Beyond Myopia: Learning from Positive and Unlabeled Data through Holistic Predictive Trends

Learning binary classifiers from positive and unlabeled data (PUL) is vital in many real-world applications, especially when verifying negative examples is difficult. Despite the impressive empirical performance of recent PUL methods, challenges like accumulated errors and increased estimation bias persist due to the absence of negative labels. In this paper, we unveil an intriguing yet long-overlooked observation in PUL: \textit{resampling the positive data in each training iteration to ensure a balanced distribution between positive and unlabeled examples results in strong early-stage performance. Furthermore, predictive trends for positive and negative classes display distinctly different patterns.} Specifically, the scores (output probability) of unlabeled negative examples consistently decrease, while those of unlabeled positive examples show largely chaotic trends. Instead of focusing on classification within individual time frames, we innovatively adopt a holistic approach, interpreting the scores of each example as a temporal point process (TPP). This reformulates the core problem of PUL as recognizing trends in these scores. We then propose a novel TPP-inspired measure for trend detection and prove its asymptotic unbiasedness in predicting changes. Notably, our method accomplishes PUL without requiring additional parameter tuning or prior assumptions, offering an alternative perspective for tackling this problem. Extensive experiments verify the superiority of our method, particularly in a highly imbalanced real-world setting, where it achieves improvements of up to $11.3\%$ in key metrics. The code is available at \href{https://github.com/wxr99/HolisticPU}{https://github.com/wxr99/HolisticPU}.Comment: 25 page

Mutational Profiling of Non-Small-Cell Lung Cancer Resistant to Osimertinib Using Next-Generation Sequencing in Chinese Patients

Purpose. To identify the somatic mutated genes for optimal targets of non-small-cell lung cancer after resistance to osimertinib treatment. Patients and Methods. Study patients all had advanced lung adenocarcinoma and acquired resistance to osimertinib as a second- or third-line treatment. These patients had harboring EGFR T790M mutation before osimertinib treatment, which was confirmed by Amplification Refractory Mutation System (ARMS) PCR or Next-Generation Sequencing (NGS). After resistance to osimertinib treatment, tumor tissue was collected by core needle biopsy. DNA was extracted from 15 × 5 um sliced section of formalin-fixed paraffin-embedded (FFPE) material and NGS was done. The genetic changes were analyzed. Results. A total of 9 Chinese patients were studied, 5 females and 4 males, age 51–89 years. After progression with osimertinib treatment, core needle biopsy was performed and next-generation sequencing was performed. Nine patients had harboring 62 point mutations, 2 altered gene copies, 2 amplifications, and 1 EML4-ALK gene fusion. No MET or HER2 amplification was found in this cohort study. Nine patients still maintained initial EGFR 19 del or L858R activating mutations, while 7 of them kept EGFR T790M mutations. Among the 7 patients, 5 had secondary EGFR C797S and/or C797G mutations, which all happened in the same allele with T790M mutation. All patients were treated with targets therapies, chemotherapy, or best supportive care (BSC) in accordance with NGS genetic results and patients’ performance status; 7 of them are still alive and 2 of them died of disease progression at last follow-up. Conclusions. EGFR C797S/G mutation and the same one presented on the same allele with EGFR T790M mutation were the most common mutation feature and played a key role in resistance to osimertinib in Chinese patients with NSCLC. Tumor cells losing T790M mutation and maintaining EGFR activating mutation might benefit from first-generation EGFR-TKI treatment

Laser beam deflection-based perimeter scanning of integrated circuits for local overheating location

4 páginas, 2 figuras.In integrated circuits, local overheating (hot spots) can be detected by monitoring the temperature gradients present in the silicon substrate at a given depth, laterally accessing the die with an infra-red laser beam probe. The sensed magnitude is the laser beam deflection, which is proportional to the temperature gradients found along the beam trajectory (mirage effect). Biasing the devices with periodic electrical functions allows employing lock-in detection strategies (noise immunity) and thermally isolating the analysed chip substrate thermal behaviour from the external boundary conditions by setting the excitation frequency (control of the thermal energy penetration depth). Measuring the first harmonic of the deflection signal components (vertical and horizontal) allows performing a fast and accurate location of devices, interconnects or circuits dissipating relatively high power levels without any calibration procedure. It has been concluded that the horizontal component of the beam deflection provides a higher spatial resolution than the vertical one when measurements are performed beyond the thermal energy penetration depth.This work has been partially supported by the Spanish Ministerio de Educación y Ciencia (under contracts TEC2005- 087392 SPACESIC Project and TEC2005-02739), FEDER funds and the Consejo Superior de Investigaciones Científicas (CSIC) (under contract ‘Junta para la Ampliación de Estudios’, JAE-Doc).Peer reviewe

BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint

The B cell-specific transcription factor BACH2 is required for affinity maturation of B cells. Here we show that Bach2-mediated activation of p53 is required for stringent elimination of pre-B cells that failed to productively rearrange immunoglobulin VH-DJH gene segments. After productive VH-DJH gene rearrangement, pre-B cell receptor signaling ends BACH2-mediated negative selection through B cell lymphoma 6 (BCL6)-mediated repression of p53. In patients with pre-B acute lymphoblastic leukemia, the BACH2-mediated checkpoint control is compromised by deletions, rare somatic mutations and loss of its upstream activator, PAX5. Low levels of BACH2 expression in these patients represent a strong independent predictor of poor clinical outcome. In this study, we demonstrate that Bach2(+/+) pre-B cells resist leukemic transformation by Myc through Bach2-dependent upregulation of p53 and do not initiate fatal leukemia in transplant-recipient mice. Chromatin immunoprecipitation sequencing and gene expression analyses carried out by us revealed that BACH2 competes with BCL6 for promoter binding and reverses BCL6-mediated repression of p53 and other cell cycle checkpoint-control genes. These findings identify BACH2 as a crucial mediator of negative selection at the pre-B cell receptor checkpoint and a safeguard against leukemogenesis

Self-Enforcing Feedback Activation between BCL6 and Pre-B Cell Receptor Signaling Defines a Distinct Subtype of Acute Lymphoblastic Leukemia

Studying 830 pre-B ALL cases from four clinical trials, we found that human ALL can be divided into two fundamentally distinct subtypes based on pre-BCR function. While absent in the majority of ALL cases, tonic pre-BCR signaling was found in 112 cases (13.5%). In these cases, tonic pre-BCR signaling induced activation of BCL6, which in turn increased pre-BCR signaling output at the transcriptional level. Interestingly, inhibition of pre-BCR-related tyrosine kinases reduced constitutive BCL6 expression and selectively killed patient-derived pre-BCR(+) ALL cells. These findings identify a genetically and phenotypically distinct subset of human ALL that critically depends on tonic pre-BCR signaling. In vivo treatment studies suggested that pre-BCR tyrosine kinase inhibitors are useful for the treatment of patients with pre-BCR(+) ALL