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01.
arXiv (CS.CV) 2026-06-18

Multi-Class Brain Tumor Classification Using Advanced Deep Learning Models: A Comparative Study

Despite recent advancements in deep learning, accurately classifying brain tumors from MRI images continues to pose challenges. In this research, we present a comprehensive evaluation of five different convolutional neural networks (CNN) architectures, including a customized baseline model and four pre-trained models - for use in classifying multi-class brain tumors using a clinically-sourced dataset of approximately 10,000 MRI images. We have utilized five different architectures; VGG16, VGG19, DenseNet121, and EfficientNetB0, which were all tested and trained within an identical experimental framework. Performance was measured by both overall accuracy and tumor-wise recall as a means to measure the clinically-relevant performance of each architecture. We found that EfficientNetB0 had the best overall classification accuracy at 95%, when compared to the other architectures tested; specifically VGG16 (94.37%), VGG19 (92.29%), DenseNet121 (90.91%) and the customized CNN (78.00%). An especially important finding of our research was the considerable improvement in detecting meningiomas; specifically, while simple CNNs could detect meningiomas with a recall rate of approximately 20%, EfficientNetB0 was able to detect meningiomas with a recall rate of 89%. Meningiomas are often difficult to detect because they can appear very subtly on MRI images. Additionally, an interesting finding was that the deeper VGG19 performed worse than the shallower VGG16. This indicates that in many cases the architectural efficiency of a CNN model may be more important than its depth when working with medical images. Overall, EfficientNetB0 appears to provide the optimal trade-off between classification accuracy, number of parameters used in the model and clinically meaningful performance.

02.
arXiv (CS.CL) 2026-06-12

AI SciBrief as a Gateway to Research: A Framework for Onboarding Students into New Research Areas

Students at all levels of higher education face a significant barrier in the form of information overload, which often paralyzes the initial stages of the research process and suppresses motivation. In response, this article introduces a pedagogical framework that leverages AI SciBrief, a platform powered by a Large Language Model (LLM) designed to automatically generate digests of scientific trends. We describe how this multidisciplinary tool - with initial coverage in finance, medicine, and education - can be integrated into the curriculum to overcome this "entry barrier." The framework provides concrete methodologies for utilizing these digests to facilitate topic selection for term papers, accelerate literature reviews for dissertations, and enable postgraduate students to continuously monitor emerging trends. We conclude that AI SciBrief functions as a "gateway to research" effectively reducing students' cognitive load and empowering them to transition more rapidly from information searching to knowledge creation.

03.
arXiv (quant-ph) 2026-06-17

Closest Accessible Symmetry reduction: a tool for Hamiltonian interpolation analysis

arXiv:2606.18161v1 Announce Type: new Abstract: We introduce a framework for analysing the spectrum of Hamiltonian interpolations without heavily relying on discretising the interpolation parameter. The method is based on the concept of accessible symmetries: a problem-class-dependent family of certifiable reflections that induce bipartitions of the Hilbert space. At each step, the interpolation Hamiltonian is projected onto the sectors of the accessible symmetry that is closest to being satisfied, yielding a hierarchy of weakly coupled pseudo-eigenspaces together with explicit residual couplings between them. We show that this representation captures qualitative signatures of quantum phase transitions, provides estimates of their location, and offers insights into their nature. The quality of the approximation is controlled by the compatibility between the accessible symmetry family and the problem instance. Although motivated in spirit by adiabatic quantum computation, our approach applies more broadly to the study of Hamiltonian phase diagrams, providing a new perspective on the spectral reorganisation of many-body quantum systems.

04.
arXiv (CS.CL) 2026-06-12

RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

05.
arXiv (math.PR) 2026-06-17

Moment generating function of the tacnode process

Authors:

arXiv:2606.17771v1 Announce Type: cross Abstract: The tacnode process is a universal determinantal point process arising in non-intersecting particle systems and random tiling models. In this paper, we study the generating function for the counting functions of the tacnode process on a union of $m$ intervals, $m\in\mathbb{N}^{+}$. Our first result provides an integral representation for the $m$-point generating function in terms of the Hamiltonian governing a system of $8m+4$ coupled differential equations. Combined with several differential identities for this Hamiltonian, the representation yields the large gap asymptotics, up to and including the constant term. As further applications, we obtain asymptotic formulae for the expectations, variances, and covariances of the counting functions, and establish a central limit theorem for their joint fluctuations. These results extend the previously known $1$-point theory for the tacnode process to the multi-interval setting with multiple discontinuities.

06.
arXiv (CS.CL) 2026-06-16

Evaluating and Preserving Lexical Stress in English-to-Chinese Speech-to-Speech Translation

Speech-to-speech translation (S2ST) systems have achieved impressive progress in semantic accuracy and speech naturalness. However, the cross-lingual transfer of lexical stress, a vital cue for emphasis and speaker intent, remains heavily underexplored, compounded by a lack of reliable automatic evaluation metrics for tonal languages like Chinese. We investigate English-to-Chinese S2ST stress transfer by constructing a stress-annotated Chinese dataset and an XLS-R-based Mandarin stress detector. Integrating this with the English EmphAssess system, we propose a novel objective metric for cross-lingual stress evaluation. Furthermore, we fine-tune CosyVoice3 to build a stress-aware S2ST system. Experiments demonstrate that our proposed S2ST architecture significantly outperforms existing systems in stress translation capability while maintaining competitive translation quality. Furthermore, our evaluation metric exhibits a strong correlation with human subjective judgments.

07.
arXiv (CS.CV) 2026-06-18

LARE: Low-Attention Region Encoding for Text-Image Retrieval

Image retrieval in crowded scenes is particularly challenging due to the salience bias of conventional visual encoders, which tend to focus on dominant objects while neglecting low-attention regions that are often crucial for fine-grained retrieval. We propose LARE (Low-Attention Region Encoding), a framework that explicitly models these overlooked regions. LARE adopts a dual-encoding strategy that encodes low-attention regions of an image and the full image in parallel, leading to more diverse and informative image embeddings. To evaluate image retrieval performance in challenging crowded scenes, we introduce Dense-Set, a challenging subset derived from COCO and Flickr30K. In this subset, images are re-captioned to provide richer descriptions of low-attention or previously overlooked regions. This dataset highlights the limitations of existing retrieval models and enables a more rigorous evaluation under densely crowded scene conditions. Experimental results demonstrate that the proposed framework improves retrieval performance by preserving subtle, non-dominant visual cues within the shared latent space.

08.
arXiv (CS.CL) 2026-06-11

The Structural Attention Tax: How Retrieval Format Hijacks In-Context Learning Independent of Content

Retrieval-augmented generation (RAG) systems inject external knowledge to improve LLM outputs, yet the format of injected content – distinct from its semantic relevance – can independently distort the model's attention distribution. We identify and formalise a phenomenon we term the structural attention tax: knowledge graph (KG) triples, due to their relational delimiters and repeated slot patterns, capture 2-3x more attention per token than semantically equivalent natural-language text ($\hat{o}$(KG) $\approx$ 0.70 vs. $\hat{o}$(neutral) $\approx$ 0.25), compressing demonstration attention by up to 42% – regardless of whether the triples are relevant or noise. We develop a formal framework decomposing attention scores into semantic and structural components (Eq. 2), derive a compression bound (Proposition 1) connecting token-level format bias to demonstration attention loss, and show that the structural term governs how much attention is diverted while the semantic term governs whether this helps or hurts. This decoupling reveals two orthogonal axes for improving retrieval-augmented ICL: optimising retrieval quality (semantic axis) and reducing format-driven attention capture (structural axis). Empirically, across two model families (Mistral-7B, LLaMA-3-8B) and three QA benchmarks, we observe that source-task alignment dominates: task-matched BM25 retrieval achieves 58-62% on HotpotQA vs. ConceptNet's 25-27%, a >30 pp gap that dwarfs all gating strategies ($\leq$2 pp). We derive five structure-aware mitigation strategies from the framework, ranging from zero-cost prompt modifications to training-time regularisation; format flattening (S3) is validated by both accuracy and attention-level evidence from a verbalized-triple control, while structural dispersal (S1) yields mixed results that illuminate the challenges of format-level intervention.

09.
arXiv (math.PR) 2026-06-17

Non-asymptotic Tail Bounds for the Kostlan–Shub–Smale Field: Tensor PCA and Spherical $k$-Spin Complexity

arXiv:2606.17665v1 Announce Type: cross Abstract: This paper builds a hierarchy of explicit, non-asymptotic tail bounds for the supremum of the Kostlan–Shub–Smale (KSS) random field on the sphere, and applies it to two problems: Spiked Tensor PCA and the landscape of the spherical $k$-spin model. For Tensor PCA, we study the non-asymptotic statistical limits of estimating a rank-$R$ symmetric signal tensor of order~$k\ge 3$ and dimension~$d\ge 3$ from a single Gaussian observation at signal-to-noise ratio~$\lambda$, through the profile maximum likelihood estimator, the MLE restricted to normalized rank-$R$ tensors of coherence at least~$\kappa$. Our analysis uses a single reduction: a deterministic geometric inequality (the Tube Method) and a rank-reduction step bound the estimation error by the supremum of the canonical KSS field, which the Kac–Rice formula turns into a Gaussian integral against the expected absolute characteristic polynomial of a shifted Gaussian Orthogonal Ensemble, controlled in turn by the four explicit tail bounds of our hierarchy (three from a Mehta–Fyodorov representation, one from a Ben Arous–Dembo–Guionnet large deviation). The same reduction yields two results, each with explicit constants. For estimation, a finite-$(k,d)$ error bound recovers the asymptotically optimal rate~$\sqrt{d\log k}$ of Perry, Wein and Bandeira, with explicit dependence on the rank~$R$ and the coherence~$\kappa$. For the landscape, a two-sided non-asymptotic bracketing of the annealed complexity of the spherical $k$-spin Hamiltonian recovers the Auffinger–Ben Arous–\v{C}ern\'y complexity function in the high-dimensional limit.

10.
arXiv (CS.LG) 2026-06-12

Positional Encoding in the Context of Memristor-Based Analog Computation for Automatic Speech Recognition

arXiv:2606.13379v1 Announce Type: new Abstract: Memristors provide a new chance for resource-efficient computation of neural models for natural language processing by enabling analog execution of vector-matrix-multiplication. Yet, computations on these devices are currently subject to larger distortion, both in weight programming and execution. In this work, we identify large output values of transformed positional encodings to cause major degradation within analog-to-digital conversion (ADC) as part of memristor-based computation. By adjusting the proportion of weight and precision bits of the ADC of specific memristor layers, we reduce the degradation of the execution by ~50% relative, while keeping the estimated energy consumption stable. Additionally, we investigate scenarios where the ADC cannot be modified. In that case the degradation can be reduced by ~30% relative after removing encoding-related linear transformations.

11.
arXiv (CS.CL) 2026-06-16

Who Should Lead Decoding Now? Tracking Reliable Trajectories for Ensembling Masked Diffusion Language Models

Masked Diffusion Language Models (MDLMs) have emerged as a distinct paradigm for sequence generation. As MDLMs become diverse in capabilities and knowledge coverage, an important question is how to combine their knowledge. Toward this, we first investigate the unique decoding dynamics of MDLMs. We find that successful generations exhibit stable confidence dynamics over answer-relevant positions, while unreliable trajectories can often be corrected by injecting promising intermediate states from other models. Guided by this observation, we propose $TIE$ ($T$rajectory-based $I$terative $E$nsembling), a knowledge fusion framework in which MDLMs iteratively identify reliable decoding trajectories and relay them across models. TIE tracks confidence dynamics over answer-relevant positions to determine which model currently follows a more reliable trajectory and selectively transfers partially denoised sequences across models. As the model on the more promising trajectory often changes across denoising steps, TIE allows different models to contribute complementary strengths at different stages of generation. Strong performance across diverse reasoning tasks, along with our analyses, suggests that TIE offers a practical approach to the underexplored problem of MDLM ensembling.

12.
arXiv (CS.CV) 2026-06-16

To forget is to preserve: Machine Unlearning for 3D medical image segmentation

With new data privacy laws such as the General Data Protection Regulation (GDPR) [1] that allow individuals to ask that any of their personal information be erased from trained machine learning models, there has been a push to investigate the unlearning of data from models as a way to comply with these laws. In this regard, based on four mechanics, we consider several approximate unlearning strategies applied to the MRBrainS18 dataset [2]. We use a 3D ResNet-50 [3] as a backbone architecture for segmentation that has been pre-trained with the Med3D framework [4]. Considering the pre-trained model as a baseline, we evaluate respective retention accuracy on 2 types of subjects, i.e., retain and forget. We assess these approaches through their Dice similarity coefficient and mean absolute error (MAE) values using two separate training horizons 20 and 50 epochs. The results show that the Noisy Label strategy had the best overall trade-off with a decrease of 93% in the forget set while maintaining 84% accuracy for the retained set after 50 epochs. All other strategies showed extreme levels of forgetting at higher epoch numbers while also demonstrating catastrophic degradation of their retain set performance. The results of this study provide a strict baseline of performance metrics for unlearning on a subject-specific level and provide practitioners with clear criteria for selecting the proper strategies.

13.
arXiv (CS.LG) 2026-06-19

VIMPO: Value-Implicit Policy Optimization for LLMs

arXiv:2606.20008v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards has become a central tool for improving the reasoning ability of large language models, but current methods face a trade-off between simplicity and credit assignment. Group-relative methods such as GRPO avoid training a critic, but typically assign a trajectory-level advantage to every token. Actor-critic methods provide denser learning signals, but require a learned value function with its own training instability. We introduce VIMPO, a critic-free policy optimization method that derives a policy-implied value function from the optimality conditions of KL-regularized reinforcement learning. For autoregressive generation, the resulting value recurrence can be written in terms of policy-reference log-ratios and anchored by the terminal condition that no future reward remains at the end of a trajectory. This gives a simple value loss that incorporates outcome-level verifiable rewards without training a critic. The same derivation also yields a critic-free actor advantage, allowing VIMPO to separate reward incorporation through the value loss from policy improvement through a PPO-style actor update. On mathematical RLVR benchmarks, VIMPO improves over GRPO across MATH-500, AIME 2024, AIME 2025, and OlympiadBench, with especially larger gains on competition-style evaluations. Under noisy rewards, VIMPO retains a consistent advantage over GRPO, suggesting that policy-implied value optimization can provide finer credit assignment while preserving the practical simplicity of critic-free training.

14.
arXiv (math.PR) 2026-06-17

Spectral recovery of a planted triangle-dense subgraph

arXiv:2606.17604v1 Announce Type: cross Abstract: Given a simple graph on $n$ vertices and a parameter $k$, the triangle-densest-$k$-subgraph problem is known to be computationally hard in the worst case. To circumvent the computational hardness, we study an average-case model where a triangle-dense subgraph on $k$ vertices is planted in an Erdős-Rényi random graph on $n$ vertices. For the recovery of the planted subgraph, we propose a simple spectral algorithm and a semidefinite program, both of which use a graph matrix whose entries are local signed triangle counts. Theoretical guarantees for these algorithms are established through spectral analysis of the graph matrix. Finally, we provide evidence showing a statistical-to-computational gap analogous to that for the planted clique problem. The computational threshold in terms of the subgraph size $k$ is at least $\sqrt{n}$ in the framework of low-degree polynomial algorithms, while the information-theoretic threshold is at most logarithmic in $n$.

15.
Nature (Science) 2026-06-17

These ‘master’ proteins protect us from deadly mutations — and could inspire new drugs

Authors:

Biology has clever ways to mask the effects of potentially harmful gene mutations. Scientists are investigating how this ‘buffering’ works — and how to exploit it. Biology has clever ways to mask the effects of potentially harmful gene mutations. Scientists are investigating how this ‘buffering’ works — and how to exploit it.

16.
arXiv (CS.LG) 2026-06-16

Learning the Geometry of Data: A Mathematical Review of Shape Space Analysis

arXiv:2606.17022v1 Announce Type: cross Abstract: A central objective of machine learning is to identify structure and patterns in data. Advances in data acquisition have increasingly produced datasets whose observations possess rich geometric form, giving rise to shape spaces that encode variability in object geometry. Such datasets arise across a wide range of disciplines, including biology, medicine, anthropology, and computer vision, where subtle geometric differences often carry important scientific information. Traditional machine learning methods, however, are frequently ill-equipped to account for the nonlinear geometric structure underlying these data. This survey synthesizes a rapidly growing body of work on shape space analysis, which provides a mathematical and computational framework for the study of geometric data. Drawing on ideas from differential geometry, statistics, and machine learning, we organize the literature around a common analytical pipeline: shape representation and parameterization, the rigorous construction of robust geodesic metrics, statistical analysis on shape spaces, and geometry-aware learning methods. We discuss how these tools enable the characterization of shape variability, the comparison of geometric objects, and the analysis of structural trajectories across populations and time. To illustrate the breadth of the field, we highlight applications spanning multiple scales of biological organization, including studies of subcellular morphology and primate tooth evolution. Across these and many other domains, researchers face common challenges arising from complex, nonlinear, and often unaligned geometric variation. The review concludes by identifying key theoretical and computational challenges, as well as emerging opportunities driven by increasingly large and diverse geometric datasets.

17.
arXiv (quant-ph) 2026-06-12

Kerr-induced nonreciprocal transparency and group delay in a hybrid cavity magnomechanical system

arXiv:2606.13412v1 Announce Type: new Abstract: We propose a scheme for realizing nonreciprocal transparency, Fano resonances, and slow/fast light in a hybrid cavity magnomechanical system containing two YIG spheres and a mechanical resonator. The nonreciprocal behavior originates from the magnon Kerr nonlinearity, which induces direction-dependent frequency shifts and modifies the interference pathways among cavity photons, magnons, and phonons. We show that the hybrid system supports multiple transparency windows arising from magnon- and magnomechanical-induced interference processes. The Kerr interaction strongly reshapes these transparency features, producing asymmetric Fano line shapes and enabling controllable nonreciprocal transmission. Furthermore, the associated dispersion exhibits pronounced directional asymmetry, leading to giant differences in the group delay for opposite propagation directions and allowing reversible switching between slow- and fast-light regimes. We investigate the roles of hybrid coupling strengths and dissipation channels and identify parameter regimes where the nonreciprocal response is maximized. These findings establish Kerr-engineered magnomechanical systems as promising platforms for integrated nonreciprocal microwave photonics and quantum information technologies.

18.
arXiv (quant-ph) 2026-06-16

Influence of the Electron's Anomalous Magnetic Dipole Moment on High-Atomic-Number Atoms

arXiv:2606.15995v1 Announce Type: new Abstract: Super-heavy atoms ($Z > 100$) are usually studied in the context of the so-called ``Quantum Electrodynamics of Strong Fields''. In this theory the problem of the singularity in the electron energy whenever $Z > 137$ is overcome. This is done by considering the finite size of the nucleus and leads to interesting phenomena, such as the spontaneous production of positrons. Here, we show that taking into account the contribution from the Anomalous Magnetic Dipole Moment of the electron (by means of an effective theory), within a point-nucleus model, is a sufficient condition to obtain regular wave functions and physically acceptable energy values for $Z > 137$.

19.
arXiv (CS.LG) 2026-06-16

GRASP: Gradient-Aligned Sequential Parameter Transfer for Memory-Efficient Multi-Source Learning

arXiv:2606.14900v1 Announce Type: new Abstract: Multi-source transfer learning faces a fundamental scalability bottleneck: existing approaches require either loading all K source models into memory simultaneously during parameter fusion, requiring O(K) memory, or deploying all models at inference time, making production deployment infeasible. We propose GRASP (Gradient-Aligned Sequential Parameter Transfer), which achieves superior knowledge integration while maintaining O(1) memory consumption through three key innovations: (1) sequential processing that merges one source at a time into an evolving target model, (2) parameter-wise gradient alignment that selectively transfers only parameters whose optimization directions align with the target domain, avoiding negative transfer, and (3) iterative fine-tuning that adapts transferred knowledge before integrating the next source. Extensive experiments across three continual learning benchmarks (Yearbook, CLEAR-10, CLEAR-100) spanning 10 to 108-year temporal distribution shifts and four architectures (1.3M to 25.6M parameters) demonstrate that GRASP achieves 93.5% mean accuracy over all datasets and architectures compared to ensemble method's 71.7% accuracy while requiring only constant memory versus K models for standard multi-source fusion. Critically, GRASP's sequential previously merged models and scales to arbitrarily many sources without memory growth, making it uniquely suitable for resource-constrained deployment and continually evolving source domains.

20.
medRxiv (Medicine) 2026-06-16

Validation of a Smartphone-Image-Based Computer-Vision Model for Lean Mass and Body Fat Estimation Against Dual-Energy X-ray Absorptiometry

Introduction Body composition, rather than body weight alone, is an increasingly important health metric, and preservation of lean mass has become a central concern in obesity treatment, aging, and chronic disease management. Dual-energy X-ray absorptiometry (DXA) provides accurate assessment of fat and lean tissue, but its cost and logistical requirements limit repeated measurement. Computer-vision approaches show promise for estimating adiposity from smartphone images, but lean-mass estimation remains less established. Methods We evaluated a computer-vision body composition model, applied to consumer-grade smartphone photographs, against DXA in a held-out validation sample of 195 adults from an ongoing cross-sectional study. Body fat percentage and total lean mass percentage were co-primary outcomes; for total lean mass percentage, an image-only configuration (no added covariates) was pre-specified as primary. Agreement was quantified using Lin's concordance correlation coefficient (CCC) as the lead statistic, with Pearson correlation, mean absolute error, root mean square error, mean bias, and Bland-Altman limits of agreement. In secondary analyses, appendicular lean mass and total lean mass percentage were each estimated with and without routine anthropometric and demographic inputs (body weight, height, age, and sex). Results Total lean mass percentage agreed with DXA from image features alone (CCC 0.916). Body fat percentage, estimated with routine inputs added, agreed at least as closely (CCC 0.930). Adding routine inputs barely changed agreement for total lean mass percentage but markedly improved it for appendicular lean mass, an absolute quantity that scales with body size. Conclusions A smartphone-image-based model estimated both body fat and lean mass with strong agreement to DXA, with lean mass percentage from image features alone. The approach needs no fixed equipment or ionizing radiation. Whether it can track change over time, including in incretin-based weight loss where lean mass preservation is a concern, was not assessed in this cross-sectional study.

21.
arXiv (CS.AI) 2026-06-18

Scaling Learning-based AEB with Massive Unlabeled Data

arXiv:2606.18864v1 Announce Type: cross Abstract: This paper studies how to scale learning-based automatic emergency braking (AEB) with massive unlabeled fleet data under production constraints. Our approach is based on meta-feedback semi-supervised learning (MF-SSL), where a teacher generates pseudo labels for unlabeled driving data and is updated using a small labeled anchor set as safety-critical feedback. In production, anchor ambiguity and labeled-unlabeled mismatch can amplify systematic pseudo-label errors, leading to spurious triggers. We propose a stabilized MF-SSL framework with (i) Noise-Aware Decoupling, which removes ambiguity-prone anchors from the teacher's supervised update path, and (ii) kinematics-gated pseudo-labeling with a teacher conflict penalty to suppress mismatch-induced risk hallucinations on unlabeled data while maintaining broad coverage. Extensive experiments show consistent gains as unlabeled data scale from 1M to 1B windows, improving safety while keeping comfort stable. The 1B-trained student model is deployed to hundreds of thousands of vehicles and validated over \$10^9$ km of driving, achieving a positive-to-false activation ratio exceeding 100:1 and a 35% improvement in accident-free driving mileage over a production rule-only baseline.

23.
bioRxiv (Bioinfo) 2026-06-14

Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell

Transcription factor (TF) cocktails used in cell identity reprogramming protocols have largely been developed from experimental approaches. A handful of computational approaches have been reported, though have not been widely adopted by the scientific community. To standardize their use and assess their performance, we built CompForce, a platform that integrates these tools. Using CompForce, we found that existing computational methods offer modest improvements over differential expression on both synthetic and literature-curated data, and that their lackluster and inconsistent performance could be attributed to a reliance on local centrality metrics. To improve upon these methods, we developed IMCell, a prediction method that is inspired by the influence maximization problem. Unlike existing tools, IMCell returns optimized TF sets rather than ranked TF lists. We demonstrate that IMCell vastly out-performs existing tools, and further extend it to dynamic, stepwise contexts. The tools presented here are available in the R packages CompForce and IMCell.

24.
arXiv (CS.LG) 2026-06-19

Phase Transition for Stochastic Block Model with more than $\sqrt{n}$ Communities

arXiv:2509.15822v3 Announce Type: replace-cross Abstract: Predictions from statistical physics postulate that recovery of the communities in the Stochastic Block Model (SBM) with a fixed number $K$ of communities is possible in polynomial time above, and only above, the Kesten-Stigum (KS) threshold. This conjecture has given rise to a rich literature, proving that non-trivial community recovery is indeed possible in SBM above the KS threshold. Failure of low-degree polynomials (LDP) below the KS threshold was also proven, as long as $K\ll \sqrt{n}$, where $n$ is the number of nodes in the observed graph. When $K\geq \sqrt{n}$, Chin et al.(2025) recently proved that, in a sparse regime, community recovery in polynomial time is possible below the KS threshold by counting non-backtracking paths. This breakthrough led them to postulate a new threshold for the many-communities regime $K\geq \sqrt{n}$. In this work, we provide evidence supporting their conjecture:\\ 1- We prove that, for any graph density, LDP fail to recover communities below the threshold postulated by Chin et al.(2025) ;\\ 2- We prove that community recovery is possible in polynomial time above the postulated threshold, not only in the sparse regime considered in Chin et al.~(2025), but also in moderately sparse regimes, by counting occurrences of some specific motifs inspired by the LDP analysis.\\ In particular, counting self-avoiding paths of length $\log(n)$, which is closely related to spectral algorithms based on the Non-Backtracking operator, is optimal only in the sparse regime. More complex motifs based on the blow-up of a cycle must be considered in denser regimes.

25.
arXiv (CS.LG) 2026-06-16

Learning the generating functional for variance reduction in lattice QCD

arXiv:2606.15986v1 Announce Type: cross Abstract: The generating functional in quantum field theory provides the natural framework for constructing correlation functions as derivatives with respect to source operators. We present a methodology that leverages machine-learned normalizing flows to reduce the variance of arbitrary $N$-point correlation functions of bosonic operators in lattice gauge field theory calculations by encoding a representation of the generating functional. We show that it is possible to systematically approach noiseless estimators of correlation functions in this framework. We demonstrate this methodology with applications to calculations of glueball correlation functions and Wilson loops in Quantum Chromodynamics and Yang-Mills theory. The results show up to three orders of magnitude variance reduction.