instructional quality. Recent LLM-based hypothesis generation methods describe such differences in natural language, but select for globally discriminative patterns without accounting for covariates that shape the data based on researchers' domain knowledge. When covariates are ignored, selected patterns can reflect confounds rather than differences of substantive interest. We introduce conditional hypothesis generation, a framework that incorporates researcher-specified covariates to steer hypothesis discovery toward differences that hold within relevant subgroups. Two challenges arise: the target subgroup may be underrepresented (stratum imbalance), and the direction of a difference may reverse across subgroups (sign reversal). We propose two econometrics-inspired methods: one introduces feature--covariate interactions to detect sign reversals, and the other applies within-stratum demeaning and inverse-frequency reweighting to equalize underrepresented strata. Synthetic experiments show each method outperforms global baselines in its targeted setting, and expert evaluation on two real-world datasets confirms that covariate-aware generation surfaces more useful hypotheses within relevant subgroups.

VerifyMAS: Hypothesis Verification for Failure Attribution in LLM Multi-Agent Systems

Large language model-driven multi-agent systems (LLM-MAS) excel at complex tasks, yet unreliable agents remain a key bottleneck to system-level reliability. Automatic failure attribution is therefore critical, but existing approaches, such as direct prediction of agent-error pairs and agent-first failure attribution, rely on local logs of agents and miss global failures that only manifest over full interaction trajectories, such as cross-step inconsistencies and inter-agent coordination errors. Moreover, directly predicting failures induces a large combinatorial search space, hindering fine-grained attribution. To address these challenges, we propose VerifyMAS, a hypothesis verification framework for agent failure attribution. Instead of directly predicting faulty agents and error types, VerifyMAS formulates and verifies failure hypotheses against full trajectories. This verification-based approach decomposes attribution into trajectory-level error validation and fine-grained agent localization, providing an error-first attribution approach that captures global failure patterns while substantially reducing the search space. We further introduce a hypothesis-based data construction strategy grounded in a structured error taxonomy and fine-tune a specialized LLM verifier model for trajectory-level failure verification and agent attribution. Experiments on Aegis-Bench and Who&When show that VerifyMAS consistently improves diverse backbone models, including open-source Qwen and API-based GPT models, outperforming prior methods without sacrificing inference efficiency for long multi-agent trajectories.

  • 5 authors
·
May 16

Phenomenal Yet Puzzling: Testing Inductive Reasoning Capabilities of Language Models with Hypothesis Refinement

The ability to derive underlying principles from a handful of observations and then generalize to novel situations -- known as inductive reasoning -- is central to human intelligence. Prior work suggests that language models (LMs) often fall short on inductive reasoning, despite achieving impressive success on research benchmarks. In this work, we conduct a systematic study of the inductive reasoning capabilities of LMs through iterative hypothesis refinement, a technique that more closely mirrors the human inductive process than standard input-output prompting. Iterative hypothesis refinement employs a three-step process: proposing, selecting, and refining hypotheses in the form of textual rules. By examining the intermediate rules, we observe that LMs are phenomenal hypothesis proposers (i.e., generating candidate rules), and when coupled with a (task-specific) symbolic interpreter that is able to systematically filter the proposed set of rules, this hybrid approach achieves strong results across inductive reasoning benchmarks that require inducing causal relations, language-like instructions, and symbolic concepts. However, they also behave as puzzling inductive reasoners, showing notable performance gaps between rule induction (i.e., identifying plausible rules) and rule application (i.e., applying proposed rules to instances), suggesting that LMs are proposing hypotheses without being able to actually apply the rules. Through empirical and human analyses, we further reveal several discrepancies between the inductive reasoning processes of LMs and humans, shedding light on both the potentials and limitations of using LMs in inductive reasoning tasks.

  • 11 authors
·
Oct 12, 2023

The Information Pathways Hypothesis: Transformers are Dynamic Self-Ensembles

Transformers use the dense self-attention mechanism which gives a lot of flexibility for long-range connectivity. Over multiple layers of a deep transformer, the number of possible connectivity patterns increases exponentially. However, very few of these contribute to the performance of the network, and even fewer are essential. We hypothesize that there are sparsely connected sub-networks within a transformer, called information pathways which can be trained independently. However, the dynamic (i.e., input-dependent) nature of these pathways makes it difficult to prune dense self-attention during training. But the overall distribution of these pathways is often predictable. We take advantage of this fact to propose Stochastically Subsampled self-Attention (SSA) - a general-purpose training strategy for transformers that can reduce both the memory and computational cost of self-attention by 4 to 8 times during training while also serving as a regularization method - improving generalization over dense training. We show that an ensemble of sub-models can be formed from the subsampled pathways within a network, which can achieve better performance than its densely attended counterpart. We perform experiments on a variety of NLP, computer vision and graph learning tasks in both generative and discriminative settings to provide empirical evidence for our claims and show the effectiveness of the proposed method.

  • 3 authors
·
Jun 2, 2023

The Specification as Quality Gate: Three Hypotheses on AI-Assisted Code Review

The dominant industry response to AI-generated code quality problems is to deploy AI reviewers. This paper argues that this response is structurally circular when executable specifications are absent: without an external reference, both the generating agent and the reviewing agent reason from the same artefact, share the same training distribution, and exhibit correlated failures. The review checks code against itself, not against intent. Three hypotheses are developed. First, that correlated errors in homogeneous LLM pipelines echo rather than cancel, a claim supported by convergent empirical evidence from multiple 2025-2026 studies and by three small contrived experiments reported here. The first two experiments are same-family (Claude reviewing Claude-generated code); the third extends to a cross-family panel of four models from three families. All use a planted bug corpus rather than a natural defect sample; they are directional evidence, not a controlled demonstration. Second, that executable specifications perform a domain transition in the Cynefin sense, converting enabling constraints into governing constraints and moving the problem from the complex domain to the complicated domain, a transition that AI makes economically viable at scale. Third, that the defect classes lying outside the reach of executable specifications form a well-defined residual, which is the legitimate and bounded target for AI review. The combined argument implies an architecture: specifications first, deterministic verification pipeline second, AI review only for the structural and architectural residual. This is not a claim that AI review is valueless. It is a claim about what it is actually for, and about what happens when it is deployed without the foundation that makes it non-circular.

  • 1 authors
·
Mar 25

Interpretable Hypothesis-Driven Trading:A Rigorous Walk-Forward Validation Framework for Market Microstructure Signals

We develop a rigorous walk-forward validation framework for algorithmic trading designed to mitigate overfitting and lookahead bias. Our methodology combines interpretable hypothesis-driven signal generation with reinforcement learning and strict out-of-sample testing. The framework enforces strict information set discipline, employs rolling window validation across 34 independent test periods, maintains complete interpretability through natural language hypothesis explanations, and incorporates realistic transaction costs and position constraints. Validating five market microstructure patterns across 100 US equities from 2015 to 2024, the system yields modest annualized returns (0.55%, Sharpe ratio 0.33) with exceptional downside protection (maximum drawdown -2.76%) and market-neutral characteristics (beta = 0.058). Performance exhibits strong regime dependence, generating positive returns during high-volatility periods (0.60% quarterly, 2020-2024) while underperforming in stable markets (-0.16%, 2015-2019). We report statistically insignificant aggregate results (p-value 0.34) to demonstrate a reproducible, honest validation protocol that prioritizes interpretability and extends naturally to advanced hypothesis generators, including large language models. The key empirical finding reveals that daily OHLCV-based microstructure signals require elevated information arrival and trading activity to function effectively. The framework provides complete mathematical specifications and open-source implementation, establishing a template for rigorous trading system evaluation that addresses the reproducibility crisis in quantitative finance research. For researchers, practitioners, and regulators, this work demonstrates that interpretable algorithmic trading strategies can be rigorously validated without sacrificing transparency or regulatory compliance.

  • 3 authors
·
Dec 14, 2025

Multi-hypotheses Conditioned Point Cloud Diffusion for 3D Human Reconstruction from Occluded Images

3D human shape reconstruction under severe occlusion due to human-object or human-human interaction is a challenging problem. Parametric models i.e., SMPL(-X), which are based on the statistics across human shapes, can represent whole human body shapes but are limited to minimally-clothed human shapes. Implicit-function-based methods extract features from the parametric models to employ prior knowledge of human bodies and can capture geometric details such as clothing and hair. However, they often struggle to handle misaligned parametric models and inpaint occluded regions given a single RGB image. In this work, we propose a novel pipeline, MHCDIFF, Multi-hypotheses Conditioned Point Cloud Diffusion, composed of point cloud diffusion conditioned on probabilistic distributions for pixel-aligned detailed 3D human reconstruction under occlusion. Compared to previous implicit-function-based methods, the point cloud diffusion model can capture the global consistent features to generate the occluded regions, and the denoising process corrects the misaligned SMPL meshes. The core of MHCDIFF is extracting local features from multiple hypothesized SMPL(-X) meshes and aggregating the set of features to condition the diffusion model. In the experiments on CAPE and MultiHuman datasets, the proposed method outperforms various SOTA methods based on SMPL, implicit functions, point cloud diffusion, and their combined, under synthetic and real occlusions. Our code is publicly available at https://donghwankim0101.github.io/projects/mhcdiff/ .

  • 2 authors
·
Oct 28, 2024

Revisiting the Hypothesis: Do pretrained Transformers Learn In-Context by Gradient Descent?

The emergence of In-Context Learning (ICL) in LLMs remains a significant phenomenon with little understanding. To explain ICL, recent studies try to theoretically connect it to Gradient Descent (GD). We ask, does this connection hold up in actual pre-trained models? We highlight the limiting assumptions in prior works that make their context considerably different from the practical context in which language models are trained. For example, the theoretical hand-constructed weights used in these studies have properties that don't match those of real LLMs. Furthermore, their experimental verification uses ICL objective (training models explicitly for ICL), which differs from the emergent ICL in the wild. We also look for evidence in real models. We observe that ICL and GD have different sensitivity to the order in which they observe demonstrations. Finally, we probe and compare the ICL vs. GD hypothesis in a natural setting. We conduct comprehensive empirical analyses on language models pre-trained on natural data (LLaMa-7B). Our comparisons of three performance metrics highlight the inconsistent behavior of ICL and GD as a function of various factors such as datasets, models, and the number of demonstrations. We observe that ICL and GD modify the output distribution of language models differently. These results indicate that the equivalence between ICL and GD remains an open hypothesis and calls for further studies.

  • 3 authors
·
Oct 12, 2023

Mela: Test-Time Memory Consolidation based on Transformation Hypothesis

Memory consolidation, the process by which transient experiences are transformed into stable, structured representations, is a foundational organizing principle in the human brain, yet it remains largely unexplored as a design principle for modern sequence models. In this work, we leverage established neuroscientific theories of memory consolidation and cross-frequency coupling to propose the Hierarchical Memory Module (HMM), a neural memory architecture composed of two functionally distinct sub-modules that operate at different update frequencies. Inspired by the transformation hypothesis, the low-frequency sub-module produces high-level representations that capture abstract, gist-level knowledge, while the high-frequency sub-module produces fine-grained representations that preserve richer episodic detail. The final memory output is dynamically reconstructed as a context-dependent combination of both representations, analogous to the reconstructive nature of human memory retrieval. We integrate HMM into a Transformer-based language decoder to form Mela, a family of memory-augmented language models that perform online memory consolidation at test time. To further exploit the multi-granularity memory representations produced by HMM, we introduce MemStack, a method that distributes different levels of memory features across the early layers of the decoder without introducing additional tokens. Experiments on language modeling demonstrate that Mela outperforms Transformer baselines across all the model sizes. Moreover, with the pretrained context length fixed at 4K, Mela maintains performance on significantly longer contexts, whereas Transformer baselines degrade rapidly beyond their training length. Extensive ablation studies validate the contribution of each component and provide guidance for practical configuration.

MusubiAI Musubi
·
May 10 1

The Master Key Hypothesis: Unlocking Cross-Model Capability Transfer via Linear Subspace Alignment

We investigate whether post-trained capabilities can be transferred across models without retraining, with a focus on transfer across different model scales. We propose the Master Key Hypothesis, which states that model capabilities correspond to directions in a low-dimensional latent subspace that induce specific behaviors and are transferable across models through linear alignment. Based on this hypothesis, we introduce UNLOCK, a training-free and label-free framework that extracts a capability direction by contrasting activations between capability-present and capability-absent Source variants, aligns it with a Target model through a low-rank linear transformation, and applies it at inference time to elicit the behavior. Experiments on reasoning behaviors, including Chain-of-Thought (CoT) and mathematical reasoning, demonstrate substantial improvements across model scales without training. For example, transferring CoT reasoning from Qwen1.5-14B to Qwen1.5-7B yields an accuracy gain of 12.1% on MATH, and transferring a mathematical reasoning direction from Qwen3-4B-Base to Qwen3-14B-Base improves AGIEval Math accuracy from 61.1% to 71.3%, surpassing the 67.8% achieved by the 14B post-trained model. Our analysis shows that the success of transfer depends on the capabilities learned during pre-training, and that our intervention amplifies latent capabilities by sharpening the output distribution toward successful reasoning trajectories.

  • 9 authors
·
Apr 7 2

Generating novel experimental hypotheses from language models: A case study on cross-dative generalization

Neural network language models (LMs) have been shown to successfully capture complex linguistic knowledge. However, their utility for understanding language acquisition is still debated. We contribute to this debate by presenting a case study where we use LMs as simulated learners to derive novel experimental hypotheses to be tested with humans. We apply this paradigm to study cross-dative generalization (CDG): productive generalization of novel verbs across dative constructions (she pilked me the ball/she pilked the ball to me) -- acquisition of which is known to involve a large space of contextual features -- using LMs trained on child-directed speech. We specifically ask: "what properties of the training exposure facilitate a novel verb's generalization to the (unmodeled) alternate construction?" To answer this, we systematically vary the exposure context in which a novel dative verb occurs in terms of the properties of the theme and recipient, and then analyze the LMs' usage of the novel verb in the unmodeled dative construction. We find LMs to replicate known patterns of children's CDG, as a precondition to exploring novel hypotheses. Subsequent simulations reveal a nuanced role of the features of the novel verbs' exposure context on the LMs' CDG. We find CDG to be facilitated when the first postverbal argument of the exposure context is pronominal, definite, short, and conforms to the prototypical animacy expectations of the exposure dative. These patterns are characteristic of harmonic alignment in datives, where the argument with features ranking higher on the discourse prominence scale tends to precede the other. This gives rise to a novel hypothesis that CDG is facilitated insofar as the features of the exposure context -- in particular, its first postverbal argument -- are harmonically aligned. We conclude by proposing future experiments that can test this hypothesis in children.

  • 2 authors
·
Aug 9, 2024 1

Towards Diverse Scientific Hypothesis Search with Large Language Models

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

  • 10 authors
·
Jun 9 2

The Cylindrical Representation Hypothesis for Language Model Steering

Steering is a widely used technique for controlling large language models, yet its effects are often unstable and hard to predict. Existing theoretical accounts are largely based on the Linear Representation Hypothesis (LRH). While LRH assumes that concepts can be orthogonalized for lossless control, this idealized mapping fails in real representations and cannot account for the observed unpredictability of steering. By relaxing LRH's orthogonality assumption while preserving linear representations, we show that overlapping concept contributions naturally yield a sample-specific axis-orthogonal structure. We formalize this as the Cylindrical Representation Hypothesis (CRH). In CRH, a central axis captures the main difference between concept absence and presence and drives concept generation. A surrounding normal plane controls steering sensitivity by determining how easily the axis can activate the target concept. Within this plane, only specific sensitive sectors strongly facilitate concept activation, while other sectors can suppress or delay it. While the surrounding normal plane can be reliably identified from difference vectors, the sensitive sector cannot, introducing intrinsic uncertainty at the sector level. This uncertainty provides a principled explanation for why steering outcomes often fluctuate even when using well-aligned directions. Our experiments verify the existence of the cylindrical structure and demonstrate that CRH provides a valid and practical way to interpret model steering behavior in real settings: https://github.com/mbzuai-nlp/CRH.

  • 10 authors
·
May 2

The Truthfulness Spectrum Hypothesis

Large language models (LLMs) have been reported to linearly encode truthfulness, yet recent work questions this finding's generality. We reconcile these views with the truthfulness spectrum hypothesis: the representational space contains directions ranging from broadly domain-general to narrowly domain-specific. To test this hypothesis, we systematically evaluate probe generalization across five truth types (definitional, empirical, logical, fictional, and ethical), sycophantic and expectation-inverted lying, and existing honesty benchmarks. Linear probes generalize well across most domains but fail on sycophantic and expectation-inverted lying. Yet training on all domains jointly recovers strong performance, confirming that domain-general directions exist despite poor pairwise transfer. The geometry of probe directions explains these patterns: Mahalanobis cosine similarity between probes near-perfectly predicts cross-domain generalization (R^2=0.98). Concept-erasure methods further isolate truth directions that are (1) domain-general, (2) domain-specific, or (3) shared only across particular domain subsets. Causal interventions reveal that domain-specific directions steer more effectively than domain-general ones. Finally, post-training reshapes truth geometry, pushing sycophantic lying further from other truth types, suggesting a representational basis for chat models' sycophantic tendencies. Together, our results support the truthfulness spectrum hypothesis: truth directions of varying generality coexist in representational space, with post-training reshaping their geometry. Code for all experiments is provided in https://github.com/zfying/truth_spec.

Toward Reliable Biomedical Hypothesis Generation: Evaluating Truthfulness and Hallucination in Large Language Models

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

  • 8 authors
·
May 20, 2025 2

The Piggyback Hypothesis of Generalization: Explaining and Mitigating Emergent Misalignment

The mechanisms behind LLMs' broad over-generalization beyond training examples remain unclear. Emergent misalignment (EM) offers a striking case study: finetuning on narrow tasks induces broad misalignment to semantically-unrelated test domains. In this work, we propose the Piggyback Hypothesis: the chat-template tokens can piggyback the finetuned behaviour onto out-of-domain queries. We validate this hypothesis by showing that subtle perturbations to the prefix (tokens preceding all user queries), or patching the prefix representations with those from the unfinetuned model, can restore alignment without changing the user query. Building on this finding, we propose Token-Regularized Finetuning (TReFT), which regularizes specific token representations during training to mitigate EM. Across different models and multiple EM-inducing datasets, TReFT reduces EM while preserving in-domain learning. On Llama-3.1-8B finetuned on the legal domain, TReFT achieves 33.5% more EM reduction than data interleaving with a retain set of aligned examples. We further show that TReFT extends to other narrow-finetuning settings, including abstention, tool use, and refusal (off-topic generalization is reduced by 54.3% on average), supporting the Piggyback Hypothesis. Broadly, our work highlights that LLMs may learn and generalize in unintended ways and suggests a path toward more constrained finetuning. It also calls for further study of how shared input features can piggyback model behavior across domains.

  • 6 authors
·
Jun 3

ProjectionBench: Evaluating Scientific Hypothesis Generation in LLMs Under Progressive Information Disclosure

Scientific discovery is an inherently creative and uncertain process, requiring reasoning beyond the recall of known knowledge. While many benchmarks have been proposed to evaluate large language model (LLM) performance on deep research tasks via multi-hop retrieval, their innovative reasoning abilities essential for true scientific discovery remain largely untested. We introduce a benchmark framework for evaluating model performance in scientific discovery and reasoning, building up from a raw problem to the classical null hypothesis test. In our framework, models initially receive only the topic and research question from a recent paper, with technical details progressively revealed. At each stage of information disclosure, the model is tasked with generating hypotheses that address the research question, which is compared with the conclusions from the original paper and evaluated via automated semantic similarity of constituent atomic claims. This progressive evaluation of semantic divergence from ground-truth conclusions enables assessment of a model's innovativeness (under minimal information) to grounded reasoning capabilities (under full experimental details), both critical for using LLMs for scientific discovery purposes. Our framework provides a foundation for systematically evaluating scientific reasoning and discovery capabilities in LLMs, crucial for advancing the development of next-generation AI scientist/co-scientist systems. Specifically, here we evaluate GPT-5, GPT-5.4, Gemini 2.5 pro, and Gemini 3.1 pro preview across 45 papers spanning bioactive materials, mechanical materials, and nanomaterials. We find that GPT-5.4 and Gemini 3.1 pro outperform their previous generation counterparts as expected, and GPT-5.4 in particular maintains 0.7 F1 score alignment with ground truth conclusions even under minimal context.

  • 3 authors
·
May 27

The Complex Brain Hypothesis: Resolving the Entropy-Content Conundrum in Minimal Phenomenal Experience

Minimal Phenomenal Experiences (MPEs) are states of consciousness in which wakefulness is preserved but phenomenal content is low or absent. The Entropic Brain Hypothesis (EBH) is a model of conscious processes that regards the entropy of spontaneous brain activity as a marker of 'phenomenal richness', exemplified by high-content psychedelic experiences (HCPEs). Yet recent human neuroimaging studies of MPEs induced by meditation -- and possibly 5-MeO-DMT -- suggest that these states, defined by their phenomenological simplicity, also show signs of increased neurophysiological entropy. This presents a conundrum for the EBH: brain entropy is elevated with increased and decreased richness of the phenomenal experience. Here, we put forward the Complex Brain Hypothesis (CBH), which proposes that the richness of experience differentiating MPEs from HCPEs is better indexed by complexity than by entropy. We argue that brain complexity is modulated by the grain of inference through which the brain resolves uncertainty: some HCPEs exemplify a fine-grained regime, in which loosened constraints amplify fluctuations into proliferating content, whereas some MPEs exemplify a coarse-grained regime, in which a simpler model dissolves variety into an experience of 'contentless' awareness. Both regimes can be associated with elevated brain entropy, but they diverge in phenomenology and perturbational signatures. By resolving the entropy-content conundrum, the CBH refines the EBH and highlights MPEs as an important test case for computational theories of consciousness.

  • 7 authors
·
May 14

The Causally Emergent Alignment Hypothesis: Causal Emergence Aligns with and Predicts Final Reward in Reinforcement Learning Agents

A hallmark of life on Earth is the ability of agents to exert causal power and be drivers of subsequent events. This is key to cognition at all scales. Causal emergence, measuring the degree to which an agent exerts unique predictive power on its future, is one consequence of causal power. Indeed, recent discoveries have shown that biological agents, even minimal ones, increase their causal emergence after learning new memories. However, there is a major knowledge gap regarding how causally emergent artificial agents are. We focused on Reinforcement Learning (RL) of neural-network agents across an array of environmental conditions, encompassing different algorithms, agent architectures, and six environments arranged on a complexity spectrum. For consistency, we computed the causal emergence of their latent-space representations over their lifetimes. We used the recently proposed ΦID to estimate causal emergence and tested how it related to learning performance. Our results suggested a Causally Emergent Alignment Hypothesis: successful agents exhibited causal emergence that was consistently predictive of final reward early in training and whose representational dynamics aligned with reward improvement in most tasks. This idea suggests that causal emergence may be a previously undisclosed axis of reorganization of neural representations in RL agents, with the potential to establish causal relationships and interventions that will lead to better RL agents. Our work also highlights the alignment between causal emergence and learning as another way biological and artificial creatures compare.

  • 2 authors
·
May 6

Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems

Neurological diseases are the leading global cause of disability, yet most lack disease-modifying treatments. We present PROTON, a heterogeneous graph transformer that generates testable hypotheses across molecular, organoid, and clinical systems. To evaluate PROTON, we apply it to Parkinson's disease (PD), bipolar disorder (BD), and Alzheimer's disease (AD). In PD, PROTON linked genetic risk loci to genes essential for dopaminergic neuron survival and predicted pesticides toxic to patient-derived neurons, including the insecticide endosulfan, which ranked within the top 1.29% of predictions. In silico screens performed by PROTON reproduced six genome-wide α-synuclein experiments, including a split-ubiquitin yeast two-hybrid system (normalized enrichment score [NES] = 2.30, FDR-adjusted p < 1 times 10^{-4}), an ascorbate peroxidase proximity labeling assay (NES = 2.16, FDR < 1 times 10^{-4}), and a high-depth targeted exome sequencing study in 496 synucleinopathy patients (NES = 2.13, FDR < 1 times 10^{-4}). In BD, PROTON predicted calcitriol as a candidate drug that reversed proteomic alterations observed in cortical organoids derived from BD patients. In AD, we evaluated PROTON predictions in health records from n = 610,524 patients at Mass General Brigham, confirming that five PROTON-predicted drugs were associated with reduced seven-year dementia risk (minimum hazard ratio = 0.63, 95% CI: 0.53-0.75, p < 1 times 10^{-7}). PROTON generated neurological hypotheses that were evaluated across molecular, organoid, and clinical systems, defining a path for AI-driven discovery in neurological disease.

  • 29 authors
·
Dec 13, 2025

Dara: Automated multiple-hypothesis phase identification and refinement from powder X-ray diffraction

Powder X-ray diffraction (XRD) is a foundational technique for characterizing crystalline materials. However, the reliable interpretation of XRD patterns, particularly in multiphase systems, remains a manual and expertise-demanding task. As a characterization method that only provides structural information, multiple reference phases can often be fit to a single pattern, leading to potential misinterpretation when alternative solutions are overlooked. To ease humans' efforts and address the challenge, we introduce Dara (Data-driven Automated Rietveld Analysis), a framework designed to automate the robust identification and refinement of multiple phases from powder XRD data. Dara performs an exhaustive tree search over all plausible phase combinations within a given chemical space and validates each hypothesis using a robust Rietveld refinement routine (BGMN). Key features include structural database filtering, automatic clustering of isostructural phases during tree expansion, peak-matching-based scoring to identify promising phases for refinement. When ambiguity exists, Dara generates multiple hypothesis which can then be decided between by human experts or with further characteriztion tools. By enhancing the reliability and accuracy of phase identification, Dara enables scalable analysis of realistic complex XRD patterns and provides a foundation for integration into multimodal characterization workflows, moving toward fully self-driving materials discovery.

  • 5 authors
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Dec 3, 2025

The Delta Learning Hypothesis: Preference Tuning on Weak Data can Yield Strong Gains

Improvements in language models are often driven by improving the quality of the data we train them on, which can be limiting when strong supervision is scarce. In this work, we show that paired preference data consisting of individually weak data points can enable gains beyond the strength of each individual data point. We formulate the delta learning hypothesis to explain this phenomenon, positing that the relative quality delta between points suffices to drive learning via preference tuning--even when supervised finetuning on the weak data hurts. We validate our hypothesis in controlled experiments and at scale, where we post-train 8B models on preference data generated by pairing a small 3B model's responses with outputs from an even smaller 1.5B model to create a meaningful delta. Strikingly, on a standard 11-benchmark evaluation suite (MATH, MMLU, etc.), our simple recipe matches the performance of Tulu 3, a state-of-the-art open model tuned from the same base model while relying on much stronger supervisors (e.g., GPT-4o). Thus, delta learning enables simpler and cheaper open recipes for state-of-the-art post-training. To better understand delta learning, we prove in logistic regression that the performance gap between two weak teacher models provides useful signal for improving a stronger student. Overall, our work shows that models can learn surprisingly well from paired data that might typically be considered weak.

  • 7 authors
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Jul 8, 2025

Analysis on Riemann Hypothesis with Cross Entropy Optimization and Reasoning

In this paper, we present a novel framework for the analysis of Riemann Hypothesis [27], which is composed of three key components: a) probabilistic modeling with cross entropy optimization and reasoning; b) the application of the law of large numbers; c) the application of mathematical inductions. The analysis is mainly conducted by virtue of probabilistic modeling of cross entropy optimization and reasoning with rare event simulation techniques. The application of the law of large numbers [2, 3, 6] and the application of mathematical inductions make the analysis of Riemann Hypothesis self-contained and complete to make sure that the whole complex plane is covered as conjectured in Riemann Hypothesis. We also discuss the method of enhanced top-p sampling with large language models (LLMs) for reasoning, where next token prediction is not just based on the estimated probabilities of each possible token in the current round but also based on accumulated path probabilities among multiple top-k chain of thoughts (CoTs) paths. The probabilistic modeling of cross entropy optimization and reasoning may suit well with the analysis of Riemann Hypothesis as Riemann Zeta functions are inherently dealing with the sums of infinite components of a complex number series. We hope that our analysis in this paper could shed some light on some of the insights of Riemann Hypothesis. The framework and techniques presented in this paper, coupled with recent developments with chain of thought (CoT) or diagram of thought (DoT) reasoning in large language models (LLMs) with reinforcement learning (RL) [1, 7, 18, 21, 24, 34, 39-41], could pave the way for eventual proof of Riemann Hypothesis [27].

  • 2 authors
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Sep 29, 2024

Revisiting the Superficial Alignment Hypothesis

The Superficial Alignment Hypothesis posits that almost all of a language model's abilities and knowledge are learned during pre-training, while post-training is about giving a model the right style and format. We re-examine these claims by empirically studying the scaling behavior of post-training with increasing finetuning examples and evaluating them using objective task-specific standardized benchmarks. Through experiments with the Llama-3, Mistral, and Llama-2 model families of multiple sizes, we observe that, similar to the pre-training scaling laws, post-training task performance scales as a power law against the number of finetuning examples. This power law relationship holds across a broad array of capabilities, including mathematical reasoning, coding, instruction following, and multihop-reasoning. In addition, for tasks like math and multihop reasoning, we observe that a handful of examples merely align the model stylistically but do not saturate performance on the benchmarks. Model performance is instead correlated with its reasoning ability and it improves significantly with more examples, illustrating the need for holistic evaluation programs leveraging objective benchmarks in addition to measurement of alignment to human preferences. We also observe that language models are not necessarily limited to using knowledge learned during pre-training. With appropriate post-training, a model's ability to integrate new knowledge greatly improves on downstream tasks like multihop question-answering. Taken together, these results shed new light on the Superficial Alignment Hypothesis, suggesting that it is, at best, an over-simplification.

  • 3 authors
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Sep 27, 2024

$CrowdDiff$: Multi-hypothesis Crowd Density Estimation using Diffusion Models

Crowd counting is a fundamental problem in crowd analysis which is typically accomplished by estimating a crowd density map and summing over the density values. However, this approach suffers from background noise accumulation and loss of density due to the use of broad Gaussian kernels to create the ground truth density maps. This issue can be overcome by narrowing the Gaussian kernel. However, existing approaches perform poorly when trained with ground truth density maps with broad kernels. To deal with this limitation, we propose using conditional diffusion models to predict density maps, as diffusion models show high fidelity to training data during generation. With that, we present CrowdDiff that generates the crowd density map as a reverse diffusion process. Furthermore, as the intermediate time steps of the diffusion process are noisy, we incorporate a regression branch for direct crowd estimation only during training to improve the feature learning. In addition, owing to the stochastic nature of the diffusion model, we introduce producing multiple density maps to improve the counting performance contrary to the existing crowd counting pipelines. We conduct extensive experiments on publicly available datasets to validate the effectiveness of our method. CrowdDiff outperforms existing state-of-the-art crowd counting methods on several public crowd analysis benchmarks with significant improvements.

  • 4 authors
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Apr 3, 2024

Generating Drug Repurposing Hypotheses through the Combination of Disease-Specific Hypergraphs

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

  • 5 authors
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Nov 16, 2023

DiffPose: Multi-hypothesis Human Pose Estimation using Diffusion models

Traditionally, monocular 3D human pose estimation employs a machine learning model to predict the most likely 3D pose for a given input image. However, a single image can be highly ambiguous and induces multiple plausible solutions for the 2D-3D lifting step which results in overly confident 3D pose predictors. To this end, we propose DiffPose, a conditional diffusion model, that predicts multiple hypotheses for a given input image. In comparison to similar approaches, our diffusion model is straightforward and avoids intensive hyperparameter tuning, complex network structures, mode collapse, and unstable training. Moreover, we tackle a problem of the common two-step approach that first estimates a distribution of 2D joint locations via joint-wise heatmaps and consecutively approximates them based on first- or second-moment statistics. Since such a simplification of the heatmaps removes valid information about possibly correct, though labeled unlikely, joint locations, we propose to represent the heatmaps as a set of 2D joint candidate samples. To extract information about the original distribution from these samples we introduce our embedding transformer that conditions the diffusion model. Experimentally, we show that DiffPose slightly improves upon the state of the art for multi-hypothesis pose estimation for simple poses and outperforms it by a large margin for highly ambiguous poses.

  • 2 authors
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Nov 29, 2022

Using multiple ASR hypotheses to boost i18n NLU performance

Current voice assistants typically use the best hypothesis yielded by their Automatic Speech Recognition (ASR) module as input to their Natural Language Understanding (NLU) module, thereby losing helpful information that might be stored in lower-ranked ASR hypotheses. We explore the change in performance of NLU associated tasks when utilizing five-best ASR hypotheses when compared to status quo for two language datasets, German and Portuguese. To harvest information from the ASR five-best, we leverage extractive summarization and joint extractive-abstractive summarization models for Domain Classification (DC) experiments while using a sequence-to-sequence model with a pointer generator network for Intent Classification (IC) and Named Entity Recognition (NER) multi-task experiments. For the DC full test set, we observe significant improvements of up to 7.2% and 15.5% in micro-averaged F1 scores, for German and Portuguese, respectively. In cases where the best ASR hypothesis was not an exact match to the transcribed utterance (mismatched test set), we see improvements of up to 6.7% and 8.8% micro-averaged F1 scores, for German and Portuguese, respectively. For IC and NER multi-task experiments, when evaluating on the mismatched test set, we see improvements across all domains in German and in 17 out of 19 domains in Portuguese (improvements based on change in SeMER scores). Our results suggest that the use of multiple ASR hypotheses, as opposed to one, can lead to significant performance improvements in the DC task for these non-English datasets. In addition, it could lead to significant improvement in the performance of IC and NER tasks in cases where the ASR model makes mistakes.

  • 6 authors
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Dec 7, 2020

Stabilizing the Lottery Ticket Hypothesis

Pruning is a well-established technique for removing unnecessary structure from neural networks after training to improve the performance of inference. Several recent results have explored the possibility of pruning at initialization time to provide similar benefits during training. In particular, the "lottery ticket hypothesis" conjectures that typical neural networks contain small subnetworks that can train to similar accuracy in a commensurate number of steps. The evidence for this claim is that a procedure based on iterative magnitude pruning (IMP) reliably finds such subnetworks retroactively on small vision tasks. However, IMP fails on deeper networks, and proposed methods to prune before training or train pruned networks encounter similar scaling limitations. In this paper, we argue that these efforts have struggled on deeper networks because they have focused on pruning precisely at initialization. We modify IMP to search for subnetworks that could have been obtained by pruning early in training (0.1% to 7% through) rather than at iteration 0. With this change, it finds small subnetworks of deeper networks (e.g., 80% sparsity on Resnet-50) that can complete the training process to match the accuracy of the original network on more challenging tasks (e.g., ImageNet). In situations where IMP fails at iteration 0, the accuracy benefits of delaying pruning accrue rapidly over the earliest iterations of training. To explain these behaviors, we study subnetwork "stability," finding that - as accuracy improves in this fashion - IMP subnetworks train to parameters closer to those of the full network and do so with improved consistency in the face of gradient noise. These results offer new insights into the opportunity to prune large-scale networks early in training and the behaviors underlying the lottery ticket hypothesis

  • 4 authors
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Mar 4, 2019

The Lottery Ticket Hypothesis: Finding Sparse, Trainable Neural Networks

Neural network pruning techniques can reduce the parameter counts of trained networks by over 90%, decreasing storage requirements and improving computational performance of inference without compromising accuracy. However, contemporary experience is that the sparse architectures produced by pruning are difficult to train from the start, which would similarly improve training performance. We find that a standard pruning technique naturally uncovers subnetworks whose initializations made them capable of training effectively. Based on these results, we articulate the "lottery ticket hypothesis:" dense, randomly-initialized, feed-forward networks contain subnetworks ("winning tickets") that - when trained in isolation - reach test accuracy comparable to the original network in a similar number of iterations. The winning tickets we find have won the initialization lottery: their connections have initial weights that make training particularly effective. We present an algorithm to identify winning tickets and a series of experiments that support the lottery ticket hypothesis and the importance of these fortuitous initializations. We consistently find winning tickets that are less than 10-20% of the size of several fully-connected and convolutional feed-forward architectures for MNIST and CIFAR10. Above this size, the winning tickets that we find learn faster than the original network and reach higher test accuracy.

  • 2 authors
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Mar 9, 2018 2